US Health Officials Talk US COVID-19 Outbreak

As a major COVID-19 outbreak in the United States looks more and more inevitable, health officials find themselves under immense pressure to address the mounting fear and anxiety. National Center for Immunization and Respiratory Diseases Director Nancy Messonnier warned that significant behavioral change may have to occur including at schools, workplaces, and social events. It is becoming clear that the viral outbreak is likely to get much worse in the United States before it gets better. This new reality was reflected in a plunging stock market.

While efforts in China appear to be having an effect on reducing transmission rates in the country, the spread of COVID-19 outside the country, and not just in neighboring countries, is getting worse. “The emergence of these new hubs underscored the lack of a coordinated global strategy to combat the coronavirus, which has infected nearly 80,000 people in 37 countries, causing at least 2,600 deaths.” While significant transmission has still not occurred in the United States, the rate of transmission in other parts of the world seems to foretell what is to come. Another factor to consider is continued uncertainty about transmission. While human-to-human transmission in close proximity is an issue what is also concerning are cases where the links of transmission are weaker.

Citation: Belluck, Pam and Noah Weiland. “C.D.C. Officials Warn of Coronavirus Outbreaks in the U.S. The New York Times, 25 February 2020. https://www.nytimes.com/2020/02/25/health/coronavirus-us.html. Accessed 25 February 2020.

Post by Richard Hackmann

Case 82: Dengue Fever and Covid-19 in Singapore

Outside China, Singapore has the 3rd large cluster of Covid-19 cases; only South Korea and Japan have more cases. Singapore is also experiencing a spike in Dengue fever. As of February 20, there have been 2,508 cases of Dengue fever reported in 2020, compared to 85 cases of Covid-19 during the same period (2). On February 20, Singapore reported one patient has tested positive for both viruses (1, 3). The patient, referred to as Case 82, went to the hospital seeking treatment for Dengue fever on February 15. She was admitted after her second visit. On February 18, she tested positive for Covid-19. The patient was then put into solo isolation.

Dengue fever shares some symptoms with Covid-19, such as fever. However, Dengue fever patients do not experience raspatory problems. When Case 82 was first admitted into the hospital, her symptoms and test results confirmed the diagnose of Dengue fever. It was only after she developed raspatory problems that she was tested for Covid-19. This indicates that hospitals in Singapore are not giving patients routine test for SARS-CoV-2 at this point.

Depending on the quality of treatment, Dengue fever’s fatality rate is between 2% - 5%. While the fatality rate of Covid-19 is still unknown, it hovers around the similar range. To control the spread of Dengue fever Singapore has implemented an active alert system letting residents know where current clusters of cases are located. Singapore also reports the number of Dengue cases daily and the location of the cases. The spike in Dengue fever is related to Singapore’s success at controlling the vector Aedes aegypti population. Because higher percentage of the residents in the city-state has never had Dengue fever before, their immunity is low. Another reason for the increase is that Singapore is seeing more DENV-3 infections, where previously DENV-1 and DENV-2 dominated.

~~ You Jia Zhu

1. Woman becomes first Singaporean to be diagnosed with both dengue and coronavirus, South China Morning Post, February 21, 2020.

2. National Environment Agency, Singapore.

3. Tee Zhuo and Timothy Goh, Coronavirus: S'pore confirms first patient with both Covid-19 and dengue, all warded with her quarantined at Ng Teng Fong, Strait Times, February 20, 2020.

China’s CDC finally provides insight into who is most impacted by Covid-19 virus

The Chinese Centers for Disease Control and Prevention (CCDC) have been working at a furious pace to collect and interpret preliminary data about the rapid spread of Covid-19 disease in China and elsewhere. The CCDC studied some 72,000 confirmed and suspected cases of Covid-19 virus disease. As described in a CNN article published on February 19 , many of 1 The CCDC conclusions and observations, as reported in a CNN article published on February 19, appear to track expectations, assumptions and speculation made through press reports and other scientific sources during the past several weeks as the virus gained a foothold and quickly evolved into worldwide menace.

The headlines include a preliminary (and expected) determination that the new virus is far more contagious that either MERS or SARS, that it is likely less fatal (2% fatality rate v. 35% and 9.6%,respectively) and, undoubtedly as a result of its more elevated contagiousness, is a much larger health event (with more than 75,000 infected in China, and more than 2,000 deaths) than either of the other two viral outbreaks. Importantly, at least according to one physician quoted in the CNN article, Anthony Fauci, M.D., the director of the National Institute for Allergy and Infectious Disease, the current fatality percentage is likely overstated because it is probable that many of the Covid-19 viral infections have not been (and may never be) reported—especially those infections where the patient is asymptomatic. He posits that, once those and other currently unconfirmed infections are considered, the denominator in the equation (number of fatalities over number of infections) will increase and the percentage of fatalities will necessarily decline. Dr. Fauci believes that the fatality rate will drop below 2 % once all of the infections that can be counted are. Notably, as reported by CNN, the CCDC report did not contain any predictions about the expected course of the virus or the epidemic.

The CCDC report also provides bona fide (but crude) analyses that will assist in assessing the virulence of the virus by providing statistical data that show who is succumbing to the virus. As with the flu virus, the Covid-19 virus seems to be causing the greatest damage among the aged and those with pre-existing— especially cardiac—conditions. The fatality rate for those over age 80 is almost 15%; it is 10% for those with cardiac conditions. This mortality analysis is consistent with medical and other scientific suspicions as reported in the press, and correlates with previous guidance from Chinese officials suggesting that, for most of those infected, the symptoms of the illness are mild. Unlike the flu virus, though, Covid-19 does not seem to disproportionately impact infants and young children. This newly released information has been a missing element in scientists’ and researchers’ analysis of the true risk of this virus.

~~ David M. Walsh

Griffith, J., and Gans, N., “Chinese CDC finds Covid-19 virus to be more contagious than 1 SARS or MERS—CNN”. CNN. Cable News Network, n.d., 19 February 2020. https://www.cnn.com/2020/02/19/health/coronavirus-china-sars-mers-intl-hnk/index.html

To Prevent Next Coronavirus, Stop the Wildlife Trade, Conservationists Say

Rachel Nuwer’s article titled, To Prevent Next Coronavirus, Stop the Wildlife Trade, Conservationists Say, reveals that history has proved that wildlife animal trade and slaughtering help viruses and diseases leap from animals to humans. With this fact known to be true, conservationists declare that the future of our public health depends on preventing wildlife animal trading and slaughtering. Conservationists are arguing that this is not a just a “conservation” issue anymore but a public health issue and even national security issue. The Chinese government is currently working on legislation to ban wild animal trading and consumption. The article stresses that live meat markets are the “perfect laboratories” for the creation of new viruses because there is a mixture of new microbes within different species of animals that are also in very close contact with humans. This mixture is also present when the multiple species of live animals are slaughtered on the same chopping block with the same knives. For example, the suspected wild animal market in Wuhan had over seventy species of wildlife sold and slaughtered there. Experts believe China did not learn their lesson from the SARS outbreak in 2003 that was linked to wild animal markets. Some critics argue that wild animal markets are simply the culture of Eastern countries like China. These same critics also say that wild animal consumption in Western countries like America occur as the “norm,” where individuals consume venison, rabbit and birds. The article also points out that answer may be somewhere in the middle by focusing on the hygiene of the markets, which lowers the risk of a new animal virus making the leap to humans. 

This article relates directly to our “Virus in the News” class because it focuses on the current coronavirus and a debate, we had in class a few weeks ago regarding the practice of wild animal markets. Furthermore, the article points out that mankind is not learning from our previous behaviors that have proved to be destructive. Although this belief can be applied to many aspects of our lives, I believe it is important to learn for the epidemic. I would be in favor of the ban of wild animal markets in China and throughout the world. As far as the consumption of wildlife in America I am unaware of live animal meat markets like the ones described in Wuhan China, where deer, rabbits, squirrels, moose, bear, ducks and turkeys are kept alive in a cage then slaughtered once purchased on the same chopping block with the same knives. 

~~ John Sikora

https://www.nytimes.com/2020/02/19/health/coronavirus-animals-markets.html

Giant Phage Viruses

Sometimes (and probably most often than not), the kind of answers we expect to arrive at for a question limits the range of answers we may arrive at. In other words, sometimes we tend to ignore or even not see certain answers because we simply did not expect to see them. The case at hand is the discovery of giant-phage viruses that exist in our mouths and until recently nobody knew about them. According to The Atlantic,1 Jill Banfield of the University of California, Berkeley, and her team have discovered that these mega viruses exist in our saliva and in our gut, and they are 10 times bigger than other phages previously known.

It is interesting that Banfield and her team have discovered these viruses by accident. They were studying the gut bacteria of people from Bangladesh who are exposed to toxic arsenic compounds because they live near arsenic-contaminated groundwater. They were interested to know if the bacteria provide any form of detoxification for the arsenic. It turned out that they don't. However, the team found huge amounts of unknown viral DNA in the DNA of the bacteria. This was a hint at the existence of new and very complex phages, since phages are viruses that attack bacteria. Later on they found these genetic material in bacteria from other parts of the world.

Traditionally, to get to a virus scientists have to grow them, and this is done by first filtering out any particles above a certain size. In other words, the traditional techniques assume that viruses have to be below a certain size, and then proceed to filter out anything that does not fit that assumption. As a result, these giant phages had not been observed previously. However, Banfield and her team utilized a different technique: they started with environmental samples and analyzed the DNA of everything within those samples to see what cames out. It was by using this technique that they were able to isolate these giant phages. While an average phage has something in the order of 50k of DNA letters, these phages have something like 500k, almost ten times as much.

Although these phages do not cause any known diseases in humans, their very complex DNA structure is a potential sign that they probably do play some role. Whatever they do, however, their functions are likely to be different from traditional viruses. For example, because of their big size, they don't easily fit inside a bacterium and therefore they cannot reproduce many copies of themselves in a bacterium before bursting it. Thus, they should be more selective and exercise more control over their host to ensure the proper copying of themselves. In that sense, they would have to act more like mammals whose strategy is to put a lot of energy in fewer offspring rather than less energy in numerous offspring. The team also found that these phages actually seem to have their own way of cutting the genes of their hosts. Even more fascinating, they seem to be able to program their hosts to attack other phages, in other words, they seem to be able to utilize the genetic machinery of their hosts to put out their competition.

These findings are fascinating not only in their own term, but also because they raise deeper questions about the meaning of life. At the very least, these discoveries show that the simple division of living vs. non-living seems to be inadequate when it comes to such boundary cases. 

~~ Moe Azadeh

1. https://www.theatlantic.com/science/archive/2020/02/oh-look-ton-giant-viruses-inside-your-mouth/606763/?utm_medium=offsite&utm_source=yahoo&utm_campaign=yahoo-non-hosted&yptr=yahoo

Gay Men Underestimate Their Risk of HPV

A recent article in the Journal of Community Health reported that young gay men are significantly uninformed regarding their risk for human papillomavirus (HPV) infection.

Interviews with gay and bisexual men in their early 20’s found that they knew little about HPV, including how it is transmitted, its symptoms, and how it can contribute to cancer.

Researchers indicated that the men erroneously believed that HPV mainly or only affects women, and therefore placed little importance on HPV vaccination.

HPV is a sexually transmitted virus that can cause several types of cancer, most commonly cervical cancer in women. However, it also causes cancers of the anus and penis. It can be particularly harmful for gay and bisexual men, due to the complicating factors of higher smoking rates and higher rates of HIV.

The study also found that the topic of HPV is rarely discussed with young men, and health care providers rarely explain the potential risks of HPV or the benefits of vaccination.

Co-author of the study, Caleb LoSchiavo, a doctoral research assistant at the School of Public Health at Rutgers University commented, “Particularly in light of the decades-long focus on gay men’s health care as HIV care, there is a missed opportunity for HPV prevention in the community.”

Rutgers postdoctoral fellow Jessica Jaiswal remarked, “Clinicians have a direct role in expanding the availability of LGBTQ-competent health care. By learning about sexual minority men’s diverse health needs and routinely offering the HPV vaccine, we can move toward a health promotion model and not only a disease prevention model.”

About 79 million Americans have HPV, and that number grows by about 14 every year, according to the Center for Disease Control and Prevention.

Perry Halkitis, director of Rutgers' Center for Health, Identity, Behavior and Prevention Studies (CHIBPS), stated, "Everyone who is sexually active -- regardless of gender, sexual orientation, partners' genders, relationship or marital status -- should talk to their doctor about receiving the HPV vaccine to prevent a future generation who may develop HPV-related cancers, such as cervical, oral and anal cancer, as we have seen emerging in baby boomers and Gen-Xers,"

~~ Amy Allebest

Source:
https://www.usnews.com/news/health-news/articles/2020-02-20/gay-men-underestimate-their-risks-from-hpv

A First Step in a Paramyxo Drug: Defining the Polymerase Complex Structure

Paramyxoviridae is an important viral family that includes diseases such as measles, mumps, respiratory syncytial virus (RSV) and human parainfluenza. As it stands, there are no specific antiviral treatments for any member of the paramyxo family. The pervasiveness and severe complications associated with paramyxoviruses make it essential for researchers to develop therapies against infection, but without knowledge of viral protein structures, drug design is really a “guess-and-check” type process. Recently, a team of researchers used cryogenic electron microscopy (cryo-EM) to uncover the structure of the parainfluenza polymerase (L-protein) and its cofactor (P-protein) together called the L-P complex. Cryo-EM essentially launches a stream of electrons at a frozen protein sample to put together a flurry of 2-D images into a reconstructed 3-D depiction with higher resolution than traditional electron microscopy. In the massive 5-protein, 2000 amino acid complex, the researchers found new, unidentified proteins and a unique methyltransferase conformation. They believe it is responsible for promoting the switch between transcription and replication. The in-depth knowledge about the key proteins’ structure will make it a viable potential drug candidate for antivirals. This research will help create new drugs not only for parainfluenza and other paramyxoviruses, but also for other viruses in the mononegavirales order with similar polymerase complexes and “switching” mechanisms.

~Avi Kaye

Article: Abdella et al. Structure of a paramyxovirus polymerase complex reveals a unique methyltransferase-CTD conformation. PNAS, 2020. https://doi.org/10.1073/pnas.1919837117

Moscow targets Chinese with raids amid virus fears

The following AP wire report details the potential for human rights abuses at the heart of political, rather than scientific, containment strategy. Public officials in Moscow ordered a fourteen-day self-quarantine period for all Chinese nationals in the city. In order to track those suspected of not following the order, city officials authorized police raids of hotels, dorms, apartments, and businesses as well as use of facial recognition software. They enlisted transit workers to stop Chinese riders and force them to complete paperwork concerning their health and travel history. Naturally, this created confusion among the bus drivers and subway operators. How exactly do you know if someone is Chinese or not? They could be Japanese, or Vietnamese, or a Russian citizen from the Yakutia region. The potential for racial profiling knows no bounds.

One of the more concerning aspects of this piece was its reference to Cossack gangs who performed a similar function without state sanction. These vigilantes approach people whom they consider Chinese, or maybe Chinese, and hand them a surgical mask and offer strong recommendations to visit local health clinic. It is not hard to envision that should Russia have more than two outbreaks in Siberia, this vigilantism will get out of hand.

Patrick Moynahan

https://abcnews.go.com/International/wireStory/moscow-targets-chinese-raids-amid-virus-fears-69157387

African swine fever virus news

As of Friday, Feb. 14, South Korea reported finding 19 more wild boars infected with African swine fever (ASF) virus, all of them near the border with North Korea.  The total number of infected boars is now 204.

Of the 19 cases, 18 were found dead in areas along the DPK border, including the eastern county of Hwacheon as well as the border city of Paju and a county north of Seoul (in western South Korea).  A wild boar captured alive in Cheorwon also was infected with the virus.

The first-ever outbreak of ASF was confirmed in September of 2019; around 400,000 domestic pigs have been euthanized to help prevent its spread.

No additional cases on farms have been reported since last October, but as noted above, authorities continue to find dead wild boars infected with the virus.  All confirmed cases so far, both wild and domestic, have occurred along the border.  The DPK announced its first case of ASF at a pig farm near its border with China last May.

African swine fever is a highly contagious and deadly disease affecting both domestic and wild pigs. ASF cannot be transmitted from pigs to humans, and it is not a food safety issue.  There are currently no vaccines or cures for ASF.  Unlike diseases like hoof-and-mouth disease, ASF is spread through direct contact with infected animals or their remains. 

ASF is found in countries around the world, particularly in sub-Saharan Africa. More recently, it has spread through China, the Koreas, Mongolia, and Vietnam, as well as parts of the E.U.

~~ Steve Blasberg

Excuse Me, But is that a Virus in Your Gut?

In recent years the “microbiome” has gotten a lot of good press.   News articles variously describe it as a complex community of bacteria and fungi that colonizes the human body.  Most people think of the microbiome as being in their gut, but it in fact also inhabits your lungs, skin and even blood.  These trillions of bugs help control digestion and benefit your immune system.   Now that you’ve heard of the microbiome, the next discovery you should know about is the “virome” — which is the name for the new realization that viruses are also a key part of your microbiome.

One of the most common viruses in your gut is a recently discovered family of viruses called Anelloviridae.   These viruses seem to be present in all humans.   So far there are no known diseases that are caused by these viruses.   In fact, instead of causing disease, scientists think these viruses help the human body by modulating your body’s immune system.

The first bacteria, fungi and viruses in your microbiome and your virome first entered your gut immediately after birth, and have persisted and flourished there ever since.   Little was known about the viruses in your body until the last two decades.  In fact, Anelloviridae was not even discovered until 1997 and even then its discovery was a bit of an accident when Japanese scientists found the Torque Teno virus (TTV) in a single patient.   Since then scientists have learned that there are at least a couple hundred different types of Anelloviridae, and that they are found in a variety of mammals.

To date there is no hard evidence that Anelloviridae cause any diseases, but there is some data that indicates that certain Anelloviridae are coincident with diseases such as hepatitis and might be associated with higher mortality rates.  Whether they are harmfully “pathogenic” is sure to be a future hot research topic.

~~ Robert Carr

Quick Speed-to-Market Ebola Vaccine – Hope for COVID-19?

As COVID-19 rages on, the Ebola outbreak in the Democratic Republic of Congo (DRC) is finally showing signs of slowing down. In the last two days, no new cases have been reported. It is a breakthrough. WHO has downgraded the risk assessment for Ebola outbreak from Very High to High.

Since the outbreak began in August of 2018, the disease has plagued DRC’s war-torn North Kivu and Ituri provinces. As of February 11, 2020, there were 3,432 cases and 2,249 deaths, with a fatality rate of 66% (1, 3). For a disease where treatment is available and vaccines have recently been approved, it is a tragedy that more people couldn’t have been saved (2).

Treatment and vaccines for Ebola have been developed in record times. Ebola first burst onto the scene in 1976; but development for treatment and vaccines was slow to gain traction because the outbreaks were confined to West Africa, a region far away from Europe and North America. The threat to the moneyed and powerful part of the global, where bioscience development happens, was minimal. In the early 2000s, a confluence of events occurred that pushed the scientific work on Ebola treatment and prevention to the top of the agenda for Europe and US. 9/11 brought terrorist threats close to home for the Americans. At this time, confirmation that Soviet Union had been developing Ebola as a bioweapon came to light. The 2013 to 2016 outbreak further demonstrated the deadliness of this virus without antidote and vaccine. Finally, the post-9/11 anthrax letters that killed five people and infected 17 others prompted the US government to invest heavily and openly in biodefense research that focused on Ebola.

On December 19, 2019, FDA approved the vaccines for Ebola developed by Merck and Public Health Agency of Canada (2, 4). The speed to market for the Ebola vaccines gives hope to many that a vaccine for SARS-CoV-2 could be developed and tested quickly, if scientists work and share their work together.

 ~~  You Jia Zhu

1.Lisa Schelin, “WHO, the Ebola Epidemic is DR Congo May Be Nearing its End”, Voice of America, February 9, 2019.

2. FDA Press Release: First FDA-approved vaccine for the prevention of Ebola virus disease, marking a critical milestone in public health preparedness and response, December 19, 2019

3. Ebola health update – DRC, 2019, World Health Organization.

4. Monica Villamizar, Despite outbreak, Ebola treatment and vaccine represent ‘resounding scientific success’, PBS Newshour, January 16, 2020.

How a Pharmacy Handles Mask Hoarders and Coronavirus Fears

 Isabella Kwai’s article titled, How a Pharmacy Handles Mask Hoarders and Coronavirus Fears, focuses on a small pharmacy, Kit Pharm in Hong Kong and how they are dealing with the Coronavirus. The article reveals that the demand of masks has increased to the point where there are shortages. The demand has also caused the prices of masks to double. Kit Pharm is a smaller store that does not have the large quantities of goods like a bigger chain store would have. The owner of the pharmacy cannot believe the prices to replace her diminished stock of masks. Due to short supplies, the owner is encouraging her customers to not panic and only buy what you need. A common practice throughout virus-stricken area involves people stockpiling masks and buying them in massive bulks. The coronavirus also has created lifestyle changes for the owner. For example, she no longer takes public transportation to limit her exposure to various germs. 

This article relates directly to our “Virus in the News” class because it focuses on the social response to the coronavirus. The shortage of masks in China is alarming, but I do not think you can place blame on individuals stock piling masks. If they have access to them and the virus is currently presenting more questions than answers I would also buy as many masks as I could to protect my family and myself.

~~ John Sikora

https://www.nytimes.com/2020/02/18/world/asia/mask-hoarders-coronavirus-pharmacy.html

Complexity of Phages Blurs Line Between Virus and Life

Large bacteria-killing viruses with capabilities usually attributable to living organisms have been discovered,  confusing the separation between microbes, considered life, and viruses. These bacteriophages are of bigger and more complex than previously known phages, and contain genes typically seen in bacteria, which these large phages deploy versus the bacterial host. The genome of the largest phage is 735,000 base-pairs long, meaning roughly 15 times larger than previously known phages, and even larger than the genomes of many bacteria.

The genomes of these large phages include components of the CRISPR system that bacteria use to fight viruses, including the Cas9 protein that has been utilized for gene editing. It appears these phages implant their own CRISPR components into bacterial cells to redirect the bacterial CRISPR system against other viruses in a kind of interviral warfare.

In addition to coding for many previously unknown proteins, these large phages contain genes that code for tRNAs and initiate translation. Herein lies one of the ways these newly discovered large phages blur the line between virus and life. “Typically, what separates life from non-life is to have ribosomes and the ability to do translation; that is one of the major defining features that separate viruses and bacteria, non-life and life,” said Berkeley researcher, Sachdeva.

~~ Pete Dailey

Disease name vs. virus name for the coronavirus

Last week I reported that the WHO proposed COVID-19 as the official name for the new coronavirus. This week, reports came to my attention distinguishing the name of the disease vs. that of the virus causing the outbreak.

COVID-19 is the name of the disease, not the virus. The virus responsible for the disease is slated with the name SARS-CoV-2.  The International Committee on Taxonomy of Viruses (ICTV) proposed “SARS-CoV-2” in a preprinted article awaiting peer review, as reported by Wired.

“SARS-CoV-2” seems like an apt candidate for a secure password rather than a name that is easily remembered. However, it does point to the similarities of COVID-19 with the previous outbreak of SARS and MERS.

A separate article reports that a team of biologists has annotated three genomes of the current coronavirus, identifying the differences and similarities with the previous outbreaks of SARS (2003) and MERS-CoV (2012). Researchers have found that “there are only five nucleotide differences—in a total genome of about 29,800 nucleotides,” suggesting a similarity in the viruses’ pathogenicity and transmissibility.

Furthermore, the researchers determined that the current coronavirus is more closely related to SARS and more distantly related to MERS. The study could help scientists understand how coronaviruses can jump into humans, and whether or not transmission to humans in the virus’ final jump. One researcher cited that control of SARS was partially due to the fact that SARS didn’t get into other animals such as dogs and cats.

The WHO has stated that case fatality rates of COVID-19 are at 2% or less.

SARS: Severe acute respiratory syndrome

 Middle East respiratory syndrome-related coronavirus

~~ Janette Canare

Sources:

“Coronavirus Has a Name: The Deadly Disease Is Covid-19," WIRED. Accessed February 17, 2020. https://www.wired.com/story/coronavirus-has-a-name-the-deadly-disease-is-covid-19/.

“Scientists Compare Novel Coronavirus with SARS and MERS Viruses,” The Scientist Magazine. Accessed February 17, 2020. https://www.the-scientist.com/news-opinion/scientists-compare-novel-coronavirus-to-sars-and-mers-viruses-67088.

“How COVID-19 Kills: The New Coronavirus Disease Can Take A Deadly Turn,” NPR.org. Accessed February 17, 2020. https://www.npr.org/sections/goatsandsoda/2020/02/14/805289669/how-covid-19-kills-the-new-coronavirus-disease-can-take-a-deadly-turn.

The Licensing of Ebola Vaccine in Africa

According to the World Health Organization (WHO), four countries in Africa have licensed the use of a recently approved vaccine for Ebola.1 They are the Democratic Republic of the Congo (DRC), Burundi, Ghana, and Zambia. The Vaccine has just recently been approved by WHO. According to WHO Director-General Dr Tedros Adhanom Ghebreyesus, the approval for the use of the Vaccine is a milestone in the fight against this "unforgiving" disease and is a sign of African countries’ commitment to protecting their people. Moreover, according to the WHO, the accelerated certification for the licensing and approval of this vaccine has been the fastest vaccine pre-qualification ever.

The vaccine is manufactured by Merck and is marketed under the name "Ervebo" and is administered in the form of an injection. Based on preliminary studies, it is very efficient. The efficacy rate is estimated to be around 97.5%. There are also signs that it reduces the mortality rate in those who are already infected with the Ebola virus.

The introduction of this vaccine is a great relief for countries and communities which have been devastated by the disease. At the same time, the whole process shows the critical importance of an international effort when it comes to fighting the disease. Because of the deadly nature of the disease, the approval process has relied on simultaneous studies of the vaccine running in parallel in several countries. Without such parallel studies, the approval could have taken many years, allowing for numerous preventable deaths.

On a more general note, this could be another case of success in humans’ fight against deadly infectious diseases. While there is no guarantee that this success can be duplicated for all other outbreaks, it certainly provides hope. Scientists worry about catastrophic events that could endanger the human civilization and even existence. For example there are programs that trace the trajectory of big asteroids that might be on a collision course with earth. Infectious diseases could pose at least a similar (if not more serious) threat, not from the macro-scale external universe, but as a result of the internal working of life on a micro-scale on earth.

~~ Moe Azadeh

Source: https://www.who.int/news-room/detail/14-02-2020-four-countries-in-the-african-region-license-vaccine-in-milestone-for-ebola-prevention

Progress in Fight Against Ebola

While much of the world’s attention has been focused on novel coronavirus, the Democratic Republic of Congo has been reeling from a deadly outbreak: Ebola. The second-largest Ebola epidemic on record has affected DRC’s North Kivu and Ituri provinces, and has killed over 2,200 people and infected over 3,400 since August 1, 2018. The grave situation has been exacerbated by ongoing fighting in the region: several health workers have been killed in what the WHO describes as warzone-like violence, and scores of people have been displaced from their homes, increasing risk of spreading infection.

However, the WHO announced an encouraging milestone this week in the fight against Ebola: a new, effective vaccine. Four African countries, including the DRC, Burundi, Ghana, and Zambia, have licensed the vaccine, called Ervebo. Dr. Matshidiso Moeti, WHO regional director for Africa commented, “The rapid approval of the Ebola vaccine by countries in the Africa region helps ensure this critical prevention tool will be available when and where it is needed most. This kind of collaboration and innovation is a model for other health priorities.” Ervebo has been shown to be nearly 98% effective, and can reduce the chances of dying for those already infected.

Ervebo, manufactured by the company Merck, is expected to be registered in additional countries in coming weeks, according to WHO. WHO leaders said the prequalification process was the “fastest vaccine prequalification process ever,” demonstrating the success the global community can achieve when commitment and motivation are high. “The development, study, and rapid prequalification of this vaccine show what the global community can do when we prioritize the health needs of vulnerable people,” said WHO Director-General Tedros Adhanom Ghebreyesus.

~~ Amy McPhie Allebest

Sources:
- https://news.un.org/en/story/2020/02/1057461
- https://www.cnn.com/2020/02/15/world/ebola-fight-milestone/index.html

Progress in DRC Ebola Fight Amid Global Focus on COVID-19

While most of the world’s attention is on the emerging COVID-19, progress is being made in the fight against Africa’s current Ebola outbreak. Since August 2018, the Democratic Republic of the Congo (DRC) has been in the midst of the second largest Ebola outbreak on record. It has killed more than 2,200 of the 3,400 that have been infected, putting the mortality rate at more than 50%.

Yet, thanks to a new vaccine, it look as though the fight against Ebola is making significant progress. “Preliminary study results of the new injectable Ebola vaccine, named Ervebo, have shown it is nearly 98% effective and can reduce the chances of dying for those who have already been infected, according to WHO.” This is a massive step forward in the fight against one of the deadliest viruses known to humanity. In an effort to get this life-saving vaccine distributed ASAP, clinical trials of the vaccine have been fast-tracked. While this inherently contains some risk, that risk is almost certainly worth it when considering the severity of Ebola infections.

Making matters worse, the current armed conflict in the DRC not only puts healthcare workers and civilians at risk of Ebola but at risk of being caught up in armed conflict as well. Also concerning for public health officials is the degree to which displacement caused by the armed conflict is exacerbating the spread of Ebola. An almost unimaginably difficult situation by any measure, but progress is being made.

Citation: Gigova, Radina. “Amid looming coronavirus crisis, progress made in fight against Ebola.” CNN, 15 February 2020. https://www.cnn.com/2020/02/15/world/ebola-fight-milestone/index.html. Accessed 17 February 2020.

Post by Richard Hackmann

When Enemies Become Friends: Using Ebola to Fight Glioblastoma

When can enemies become our ally? George Orwell said it succinctly in 1984: ““We do not merely destroy our enemies; we change them.” One of the deadliest viruses in the world - the infamous Ebola virus - may actually be a tool to fight glioblastoma - an aggressive brain tumor that is notoriously difficult to treat. Many cancer cells inherit a major weakness, which is an impaired innate immune response to foreign invaders like viruses. A team from Yale experimented with chimeric viruses containing genes from different viral species to target the cancer cells without causing a deleterious infection to the patient. They found success with an Ebola gene called glycoprotein with a mucin-line domain (MLD) which helps the virus evade the immune system. When a chimeric vesicular stomatitis virus virus was introduced into the brains of mice with glioblastoma, it selectively targeted and killed the tumor cells. The study marks an incredibly exciting and promising approach to making safer and more efficacious treatments of invasive cancers such as glioblastoma which remains a death sentence for its victims. This experience can also teach us that our greatest enemies can be “changed” into allies with an open mind and a larger cause. 

~Avi Kaye

Article: Zhang et al. Mucin-like domain of Ebola virus glycoprotein enhances selective oncolytic actions against brain tumors. Journal of Virology, 2020. DOI: 10.1128/JVI.01967-19

Fact-Checking 'Contagion' — In Wake Of Coronavirus, The 2011 Movie Is Trending

Pandemics in general and viruses in particular provide rich material for Hollywood. The outbreaks provide an ideal backdrop to explore the dark underbelly of the human condition. It is no wonder why the zombie virus archetype has lived on for more than sixty years. In light of the coronavirus in Asia, the 2011 movie Contagion has experienced a rebirth in cultural circles, among the top-trending movie rentals and downloads this winter. Starring Gwyneth Paltrow, Matt Damon, and a host of other A-listers the film proves ideal for the current crisis because its plot closely mirrors that of the coronavirus. What proves particularly noteworthy is its level of scientific accuracy. Starting with bats, then transmitted to pigs, then to humans the film offers a plausible series of events for how the virus came to be transmitted. Once the outbreak hits, EIS agents find a prominent role. Their representation is consistent with standard practices in the field. While Hollywood plays fast and loose with speed of transmission, the movie nonetheless offers the term fomite into a broader cultural lexicon. R-naught is even discussed in the film!

Patrick Moynahan

https://www.npr.org/sections/goatsandsoda/2020/02/16/802704825/fact-checking-contagion-in-wake-of-coronavirus-the-2011-movie-is-trending

Pneumonia: how to treat it following COVID-19 infection

When individuals die of COVID19 or influenza virus, they often have developed an infection, such as pneumonia. The flu can cause pneumonia directly, but often pneumonia is caused by a bacterial opportunistic infection. Though the cause is often difficult to isolate completely, treatment regimes for viral vs bacterial pneumonia can be very distinct. Doctors often turn to antibiotics for pneumonia when the etiology is uncertain. In cases of viral pneumonia, anti-virals such as Tamiflu are used, but studies have yet to show the effectiveness of these medications against pneumonia.

COVID19-related pneumonia seems to be different and there is much uncertainty surrounding best treatment practices in this case. Current practices include oxygen supplementation and giving fluids and medicines for nausea, dehydration and other symptoms.

- Micah

https://www.inquirer.com/health/flu-coronavirus-covid-19-pneumonia-vanderbilt-penn-johns-hopkins-jefferson-20200214.html 

Debunking Fake News often unsuccessful

Emerging infectious disease are the perfect scenario for media to capitalize on the publics' emotions. Researchers at Dartmouth College, IE University in Spain and other institutions conducted social science experiments showing that attempts to combat false information about the Zika virus with information from the World Health Organization often was counterproductive. Individuals tended to maintain their perspective and lost confidence in the accurate information concerning the virus. 

A major takeaway from these studies is to use news platforms in order to promote simple best practices for preventing and protecting against specific pathogens rather than overemphasizing attempts to debunk misconceptions. This perspective could also be important in promoting vaccination. 

-Micah

https://www.scientificamerican.com/article/attempts-at-debunking-fake-news-about-epidemics-might-do-more-harm-than-good/ 

China’s reclassification of Novel Coronavirus diagnosis results in spikes in infections and death toll

After a flurry of hopeful reports that the number of new infections was beginning to decline, China reported significant increases in both new coronavirus diagnoses and suspected coronavirus deaths late on February 12. As reported by CBS News , new coronavirus diagnoses in China totaled 14,480 and deaths totaled 242. Of the new diagnoses, some 13,332 (92 percent) and half of the reported deaths are ascribable to China’s adoption of a new, broader definition of a confirmed coronavirus cases. The new definition was enabled by the utilization of lung imagining, in addition to the standard nucleic acid test protocol, to identify new infections.

While the expansion of the epidemic is troubling (though seemingly not surprising), China’s revised numbers are a positive development in at least three keys ways critical to the eventual management and control of the virus’s spread. First, the numbers demonstrate that China is investing time and resources into rapidly reaching a better and more accurate means of diagnosing and better understanding the illness caused by the virus. In fact, more accurate diagnoses are important to limit the spread and impact of the illness but, at least in the near term, they are not helpful to China’s efforts to suggest that it is gaining control over the epidemic or its economic stability. That China sees the benefit of investing in developing a better medical understanding is a good sign.

Those realities play into the second point, which is that China’s revised numbers help bolster the credibility of its data and the justified reliance on that data by third parties trying to track the trajectory of the epidemic. China had a slow start regarding transparency, delaying the release of reports of the illness and then underplaying its spread and numbers. The new diagnostic protocols (and the concomitant increase in cases and deaths) does not aid China’s efforts to contain the now international damage it is suffering at many levels, nor does it reassure its own populace that the government has gained control over the spread of the virus internally. But it does show that, at least until demonstrated otherwise, China sees the benefit of valid data even if the data is derived at the expense of its own reputation. That gives greater credence to the data.

Finally, about the people, the new diagnostic tools enable China to offer better and faster treatment for its affected citizens. Knowing who actually has the virus is key to quarantine and other responsive measures. In addition, knowing who has the virus earlier may lead to better and more timely interventions which, in turn, may lessen the mortality rate. While the urgent construction of temporary hospitals belies chaos in a medical response, at least there is a chance that these newly diagnosed patients will get the right treatment sooner.

~~ David M. Walsh

Coronavirus came from bats or possibly pangolins amid ‘acceleration’ of new zoonotic infections

Joel Achenbach’s article titled, Coronavirus came from bats or possibly pangolins amid ‘acceleration’ of new zoonotic infections, reveals the danger of a zoonosis, which is the ability of viruses to infect humans from an animal host. The article points out that the coronavirus is very similar to two viruses found in bats but there is a chance that the virus affected another species before infecting humans. Some researchers believe the “pangolin” might be responsible for this occurrence because the coronavirus that infects pangolin’s “is more closely related” to the coronavirus infecting humans. Researches also hint that if the pangolin is responsible for the coronavirus it will be extremely difficult to track down and trace because it is sold on the black market. Pangolins are endangered and trading them are illegal. When studying overall diseases since 1940, more than sixty percent of emerging diseases have been zoonotic according to a British Medical Journal. This can be explained because of new contact humans are having due to land and global changes

This article relates directly to our “Virus in the News” class because it focuses on a virus depending on hosts. In our class we learned that some of the hosts can be animals. These vectors make efforts to slow the spread of the virus very difficult because scientists cannot pinpoint the cause or host. For example, yellow fever wreaked havoc for close to 250 years before researchers figured out the mosquitos were spreading and infecting humans. Hopefully, the coronavirus will not take 200 years to pinpoint the cause and spread of the virus.

~~ John Sikora

https://www.washingtonpost.com/health/coronavirus-came-from-bats-or-possibly-pangolins-amid-acceleration-of-new-zoonotic-infections/2020/02/07/11eb7f3a-4379-11ea-b503-2b077c436617_story.html

Bats as Viral Resevoirs

Bats’ unique immune systems may amplify the lethality of zoonotic viruses passed to other animals and humans, a new UC Berkeley study finds. Bats seemed to have developed an important adaptation related to flight that allows them to avoid inflammation. Because the metabolism of bats in flight operates as twice the speed for similarly sized rodents who don’t fly, one would expect the life span of bats to be very short. In general the faster the metabolism in small animals, the shorter the life span due to the accumulation of free radicals and other malign molecular detritus. Yet Bats can live as long as 40 years where similar sized rodents are good for just a couple of years. The same quirk of bat physiology that enables them to clean up free radicals also enables them to avoid inflammation. This adaptation in turn allows the bat immune systems to run at much more aggressive tempo than seen in any other mammals. Humans for example would suffer debilitating inflammation if our immune systems ran at the same pace that bats’ systems run.  Cara Brook, a postdoctoral Miller Fellow at UC Berkeley and the first author of the study noted, “Our immune system would generate widespread inflammation if attempting this same antiviral strategy. But bats appear uniquely suited to avoiding the threat of immunopathology.”

Brook and her colleagues believe that viruses confronted with the bats’ intense immune response are triggered into a much more rapid replication cycle. The accelerated replication rate carries through the zoonotic transition. Thus even when the viruses jump to an intermediate host like civets in the case of SARS; Camels in the case of MERS;  chimpanzees and gorillas with Ebola; pigs and Nipah; horses with Hendra; and African green monkeys with Marburg,  the viruses still exhibit intense lethality after making the final jump into humans.

~~ Pete Dailey

Sources:

eLife 2020;9:e48401cited in Sanders, Robert. Berkeley News, “Corona Virus Outbreak Raises Question: Why are Bat Viruses So Deadly?” 10 February, 2020. https://news.berkeley.edu/2020/02/10/coronavirus-outbreak-raises-question-why-are-bat-viruses-so-deadly/fbclid=IwAR3bHR5WODiHaDHArSuTyp7E0Hg1y2ANkFm4ypRUboWwuBbM_BtQyd_hqVM

Do You Know Which Part of Your Body Has a Memory Like an Elephant?

Modern research shows that Elephants do indeed have a tremendous memory.  It helps the herd survive because the matriarch can remember other Elephants’ identity and recognize them as familiar or foe.   Memories last for decades and also include how the herd survived a drought three decades earlier by migrating to a distant land that had more water and food.   Recognition techniques include using their trunk to feel another elephant’s pattern of scars on its body.   Wow.


Well, your own body has its own internal, elephant-like memory system in its “immunologic memory.”   Your immune system is your body’s front line of defense against a wide range of pathogens (viruses and bacteria).   If your body had previously fought that pathogen, your immunologic memory will help your system marshal a strong and almost immediate defense against a new invasion, even if its decades later.


Here’s a simple example:   in 1781 the Faroe Islands (between Norway and Iceland) were ravaged by a Smallpox epidemic.   Many died, but many also survived.   The survivors were all immune to Smallpox, and the islands did not have any small pox for 65 years later, when a visitor brought it back.   In that 1846 re-infection, not a single one of the elderly who had been exposed in in 1781 became ill.    Sixty-five years — how’s that for a memory as good (or better?) than an elephant’s?


~~ Robert M Carr

sources:
https://www.sciencemag.org/news/2019/04/how-long-do-vaccines-last-surprising-answers-may-help-protect-people-longer

https://www.scientificamerican.com/article/elephants-never-forget/

WHO proposes an official name for the new coronavirus: COVID-19

The World Health Organization unveiled a new name for the coronavirus: COVID-19. According to the director general of the WHO, Tedros Adhanom Ghebreyesus, this name does not refer to a “geographical location, animal, an individual or group of people” in an effort to avoid stigma by association with the disease.

As of Tuesday, Dr. Tedros reported that 1,017 people have died from the coronavirus, with the number of confirmed infections in China at 42,700 people. This is approximately 2,700 more than a day ago. Over 24 countries have reported cases of the coronavirus with 393 cases abroad.

The United States has 13 confirmed cases, including a 25-year-old man in Washington state, a couple in their 60s in Chicago, seven people in California, as well as single cases in Wisconsin, Arizona, and Massachusetts.

The New York Times has provided maps showing the spread of the outbreak, including one showing railway networks centered around Wuhan and neighboring Huanggang and Ezhou. As previously reported, Chinese authorities have continued to close off Wuhan canceling planes and trains and suspending buses, subways and ferries.

In the United States and other countries, several major airlines have reported plans to halt direct service to mainland China for months. While experts warn that closing borders to highly infectious pathogens does not fully succeed, such closures are hoped to allow more time to develop treatment and vaccines.

~~ Janette Rose Canare

Sources:
• “Coronavirus Updates: The Illness Now Has a Name: COVID-19.” The New York Times, February 12, 2020,. https://www.nytimes.com/2020/02/11/world/asia/coronavirus-china.html.

• Lai, K. K. Rebecca, Jin Wu, Allison McCann, Derek Watkins, Jugal K. Patel, and Richard Harris. “Coronavirus Map: Tracking the Spread of the Outbreak.” The New York Times, February 11, 2020. https://www.nytimes.com/interactive/2020/world/asia/china-wuhan-coronavirus-maps.html.

U.S. public health response to Wuhan CoV

According to an article in the February 10, 2020 issue of the San Francisco Chronicle by Erin Allday, experience with the earlier epidemics of SARS and MERS are guiding U.S. authorities in responding to the novel coronavirus. The U.S. public health response has been both more aggressive and less chaotic than it was with the earlier outbreaks.

Compared to SARS and MERS, the new coronavirus is both better and worse. It has produced far more cases (40,500 in 3 months vs 8,100 in 5 months for SARS and 2,500 cases total for MERS), but the mortality rate is much lower (2% vs 10% for SARS and 30% for MERS). Although China can be faulted for its response, it is still a big improvement over the situation with SARS (it took China 4 months to report SARS, but only a little over a month to report the novel coronavirus). Improved technology has played a big role in tracking this outbreak -- with SARS, testing could take weeks and often wasn’t done at all, while the current virus was identified within weeks and testing can be done in under 24 hours, including time to transport samples to a central testing location.

The other lesson is that it all starts at the airports. As a result of the experience with SARS, travelers from China are being funneled to specific airports which are equipped to screen them. As a result, potential sufferers are being identified early, both preventing them from being at large and making it easier to identify their contacts (since the number of contacts is much smaller).

~~ Steve Blasberg

Outbreaks in the Light of Quantitative Information

When faced with an outbreak of global proportions, it is easy to get overwhelmed. Clearly there is no shortage of rumors, conspiracy theories, and false news. But in such situations it is hard even to make sense of the "facts" because it is difficult to put those facts in the proper perspective or context. Without such a context, facts can be as confusing as rumors. One of the main ways in which a context can be provided is through comparing the current scenario or case of interest with other similar scenarios or cases which are not currently the news.  And what makes such comparisons even more effective is when they include quantitative information.

Such a context is exactly what I encountered in a recent article by the New York Times.1 The article includes a chart that characterizes the Corona virus against the background of other well-known (or well publicized) outbreaks (Fig. 1). The chart has two axes. The horizontal axis represents the average number of people who can be infected by a single sick individual. The range of the horizontal axis is 0 to 15, with MERS being the lowest (~0.7 infections per person) and Measles the highest (15 infections per person). The vertical axis represents the mortality rate, which starts from 0 (with common cold and Chickenpox) and goes as high as 70% (with Bird flu). Ebola, for instance, is rated at 50% fatality rate. Within this chart, currently the coronavirus occupies a relatively large area with an estimated transmission rate of 1.5 to 3.5 (persons infected by a single sick person) and the mortality rate estimate of 0.1% to 3%. The wide range is due to the evolving nature of the situation and is expected to narrow down as more data and statistics become available.

Apart from putting the current outbreak in perspective, the advantage of this chart is that it quantifies the risk and provides a more accurate and nuanced picture of viral infectious epidemics. As such, it provides a valuable counter balance to the massive mixture of qualitative and often emotionally charged forms of news that we encounter on a daily basis.

~~ Moe Azadeh

1. https://www.nytimes.com/interactive/2020/world/asia/china-coronavirus-contain.html

Cruise Ship 2019-nCoV Outbreak Creates Uncertainty, Fear

At a port in Yokohama, Japan, just outside of Tokyo, a quarantined cruise ship is becoming ground zero for the complexity that results from global health issues in the 21st century. The stranded Princess Cruises ship, with more than 3,500 passengers and crew onboard, is in the midst of a 2019-nCoV outbreak that is leaving passengers, crew members, public health leaders, and government officials scrambling for solutions to address the deteriorating conditions onboard.

While the close quarters of cruise ships are known for facilitating the spread of norovirus, an uncomfortable but normally not lethal viral infection, addressing the current 2019-nCoV outbreak onboard is presenting a far more complex set of problems as officials try and balance quarantine efforts with the realty that prolonged exposure is likely to result in a significantly higher rate of infection.  As of February 10, 2020, 135 people onboard the ship had been infected. That is approximately 3.8% of the onboard population and is a significant increase from previous totals. “According to Princess Cruises, which operates the ship, at least 20 of them are American. The ship already has the largest number of coronavirus cases outside the epicenter in China, where more than 40,000 have been infected.”

The crew in particular is facing significant risk since they live in closest proximity to one another and undergo the greatest amount of daily interaction with passengers (who are currently quarantined to their rooms for most of the day). “While the quarantine slapped on the Diamond Princess was meant to contain the virus, the conditions facing the crew could end up doing the opposite and help spread the illness, disease experts say.” So far it does not appear that a majority of the identified cases have impacted crew members but the situation is fluid.

The reality of quarantines is that they project those outside but it can be to the detriment of those within. The difficult balancing act becomes doing what is best for the majority without sacrificing or endangering the well-being of the minority.

Citation: Dooley, Ben and Motoko Rich. “Cruise Ship’s Coronavirus Outbreak Leaves Crew Nowhere to Hide.” The New York Times, 10 February 2020. https://www.nytimes.com/2020/02/10/business/coronavirus-japan-cruise-ship.html. Accessed 11 February 2020.

Post by Richard Hackmann

Pump the Breaks! Flavivirus Protein Intentionally Slows Replication

Most viruses seem to follow a shared 8-step lifecycle where they enter the host cell, replicate, and after some period of time egress to spread their viral progeny. However, we still have much to learn about how viruses complete their lifecycle. A research team at Colorado State University (my home state!!) focused on the Non-structural protein 3 (NS3) in flaviviruses - Zika, Dengue and West Nile - to uncover replication mechanisms. NS3 is a viral helicase that utilizes ATP to unwind transient double-stranded RNA that is formed during replication. Surprisingly, they found that NS3 actually “pumps the brakes” on viral replication, and with mutations that impaired the braking system, the virus replicated less efficiently. Furthermore, they identified Motif V in the NS3 protein as a ‘communicator’ between the ATP and RNA binding pockets. The study represents an initial step in learning how flaviviruses might regulate an optimal replication speed using protein structure, and similar motifs are used across different viral families. With additional knowledge about the NS3 protein structure and function, researchers will be able to investigate the Motif V as a potential antiviral drug target or even a method of efficiently creating an attenuated vaccine! 

~Avi Kaye

Article: Du Pont et al. Motif V regulates energy transduction between the flavivirus NS3 ATPase and RNA-binding cleft. Journal of Biological Chemistry, 2020; 295(6) 1551–1564.

Scientists Discover Mysterious Virus in Brazil With No Known Genes They Can Identify

A team of South American researchers discovered a new virus whose genome has never before been documented in viral research. Named Yaravirus, after a mythic Brazilian water-queen figure, scientists recovred the virus in Lake Pampulha, Brazil. The same team discovered a “giant” virus which existed in watery habitats. Yara represents a new lineage of amoebal virus, previously unknown to science. Nearly 90% of its genes had not been transcribed before. While Yara is not a giant virus, composed of 80 nm-sized particles, nonetheless this discovery illustrates how much there is still to learn about viruses and viral agents. It could be an isolated case of an unknown group of amoebal virus, or a giant virus which evolved in a reduced form.

-          Patrick Moynahan

https://www.sciencealert.com/mysterious-virus-discovered-in-brazil-has-no-known-genes-scientists-can-identify

Despite herculean human efforts, it may be weather that stops the virus

History tends to repeat itself and so it may be in the case of the Novel Coronavirus, which has already infected more people worldwide that its cousin, the SARS virus, when the weather in China warms in late spring.1 According to epidemiology statistics, the infection rate for both SARS and more common influenza virus strains subsides as the weather improves (the peak month for new infections is usually February). While the frenzied efforts to identify, map, contain and eradicate the Novel Corona virus will likely continue apace or intensify in the coming weeks, the hard lesson for human kind may be that, despite our best efforts, things completely out of our control such as higher temperatures and higher humidity may be far more effective than the weapons in our man-made disease fighting arsenal. Obviously, that reality has far reaching implications if, as some scientists suspect, human interaction with life threatening viruses increases as the population expands. Of course, that is not to say that current measures—quarantines, contact tracing and travel bans—are not good emergency efforts to control the spread of the virus but, by their very nature, they are and must be temporary, especially where, as here, the virus has already spread on such a global scale.

Scientists in Hong Kong have completed studies regarding the response of the SARS virus, another coronavirus that had spread convulsively during the winter of 2003, to climate effects such as temperature and humidity. The research, conducted at Hong Kong University by Professors Malik Peiris and Seto Wing Hong, demonstrates that the SARS virus is able to survive much longer at lower temperatures and humidity. Interestingly, the research team linked its observations to the anomalously low incidence of SARS in humid Southeast Asian countries and to its virulence in locations where air conditioning keeps temperature low and the air dry, such as Hong Kong.

As it appears that the Novel Coronavirus is spread from human to human through the same channels as influenza, these same environmental factors (cold weather) compel human behaviors (long periods of time indoors in close contact with other humans) that may enhance the spread of the virus.

The weather is a big deal. By comparison, and as the past weeks have shown, human tools to combat the spread of an infectious virus seem to have limited efficacy. Even with the panic and attention being lavished on this coronavirus, and the availability of almost instantaneous updates around the world, human ability to control the virus’ spread seems disturbingly limited. Waiting for the weather could be a costly alternative in terms of human life and damage to world economies.

~~ David M. Walsh

1: Somani, J., and Tambyah, P., “Hot and humid weather may end the Novel Coronavirus." NUS News, 07 February 2020. https://news.nus.edu.sg/research/hot-and-humid-weather-may- end-novel-coronavirus. Accessed on 08 February 2020.

Big Data Payoff in 2019-nCoV Virus Illustrates the Value of Knowledge

What value do we put on knowledge? It is a core topic of epistemology. A few weeks ago, I wrote about the Global Virome Project (GVP) and its mission to map the genomes of the viruses in the animal kingdom. I also mentioned critics of the project believe money should be spent on fighting infectious disease outbreaks, not on identifying non-human viruses that may or may not ever cause an outbreak (4). In other words, the skeptics do not see any human or scientific value in the GVP vision—a virus database.

These critics may reconsider and re-evaluate their position in light of the current coronavirus outbreak in China. The probable natural reservoir of the culprit coronavirus, bat, was quickly identified due to works by virologist Dr. Shi Zhengli 石正麗 and her team. Dr. Shi has set herself and her team the task of mapping all the viruses bats carry (1). Dr. Shi was one of the scientists who identified that bats are the natural hosts for Sars. She is also the builder of the world’s largest database on bat-related viruses. For the past eight years, she and her team have been “caving” for bats in China. They have “caved” in 28 Chinese provinces and collected samples from over 10,000 bats and 2,000 other species (3). When her team ran the genome of the new coronavirus against their database, they found a 96% match in a ragt13 coronavirus found in a fruit bat in the Yunnan province (5). If her database hadn’t existed, the path to knowledge of the current coronavirus outbreak would have taken much longer.

~~ You Jia Zhu

1. Stephen Chen, “Coronavirus: bat scientist’s cave exploits offer hope to beat virus ‘sneakier than Sars’, South China Morning Post, Feb. 6, 2020.

2. Guojie Zhang, Christopher Cowled, Zhengli Shi, et al, “Comparative Analysis of Bat Genomes Provides Insight into the Evolution of Flight and Immunity”, Science 339, No. 6118: 456-460.

3. Jon Cohen, “Mining coronavirus genomes for clues to the outbreak’s origins”, Science, Jan. 13, 2020.

4. Olga Jonas and Richard Seifman, “Do we need a Global Virome Project?”, The Lancet Global Health, vol. 7, issue 10, October 2019, pp. 314-6.

5. 杨睿, 冯禹丁, 赵今朝, “石正丽回应质疑 专家一致认为新冠病毒非人造”, 《财新》2020年2月5日。Yang Rui, Feng Yu-ding, Zhao Jinzhao, “Shi Zhengli Responds to Questions, Experts Agree the New Coronavirus Are Not Created in a Lab”, Caixin, Feb. 5, 2020.

Doctor who was silenced for sounding alarm about coronavirus dies of disease

The Washington Post reported this morning that 34-year-old Dr. Li Wenliang, an ophthalmologist at Wuhan Central Hospital, died today of novel coronavirus disease.

As early as December 30, Dr. Li tried to warn his medical school classmates about the existence of a contagious new virus that resembled SARS. Li’s warning began to spread throughout China, but his posts were censored, and on January 1 he was detained by police for “rumor-mongering.” He was released two days later, after signing a document admitting the illegality of making “untrue statements” on social media and promising that he would “earnestly reflect” on his mistakes.

After detaining Li, Wuhan police appeared on Chinese state television to discourage the public from spreading rumors. That same day, a coordinated media initiative told Internet users throughout China to not believe online rumors and help maintain a “clear and bright cyberspace.”

Within a week of his release from police detention, Li returned to work and began to receive a flood of patient checking into Wuhan’s hospitals with respiratory distress. He began coughing on January 10, he later recalled, and checked himself into the hospital as a patient around January 16. On February 1 he posted on social media that he had tested positive for coronavirus. He shared with his followers that he had quarantined himself as soon as he suspected infection, but his mother and father had recently been hospitalized for fever and he did not know whether they had contracted the virus. Also at risk were Li’s pregnant wife and young child.

The outpouring of support lifted Li’s spirits after the crackdown on his warning. “I’ve seen the support and encouragement so many people online have given me,” he wrote. “It makes me feel a little more relaxed in my heart.” Luo Yu, a technology industry executive who was one of Li’s college classmates, wrote that “The Wuhan government owes Dr. Li Wenliang an apology,” in a widely circulated post. And in a rare censure of police, China’s judicial authorities wondered whether the epidemic might have unfolded differently if Li had not been silenced. Upon learning of his death, Michael Ryan, the executive director of the World Health Organization’s health emergencies program, commented, “We are deeply saddened by the passing of Dr. Li Wenliang. We all need to celebrate work that he did.”

Shortly after his death was confirmed a literary verse began to circulate on social media, in response to Li’s courage: “He who holds the firewood for the masses,” they wrote, “is the one who freezes to death in wind and snow.”

~~ Amy McPhie Allebest

https://www.washingtonpost.com/world/asia_pacific/chinese-doctor-who-tried-to-raise-alarm-on-coronavirus-in-wuhan-dies-from-disease/2020/02/06/8bf305a2-48f9-11ea-8a1f-de1597be6cbc_story.html

As virus fallout widens, China readies more measures to stabilize economy

As the coronavirus spreads through China, the economic fallout is not something to overlook. Operating under the expectation that the virus will seriously hamper first quarter growth, the communist party plans to introduce quantitative easing measures to help curb the slide. As the article stresses, the top brass obsesses over social stability. This outbreak itself on top of a backsliding economy has led to an increase in monetary policy. Such actions illustrate the effects a widespread outbreak can have beyond public health. Actions such as increased government spending, tax relief, and incentives for bank lending alongside lower borrowing costs for businesses are all on the table to lessen the economic fallout.

In 2019 China’s economy grew by 6.1%, the weakest in nearly thirty years. A slow start to the first quarter of 2020 would indicate that this year would be even lower. Unlike the SARS virus China endured last decade, this economy depends more on consumption and services. The coronavirus has curtailed both as major cities and transit lines have been shut down. As always the threat of further spread could curtail growth even further.

-          Patrick Moynahan

https://www.reuters.com/article/us-china-health-economy-exclusive/exclusive-as-virus-fallout-widens-china-readies-more-measures-to-stabilize-economy-sources-idUSKBN1ZY103

The non-obvious costs of the corona virus: measured reaction or panic?

The U.S. stock market fell 600 points on Friday, January 31. China is closed. Tech stocks are vulnerable. Airline travel is down precipitously. More than 10,000 people have been infected in the past two months and, of those, at least 213 have died (as of the end of the day on Friday)[1]. All in all, a pretty big impact for a pretty tiny virus. Speculation regarding the longterm economic impacts of the Wuhan coronavirus continues apace with experts predicting potentially significant and lasting damage to (at least) China’s economy.

The availability of instantly available information—a stream of “data” addressing the spread of the virus, new cases, speculation on modes of transmission, efforts to contain it—has likely magnified its impact materially. On the positive side, that information is absolutely critical to public health officials efforts to track and contain the spread of the virus. At the same time, the easily available but not-always-reliable information stream has exacerbated the response and the panic surrounding spread and risk of infection. Interestingly, while the virus is a cousin of the SARS virus, and while there is a world of information available regarding the spread, containment and trajectory of SARS, little or none of that real data seems to be filtering into either public or market response. The evident impact that the Wuhan virus is having foreshadows greater risk to world stability arising from other more and less deadly viruses in the future. As the human population expands, it will undoubtedly encounter new viruses and will have to address the risk of exposure and illness in a thoughtful and more targeted fashion. It seems unlikely that humans can rely on that these exposures will obtain on a once every decade and a half time frame.

~~ David M Walsh

1: Veiga, Alex. “Stocks sink on fears virus outbreak will dent global economy.” The Seattle Times (Seattle) 31 January 2020. 

HIV vaccine hopes dashed by trial results

Michelle Robert’s article titled, HIV vaccine hopes dashed by trial results, reveals the preventive vaccine called HVTN 702 was ruled “non effective” toward HIV. Doctors have vowed that the research much continue to develop a safe and effective HIV vaccine to end the “global pandemic.” The article does point out that a drug called, Pre-Exposure Prophylaxis does exist in preventing HIV but needs to be takes regularly unlike a vaccination.

This article relates directly to our “Virus in the News” class because it focuses on a vaccine to eradicate HIV. Last week, Dave had a very informative presentation on HIV. This article gives the most up to date information on HIV vaccinations. Doctors are not giving up the fight despite this recent setback.

~~ John Sikora

Source: https://www.bbc.com/news/health-51361955

Coronavirus Zoonoses

Coronaviruses commonly infect animals but notable examples have made news by jumping to people. This transition is called zoonosis. Subsequent to zoonosis, some coronaviruses can also pass from human to human. A variety of animals are known sources of coronaviruses. The Middle East respiratory syndrome coronavirus (MERS-CoV) originated from camels and the Severe Acute Respiratory Syndrome (SARS) originated from civet cats. Wuhan NCoV 2019 appears to have originated from bats.

Coronaviruses, named for the crown-like appearance of the virions under electron microscopy,  are enveloped RNA viruses from the Coronaviridae family. Coronaviruses infect the respiratory and gastrointestinal systems as well as occasionally affecting the liver and the neurological systems.

When Coronaviruses infect humans, the Case–fatality ratio (CFR) varies. Zoonotically contracted MERS CFR is comparatively high, probably about 40%, with mortality rates increasing with age or co-morbidity. Secondary cases, including among healthcare workers, appear to have a lower CFR. Early indications for Wuhan NCoV are that the CFR is around 2% or perhaps lower. There is still insufficient data to make a more reliable determination.

The most concerning aspect of Wuhan NCoV 2019 appears to be that the pathogen is easily transmitted from person to person. “It’s very, very transmissible, and it almost certainly is going to be a pandemic,” said Dr. Anthony S. Fauci, director of the National Institute of Allergy and Infectious Disease, quoted in the NY Times. The spread of NCoV is not as rapid as the flu or measles, but it is much more rapid than the other recent outbreaks in the news, SARS and MERS.

~~ Pete Dailey

Sources:

https://www.ecdc.europa.eu/en/facts-0#C3

https://www.ecdc.europa.eu/en/novel-coronavirus-china/questions-answers

https://www.nytimes.com/2020/02/02/health/coronavirus-pandemic-china.html

R0 Is Not All that Matters

I previously posted about ‘Why R0 Matters,” explaining that R0 (that’s “R-zero” or “R-naught”) is medicine’s measurement of how infectious a pathogen (such as a virus) is in a host population.   In the current Wuhan Coronavirus outbreak (2019-ncov), much press coverage is mentioning that scientists don’t know that R0 for this new virus is, but estimates place it in the 1.5 to 2.5 range.  That means that if someone has 2019-ncov, they will, on average, transmit it to about 1.5, 2 or 2.5 other people.   That’s pretty infectious, but not nearly as bad as other viruses (Smallpox had a R0 of 3.5-6). 

But R0 is not all that matters when it comes to trying to limit or stop a virus from spreading.   One way to stop spread is through quarantine, but quarantines do not always work, and the best way to protect a population from a virus is for the population to have immunity to the virus.  A population can sometimes develop immunity by catching the virus (or a weaker version of it) through natural exposure, but the best way (at least in developed countries) to immunize a population is through immunization.   Which leads to the question of how many in the population need to be immunized to stop a virus from spreading?  This number of what percentage of a population needs immunization is called the “threshold.”

The answer depends on on how “effective” the vaccine is. The WHO states “no vaccine is 100% effective. To make vaccines safer than the disease, the bacteria or virus is killed or weakened (attenuated). For reasons related to the individual, not all vaccinated persons develop immunity. Most routine childhood vaccines are effective for 85% to 95% of recipients.” (see https://www.who.int/vaccine_safety/initiative/detection/immunization_misconceptions/en/index2.html )

Just as a stool has 3 legs, the answer to ‘how many need immunization’ (that is, the “Threshold”) has 3 variables:   R0 (how infectious), the Effectiveness of the Vaccine, and the Threshold number.

Imagine the extreme of a virus with very low R0 of 1.1 — it is barely infectious at all.  Therefore, if you have a highly effective vaccine, you don’t need the Threshold percentage of the population to be high.   But if the vaccine is relatively ineffective, then you need to inoculate a higher Threshold.

At the other extreme, if a virus has a very high R0 of 5 or 8, then you need both the vaccine to be quite effective, and you need to vaccinate a very high Threshold percentage of the population.

~~ Robert Carr

The Trump administration has made the U.S. less ready for infectious disease outbreaks like coronavirus

As the Wuhan coronavirus outbreak continues, an article by Linda J. Bilmes  (Senior Lecturer in Public Policy and Public Finance, Harvard Kennedy School) considers how the Trump administration has harmed the ability of the U.S. to respond to infectious disease outbreaks. The article cites a decrease in appropriation levels for relevant CDC programs, down 10% from 2016, adjusting for inflation. Moreover, in 2018, Trump attempted to cut $65 million from the agency’s budget, a 10% reduction. In 2019, he sought a 19% reduction. In 2020, he proposed to cut federal spending on “emerging and infectious zoonotic diseases by 20%.” Congress, however, reinstated the funding with bipartisan support.

Changes in personnel, however, have resulted in the loss of qualified and respected leadership that would be critical to navigating a course capable of thwarting the crisis of an infectious disease outbreak.

In 2018, the Trump administration disbanded the global health security team, the group that had been tasked with helping the U.S. build its resiliency to epidemic threats. The global health security team was a casualty of a reorganization of the National Security Council (NSC) as ordered by John Bolton, the then national security advisor.

In response to Bolton’s elimination of the global health security and biodefense directorate, two respected leaders left the White House: Rear Admiral Tim Ziemer who served as the NSC’s senior director for global health security and biodefense, and Homeland Security adviser Tom Bossert.

During his tenure under Presidents George W. Bush and Barack Obama, Zimmer

Ziemer’s track record during his tenure under Presidents George W. Bush and Barack Obama included a global anti-malaria campaign that reduced deaths by 60% over 15 years. Zimmer estimated in 2016 that “funding initiatives to reduce malaria generated a 36-to-1 return on investment because it averted so many deaths and debilitating interests. In 2018, he traveled to the Democratic Republic of the Congo to assist with the fight against the reemergence of Ebola.

~~ Janette Canare

Source:
Bilmes, Linda J. “The Trump Administration Has Made the U.S. Less Ready for Infectious Disease Outbreaks like Coronavirus.” The Conversation. Accessed February 3, 2020. http://theconversation.com/the-trump-administration-has-made-the-u-s-less-ready-for-infectious-disease-outbreaks-like-coronavirus-130983.

Viruses, False News, Rumors, and Conspiracy Theories

The Corona virus outbreak provides an interesting case to observe and study a wide range of phenomena, bringing to light issues one would generally not associate with a virus outbreak. One of the fascinating issues that has emerged is the proliferation of false news.

Ever since the news of the outbreak broke out, there have been wild speculations about the source of the virus. Among those, a slew of Videos that purportedly showed people in China eating bat soup contributed to the claim that the virus has jumped from bats to humans. According to the BBC1, one such video that has attracted a lot of attention (and anger) showed a smiling Chinese woman holding a cooked bat and claiming that it tasted like chicken. However, BBC asserts that that video has not been shot in Wuhan or even in China. Instead, it has been filmed in 2016 in Palau, an archipelago in the western Pacific Ocean and by a blogger and travel show host. Mengyan Wang, the show host and blogger, has now apologized and has said that she had just wanted to introduce the customs of the people of Western Pacific. It turns out that bat soup is not particularly common in China after all.

Another interesting case, according to BBC, is that of conspiracy theorist and YouTuber Jordan Sather. He has shared a link to a patent filed in 2015 by the Pirbright Institute in Surrey, England. The patent talks about the development of a version of coronavirus for use in vaccines. This video has been shared mainly by conspiracy and anti-vaccination groups. Sather suggests that the Gate foundation has released the virus intentionally to attract funding. Others claims that the virus has been part of a covert biological weapons program in China. There is also an unsubstantiated video of a woman (supposedly in Wuhan) wearing protective suit in an unknown location who claims that the actual number of infections in China are more than 90,000. She also claims that there is a “second mutilation” of the virus that can infect up to 14 people (as opposed to 1-2 people).

The explosion of conspiracy theories, fake news, fand acts mixed with fiction, I think, shines a light into the human psyche more than the actual situation. We humans are proud of our claim to rationality. However, it is in such occasions that the irrational forces within us surface and show their power over us.

~~ Moe Azadeh

1. https://www.bbc.com/news/blogs-trending-51271037