Monday, March 23, 2020

Mosquito salivary gland protein

Mosquito-transmitted viruses have evolved ways to enter and persist in human populations. Evidence has shown that mosquito salivary gland proteins can manipulate host cellular and immune responses in a manner that enhance viral transmission efficiency from mosquitoes to humans, an essential step in the lifecycle of flaviviruses.

This study focused on AaVA-1, an Aedes aegypti salivary protein, which promotes flaviviral replication in human monocyte-lineage immune cells, a primary intradermal target of flaviviruses during mosquito bite. Adding AaVA-1 to DENV or ZIKV results in high viremia and disease onset, while removal of AaVA-1 promotes low viral load. Not only does AaVA-1 play a role in transmission  efficacy, it also was found to be a positive regulator of autophagy, a cellular process that flaviviruses have usurped to promote viral replication in host cells.


-Micah

https://www.nature.com/articles/s41467-019-14115-z#Sec7 

Novel antiviral targets host nuclear transportin  α/β1 heterodimer

Currently, Dengue virus is treated primarily symptomatically, and, while there is a vaccine, it is not recommended for all people nor is it licensed in many countries. Thus, antivirals are still being investigated and could play a major role in treating this virus whose geography has expanded in recent years.

According to this study, GW5074 has potential as an anti-viral for flaviviruses. The mechanism of inhibition involves limiting NS5 nuclear targeting by halting NS5–IMPα/β1 interaction in vitro as well as NS5 nuclear localisation in infected cells. Inhibitors able to prevent nuclear import of viral proteins like NS5 are promising for anti-DENV treatment. The role of NS5 protein seems to be to suppress host antiviral response, partly through impacting host mRNA splicing. Thus, establishing that GW5074 has strong antiviral activity against DENV-2 as well as other flaviviruses, ZIKV and WNV, confirms that NS5 nuclear localization is a viable target for antiviral therapies.


- Micah


https://www.mdpi.com/2073-4409/8/3/281/htm

Tuesday, March 17, 2020

Aspirin able to reduce liver cancer risk?

Hepatocellular carcinoma is the fourth-leading cause of cancer mortality worldwide. This cancer primarily is driven by infection with viral Hepatitis B and C. While many cancers are declining in incidence, HCC is not.

A nationwide observational study based in Sweden identified low-dose aspirin as reducing risk of liver cancer and liver-related death in individuals with viral hepatitis. Though it is too early in studies to begin regularly prescribing low dose aspirin to all patients with viral hepatitis, the results of this particular study are promising. This study confirms a duration-response relationship with low-dose aspirin.  One next step would be a study with randomized participants in order to gather prospective data.

- Micah


Tuesday, March 10, 2020

Some good news: China appears to be getting the upper hand

While the news around the globe surrounding the spread of the Covid-19 virus continues to be bleak, with outbreaks and deaths in new places almost every day, the tide seems to have turned in China where it all started.   According to an Associated Press dispatch , China reported just 119 new diagnoses on Tuesday, March 4. That number is significantly below the diagnosis rate just 10 days earlier and marks a major shift in the virus’s momentum within China.   In addition, China, which has both the bulk of the world’s infections (more than 80,000) and 95% of the reported deaths caused by the virus, announced that more than 50,000 people have fully recovered from illness associated with the virus and the city of Wuhan, ground zero for the spread of the virus, closed the last of its emergency hospitals and discharged its final patients.    While these early week reports of diminishing infection rates encouraged observers to believe that the virus had largely run its course in China, China’s infection rate ticked up in a real but statistically insignificant way by the end of the week.   Notwithstanding the minor variation in reported infections, experts still believe that the worst if over in China.

Meanwhile, the West is bracing for the epidemic with equal measures of panic and fear.   The U.S. reported more than 230 active cases by weeks’ end, with major universities including Stanford, NYU and three in the Seattle area , announcing that they would suspend classroom and other meetings for the foreseeable future to try to inhibit further infection.  As detailed in countless news and online reports and dramatically reflected in the U.S. and other stock markets, the impact of the virus’ spread—and even more so, the fear of the virus’ spread— on the world’s economies has been extraordinary.


~~ David M. Walsh

Hinnant, L. And Moritsugu, K., “Virus crisis ebbs in China, spreads fear across the West.”  Associated Press.  (Paris) March 3, 2020.  Republished in the Marin Journal, March 4, 2020.  https://www.marinij.com/2020/03/03/virus-crisis-ebbs-in-china-spreads-fear-across-the-west/

Evolution of Coronavirus, seen from Wuhan

Last week, on March 3, 2020, an article (accepted manuscript) was published in the National Science Review. The article, titled “On the Origin and Continuing Evolution of SARS-CoV-2”, was authored by scientists from Peking University, Chinese Academy of Sciences, Peking Union Medical Collage, and Shanghai University. The authors discussed their findings of a single nucleotide mutation of the SARS-CoV-2 in the early days of the epidemic, or single nucleotide polymorphism (SNP). According to the authors, this new mutated type, given the name L-Type, is more “aggressive” than the ancestral S-Type. While L-Type is sending more people to the hospitals, the S-Type is one that is spreading more widely. Hence the apparent larger number of people with milder cases of Covid-19. (1) [NOTE: for a summary of the findings, see Coronavirus Epidemic Update 31, 2:21]

Another scientist, in his response to the article by the Chinese scientists, pointed out that when an RNA virus changes hosts, mutation often happens because the virus needs to adopt to the new host. In the case of SARS-CoV-2, that new host is us! (2)

Back in 2004, when the first SARS were happening, scientists already wrote about the viral evolution of coronavirus, and noted that among the emerging viruses, majority are RNA rather than DNA viruses. RNA’s higher mutation rate is one reason why RNA viruses adopt better to new hosts than DNA viruses, and accounts for its agility to cross species. (3)

Looping back to my first blog on the Global Virome Project, it is more apparent now than ever the need to invest in the project to map the viruses in the animal kingdom and other kingdoms, such as the marine viruses, to gain data and knowledge in the understanding of future emerging viral diseases.

~~ You Jia Zhu

1. Xiaolu Tang, Changcheng Wu, Xiang Li, Yuhe Song, Xinmin Yao, Xinkai Wu, Yuange Duan, Hong Zhang, Yirong Wang, Zhaohui Qian, Jie Cui, and Jian Lu, “On the origin and continuing evolution of SARS-CoV-2”, National Science Review, March 3, 2020.

2. “Expert Reaction to Study Looking at Whether There Are Two Strains of the Novel Coronavirus”, Science Media Center, March 4, 2020.

3. Edward C. Holmes and Andrew Rambaut, “Viral Evolution and the Emergence of SARS Coronavirus”, The Royal Society, July 29, 2004.

The ‘London Patient'

Apoorva Mandavilli’s article titled, The ‘London Patient,’ Cured of H.I.V., reveals that Adam Castillejo formerly known as the “London Patient” to protect his identity is just the second person in the world to ever be cured of the Human Immunodeficiency Virus. Mr. Castillejo battled HIV for ten years and recently underwent a bone marrow transplant to help treat his lymphoma cancer, which was a result of HIV. This transplant cured his HIV because the donor “carried a mutation that impeded the ability of HIV to enter cells, so the transplant essentially replaced Mr. Castillejo’s immune system with on resistant to the virus.” Bone marrow transplants is “not a practical option for curing HIV” because the procedure is extremely risky. Mr. Castollejo was diagnosed with HIV in 2003 and immediately adapted a healthy lifestyle regarding exercising and eating better.  But in 2011 he was diagnosed with Stage 4 Lymphoma and underwent chemotherapy, which also made complicated his treatment (medications) for HIV more difficult. In the spring of 2015, doctors revealed that Mr. Castillejo would live to see Christmas. Fortunately, Mr. Castillejo found one of the few hospitals who agreed to perform a “last ditch effort” of a bone marrow transplant with a patient who has HIV. As of today, Mr. Castillejo’s body shows no signs of the virus.

This article relates directly to our “Virus in the News” class because it focuses on the Human Immunodeficiency Virus that we have covered in class through lectures and two presentations involving the virus. After learning more about viruses and specifically the havoc HIV wrecks on the immune system it makes sense that the bone marrow transplant worked. By essentially “giving” Mr. Castillejo a new immune system that blocked HIV from entering the cells the virus was defeated. I do have a question for the class, why is a bone marrow transplant extremely? The article did not elaborate on this subject.

~~ John Sikora

Why is the coronavirus mysteriously sparing kids and killing the elderly?

Why is it that COVID-19 manifests itself so drastically different between young children vs. the elderly? In China, 2.4 percent of reported cases were children and of these, 0.2 percent were chronically ill. In contrast, the fatality rate for those over 80 in China is particularly deadly, estimated at 21.9 percent, according to the WHO, based on over 44,000 confirmed cases. Moreover, fatalities and severe symptoms for children under the age of 10 are almost nonexistent.

The previous coronavirus outbreak, SARS in 2002 killed 774 people, but also spared the young. No children died from SARS in 2002. Similarly, few children developed symptoms from MERS coronavirus which has counted 858 fatalities since 2012.

A virologist from the University of Texas, Vineet Menachery stated that respiratory infections typically show a U-shaped curve with children on one end and older adults on the other, as the immunity of the former group isn’t fully developed and that of the latter group is weakened. However, the U-shaped curve does not apply to COVID-19.

While numerous questions have been explored as an explanation, research to date remains inconclusive. Frank Esper, a pediatric infectious disease specialist at Cleveland Children’s Clinic suggests the possibility that the answer may have “nothing to do with the virus and has to do with the host, like underlying conditions in the lungs, diabetes, or hypertension.”

Menachery and his lab have conducted experiments with mice, finding that baby mice ward off coronavirus infection, while the lungs of older mice become ravaged from the disease. Moreover, Menachery found that the cause of the older mice’s fatalities were related not only to compromised immune systems, but a “disregulation’ that caused their immune systems to overreact to the SARS coronavirus. That’s similar to how humans die of infections from (COVID-19).”

Interestingly, Esper ads, “I suspect there’s something more mechanical than immunological going on…Something about the receptors in children’s bodies or their lungs is interfering with the virus’ ability to attach itself.” This comment from Esper is particularly relevant to my recent research of the coronavirus and the relationship between the spike protein trimers and the host receptors of ACE2 located deep in the bronchii.

The article also states that while children show much milder symptoms of COVID-19, contact testing—testing people who come in contact with a confirmed case—shows that children are getting infected at similar rates as adults. Thus, children are potential drivers of infection, spreading the virus to parents, relatives, and the wider community. For this reason, closing schools could help protect adults and staff from the outbreak.

~~ Janette Canare

An unusual solution

My son-in-law Matt is a lawyer working at the Securities and Exchange Commission (SEC) in Washington DC (the office he works out of is behind Union Station, only about six blocks from the apartment building where he, my older daughter Amy, and their five-month old son Tate (my only grandchild) live). Normally he takes Tate to a daycare operated by the SEC in his office building. Unfortunately, Tate developed an intestinal problem (NOT Covid-19!) that caused him to throw up several times on Sunday. The daycare has a policy that no child can go to daycare within 24 hours of throwing up, so Matt and Amy were going to have to find alternative daycare for Tate for Monday. But on Sunday night Matt was informed that the SEC was shutting down the office as of yesterday because of Covid-19 and everyone was to work from home. Problem solved!

~~ Steve Blasberg

Mismanagement of COVID-19 by US Federal Government

 The Trump administration’s mismanagement of the COVID-19 Pandemic will cost American lives. The mismanagement started not when the disease first came to the attention of the western world at the end of 2019, but much earlier in the administration. In the summer of 2018, Trump eliminated the National Security Council’s Global Health Security Unit and the Department of Homeland Security’s Epidemic Response Team. Neither team was replaced. This left the Administration without adequate insight into the threat to American life, and without several key organs of response.

The administration’s mismanagement was not confined to craven elimination of key NSC and HHS staff perspective extends to other key agencies as well. The administration chose Tom Price to be the Secretary of HHS, a partisan politician who would soon be forced to resign ignominiously after his improper use of chartered jets came to light. But who could really claim surprise? After all, Price was criticized during his confirmation hearings for insider trading in healthcare stocks while serving in the congress on the Ways and Means subcommittee on health. That subcommittee was responsible for writing legislation regulating the companies in which Mr. Price was trading. The administration then chose Alex Azar to run HHS. Azar was a lobbyist for drug giant Eli Lilly & Co for past decade. This is a post normally staffed by a scientist, a physician, or a public health expert, or even better, somebody whose credentials encompass all of the above bona fides. Instead, the Trump administration chose Azar, a lobbyist, to replace the disgraced former secretary. Azar by no means the only lobbyist at HHS, where at least 27 other lobbyists of lesser stature run departments.

Within HHS the administration made questionable choices to staff other key leadership roles. After the first CDC Director appointed by President Trump was forced to resign over ethical breaches pertaining to investments in the tobacco industry, President Trump appointed Robert Redfield, a virologist and physician with no experience leading a public health agency. Peers in the scientific community were concerned that some of Redfield’s religious and discriminatory policy positions were inconsistent with best practices in public health. More over, Redfield faced criticism for misrepresenting data on an experimental HIV vaccine in the 1990’s.

So it is within this context of leadership choices by the administration that specific actions, or in some cases lack of action, must be viewed. For example, HHS sent more than a dozen workers to process the first Americans evacuated from Wuhan, without proper training, personal protection equipment, or proper procedures in place to insure containment of the disease. The HHS employees were then dispersed back into their communities after being exposed to the virus. Shortly thereafter, the first known case of community transmission was confirmed within miles of where the HHS employees had processed the evacuees from Wuhan.

The CDC botched the rollout of tests, and because of poor management, failed to correct the problem for weeks. As a result, to this date, only a few thousand Americans have been tested for COVID-19, where in other places around the world, nations like South Korea and Italy test that many or more on a daily basis. Not only would professional management have enabled the CDC to correct the issue with the test kits, but other institutions should have been allowed to produce test kits beginning in January. They are now allowed to do so. Stanford has developed a test, as have various state labs and other institutions, and hopefully this will help the United States overcome the glaring deficit in preparation.

The list of public health mistakes made by this administration is manifold. When the above-mentioned evacuees from China came home, despite recommendations to segregate confirmed infections, the uninfected and the infected were put on the same plane by the US Department of State. This is what happens when lobbyists and political partisans are put in charge of public health. They lack the credibility and gravitas to impress upon another cabinet agency like State to implement the best public health decisions. What’s the administration’s response to these initial missteps?

The President has responded by lying to the American public. On Friday of last week, the President visited the CDC and told the media that “Anybody that wants a test can get a test.  That’s what the bottom line is. But — but I think — I think, importantly: Anybody right now and yesterday — anybody that needs a test gets a test.  We — they’re there.  They have the tests.  And the tests are beautiful.  Anybody that needs a test gets a test.” This of course was not true. The nation still short hundreds of thousands of tests and has no ability to understand the extent of the problem yet. Sadly though, the President’s penchant for lying to the American people is no surprise. He also told the media last week that there were 15 cases of COVID-19 and that with those people recovering there would soon be zero. Obviously not true. In addition to disinformation from the President, the administration has further tasked the Vice President to coordinate messaging.             

The President appointed Vice President Pence to coordinate White House policy and communication on COVID-19. To some this was an odd choice because of Mr. Pence’s troubling public health record in his previous capacity as governor of Indiana. When Scott County, Indiana, suffered one of the most severe outbreaks of HIV in many years, Pence failed to follow the recommendations of the CDC. Later a study conducted by the Yale School of Public Health concluded Pence’s decision caused the epidemic to infect as many as 20 times more people than would have been infected had then Governor Pence immediately followed the CDC’s recommendations. It turns out Pence’s history of ignoring the best advice of public health professionals was a harbinger of things to come. Mike Stobbe of The Associated Press reported on March 7 that the CDC advised the White House that elderly Americans should not fly on commercial airlines. The White House chose to overrule the CDC and did not issue that guidance.

How many elderly Americans, who are known to be at such risk, will get sick because the administration has chosen disinformation as a management technique? How many Americans will get infected because the administration made personnel choices based on partisanship and cronyism, and those political hacks allowed the disease to break containment and lead to early community spread? How many Americans will get sick and how many will die because that community spread has been unchecked by adequate testing and quarantines?

~~ Pete Dailey

Sources:

https://apnews.com/921ad7f1f08d7634bf681ba785faf269?utm_medium=AP&utm_source=Twitter&utm_campaign=SocialFlow&fbclid=IwAR0y4OP50E5d3-JbGeHjiowBclJzT7g0neYPEqiFiGfnipFXtapqA74AcLo

https://www.npr.org/2020/02/27/809930094/pences-new-coronavirus-role-raises-questions-about-his-public-health-record

https://www.vox.com/2018/3/22/17150322/robert-redfield-cdc-director-trump

https://cspinet.org/news/cspi-urges-administration-not-appoint-dr-robert-redfield-history-scientific-misconduct-cdc

https://foreignpolicy.com/2020/01/31/coronavirus-china-trump-united-states-public-health-emergency-response/

https://www.pbs.org/newshour/nation/hhs-pick-tom-price-made-brazen-stock-trades-committee-scrutiny

 https://www.technologyreview.com/s/615323/why-the-cdc-botched-its-coronavirus-testing/

 https://www.nytimes.com/2020/03/07/us/politics/trump-coronavirus-messaging.html

As Covid-19 Spreads, Will It Be Dangerous to Grocery Shop?

I did a mental exercise in comparing chances of exposure to Covid-19 in two hypothetical outings I might take in a community that has some level of the infection spreading.  One outing is going to Safeway to buy 20 grocery items like apples and boxed pasta.  The other outing is attending a church service followed by coffee hour.   Don’t go to church?  Then replace it with some other social gathering with people surrounding you for a time.  Say the Symphony with an intermission.  To  be comprehensive, let’s examine them each of these outings for a combination of both fomite-based exposure and respiratory-droplet exposure.

Safeway:  I grab a cart and take the disinfectant tissue to wipe the cart handle and my hands.  I enter through doors that open automatically.  I pick up items such as pasta in a box and apples that, even if they were touched by another person, it was hours and hours if not days ago and any Covid-19 virons, as a fatty-enveloped virums, probably died from desiccation and temperature changes a good while before I touched the item.  In the aisles, there are at most 1 or 2 other shoppers, 10 or 30 feet from me — not too much exposure to their respiratory droplets.   At checkout I pick my items from my basket and place them on the checkout conveyor belt, but I’m not touching any surfaces, and there’s at least 4-5’ between me and the other people in the checkout line.  I advance to the Point-of-sale terminal, which I do not have to touch, but simply wave my Apple Pay iphone or insert my credit card and withdraw it.   Perhaps I have to pick up a pen and sign the screen, but I can use my finger nail for this too.  My items are placed into my bags by either my hands or the bagger’s hands.   I guess I’ll bag my own groceries, though I could also just make a mental note that at home, when I unbag my groceries and place them away, I should wash my hands again, which I should do after any outing anyways.   All-in-all, it’s a pretty low transmission experience.

Church:  I open a door by my hand—50 other members have touched that same door handle in the previous 15 minutes before service starts.  Yipes, that’s worse than an elevator button!  I sit shoulder to shoulder, row to row with 100 or 200 other people for an hour, sitting, standing, singing — lots of chances for respiratory droplets, seems like we have an average spacing of 1-3 feet.  We greet each other at some point but that we do with elbows and fist bumps (because we’re trying to be safe).   After the service I go to the bathroom and touch these surfaces that were recently touched by dozens of others:  door handle (twice), flush handle, stall handle, faucet handles.   At coffee hour I use the black lever on the coffee urn to fill my mug (the coffee urn lever has had 100 touches in last 10 minutes!) and then I pick up the half-n-half container (30 touches in last 10 minutes), and I mingle more at close speaking distance in midst of scores of others.  Hopefully no hand shaking.   (note:  hmmm…. at this point I remember that the initial hot spot in South Korea was a church…).

Conclusion:   grocery stores shopping outings are pretty safe, but I’m going to shut down church visits for a month or two as part of my civic duty for Bay Area social distancing!

~~ Robert Carr

Genomic Tracing of Covid-19 Epidemic in Seattle

Among numerous news items related to the Covid-19 epidemic, I recently came across an interesting item which included some new and interesting information. I am referring to a post by Trevor Bedford, who is an Associate Member at Seattle’s Fred Hutchinson Center in the Vaccine and Infectious Disease Division. He is also an Affiliate Associate Professor in the Department of Genome Sciences and the Department of Epidemiology at the University of Washington.1

The post to which I am referring is a blog titled “Cryptic transmission of novel coronavirus revealed by genomic epidemiology.”2 Bedford and his team track the patterns of transmission and spread of pathogens by using the genetic mutations in the pathogen’s genes. This is very similar to the tracking of patterns of migration and ancestry in human history using the mutations in human genome, especially when we know the rate at which certain mutations on average take place.

In terms of the novel coronavirus, we know that the rate of mutation is roughly two per month. Moreover, we know that on average, it takes about 7 days for the infection to transmit from one person to the other. Combining these two pieces of information, the transmission of the virus can be visually represented as follows:

Here each mutation is represented by a change of color. Using this information, by sequencing the genome of the virus from two different infected patients, it is possible to tell if they are related (i.e., one is the parent of the other) and if yes approximately through how many transmissions or over what period of time.

This is exactly what Bedford has done on two infection samples from COVID-19 patients in Seattle. The first case, known as USA/WA1/2020, is the first identified case in US. The patient had returned from Wuhan to Snohomish County on Jan 15. The second case, detected around end of February, is known as USA/WA2/2020 and is a “community case,” which means the patient had not traveled to Wuhan and had not come into contact with a known Covid-19 patient. The remarkable result that Bedford and his team arrived at was that the WA2 case was identical to the WA1 case expect for 3 extra mutations. According to Bedford, based on the statistical mutation rate of the virus, this means that with overwhelming probability (~97%), WA2 is a descendent of WA1. Most probably, the infection has been transmitted undetected from WA1 around 5 times before getting to WA2. Bedford calls this “cryptic transmission.” One can conclude that in all likelihood there have been many cases of infection with mild or no symptoms at all. Bedford’s analysis shows that the number of infections in WA should be around 570 (as of March 2), with a 90% uncertainty interval of between 80 and 1500 infections.

What is remarkable about this conclusion is the number of unreported or unnoticed infections, most likely due to lack of severe symptoms. This underlines the importance of more testing to identify possible patterns of infection. For example, random checking of various individuals could provide a basis for a more accurate statistical picture of the spread of the infection. But I wonder if this also could be a sign of hope, in the sense that the death rate of the disease may be much lower than the nominal 2% often quoted. Moreover, I wonder if this means that a large number of people have developed (or will develop) immunity to the disease due to mild infection, and as a result, eventually the infection would dissipate because of herd immunity. Whatever the case, the picture is fast evolving and we must wait for new information.

~~ Moe Azadeh

References

https://bedford.io/team/trevor-bedford/
https://bedford.io/blog/ncov-cryptic-transmission/

Last Ebola Patient Discharged in the DRC

Having read the Hot Zone for my first book report, researched the 2014 Ebola outbreak for my second class presentation, and enjoyed Richard’s Ebola model presentation last night, I have had Ebola on my mind throughout the quarter. I’ve kept an eye on the current outbreak in the DRC, and decided to check back in this morning in hopes of good news for my New and Hot article. And what a wonderful surprise!! Parting the clouds of the apocalyptic coronavirus news storm, Al Jazeera shone a ray of light five hours ago with news that the last Ebola patient in the DRC has been discharged.

The Democratic Republic of Congo is consistently plagued with Ebola, as its dense tropical rainforests are a natural reservoir for the disease. The country has endured ten outbreaks since 1976, the most recent one closely following another, smaller one in 2018.

The DRC has also suffered from civil war, which has made diagnosis and treatment extremely difficult. Complications resulting from the conflict prevent the WHO from declaring the outbreak officially over, as militia violence in the eastern DRC makes cases difficult to track. “Because of the complex security environment, Ebola transmission outside of groups currently under monitoring cannot be ruled out,” said WHO spokesman Tarik Jasarevic. “A single case could reignite the epidemic.”

The virus killed 2,264 people and infected nearly 1,200 more since August 2018, making it the second-worst Ebola outbreak in history, exceeded only by the 2013-2016 epidemic in Guinea, Liberia, and Sierra Leone, which killed more than 11,000.

The last known Ebola patient in the DRC, Semida Masika, was released yesterday and allowed to go home, to the sound of rejoicing hospital staff singing, dancing, and drumming on trash cans in celebration. “As I am the last survivor,” Masika said, “I say thank you very much and praise be to God.”

The DRC has now gone 14 days without any new confirmed cases, so the end is almost insight. The virus has an incubation period of 21 days, so a precautionary period of two cycles of incubation (42 days) is observed before the outbreak can be officially declared over. WHO Director-General Tedros Adhanom Ghebreyesus said the developments were “very good news,not just for me, but for the whole world.”

~~ Amy McPhie Allebest

https://www.aljazeera.com/news/2020/03/drc-ebola-patient-discharged-outbreak-sight-
200304130826905.html

It Was Not Pneumonia, It Was Coronavirus

When a lawyer in suburban New York City checked into the hospital staff thought he had pneumonia. Turns out it was not pneumonia, it was coronavirus. Days after he was admitted to the hospital, where he was in close proximity to both other patients and medical staff, it would be discovered that he was one of the first people in the state of New York to contract coronavirus through community spread. “Within days, it would emerge that Mr. Garbuz — who is from New Rochelle, N.Y., and had not traveled to one of the known hubs in the world for the illness — was part of a cluster of more than 90 cases, the largest concentration on the East Coast.” 2019-NCOVID was now present and spreading in New York, the home state to the most populous metropolitan area in the country.

The result of this mishap is not good. At least one healthcare professional at the hospital contracted the virus and a number of other healthcare workers are now in quarantine because of their exposure to the patient. This not only puts healthcare workers at risk of contracting the virus but it also limits the number of staff members available to treat other patients due to the quarantine at a time when medical staff is needed most. Additionally, this prolonged unidentified case means that the possibility of secondary exposure within the hospital was that much greater, a concern for workers at the facility who may have not been in direct contact with the patient but were with those who worked on him and visited him.

This example represents the new reality that healthcare workers and hospital support workers face. Knowing exactly who has 2019-NCOVID and who does not is a difficult task. At times doctors will be wrong and, when they are, the infection is likely to spread to others. If those others are patients in vulnerable states of health, the impacts can be devastating. How this example plays out is still too be determined but it underscores the importance of being cautious and being careful. At this point in time it seems the best thing for healthcare workers to do is error on the side of caution.

Citation: Goldstein, Joseph and Andrea Salcedo. “For 4 Days, the Hospital Thought He Had Just Pneumonia. It Was Coronavirus.” The New York Times, 10 March 2020. https://www.nytimes.com/2020/03/10/nyregion/coronavirus-new-rochelle-pneumonia.html. Accessed 10 March 2020.

Post by Richard Hackmann

Information Spreads and Evolves Like a Virus

One of the many things we’ve learned from the COVID-19 epidemic is that a piece of information can take hold, evolve and spread like a virus. While mathematical epidemiological models are far from perfect, they can still provide insight into the patterns and extent of proliferation. Recently, a team of scientists attempted to predict the spread of “viral” elements. What they found is that whether you are looking at a virus or misinformation, the evolution of it significantly impacts how much it proliferates. Take coronavirus coverage as an example. On March 5, 2020, CNN had to put out an article addressing common COVID-19 rumors that ‘evolved’ and ‘spread’ including: The virus was man-made, homemade remedies can prevent or cure it, you NEED to get a mask for protection, the virus can pass through the mail, and finally, the virus will kill you. When taking into account how this information changes, a mathematical model does surprisingly well predicting its expansion. And the simulation mirrors the propagation of evolving viral diseases. Of course, models will never be 100% accurate, but with a more realistic simulation that accounts for evolution, epidemiologists can get a better idea of the possible extent of an epidemic.
~Avi Kaye

Mathematical Model Article: Eletreby et al. The effects of evolutionary adaptations on spreading processes in complex networks. PNAS, 2020. https://doi.org/10.1073/pnas.1918529117 
CNN Article: Kaur, M. Coronavirus myths and misinformation, debunked. https://www.cnn.com/2020/03/04/health/debunking-coronavirus-myths-trnd/index.html

Monday, March 9, 2020

American sports leagues closing locker rooms and clubhouses to non-essential personnel


The coronavirus has now impacted the sports world, both in the US and abroad. On the heels of Italy announcing that Serie A would play their remaining games in empty stadiums, the Italian government decreed that all sporting events would be postponed until April, 3rd; this policy includes qualifying events for the 2020 Summer Olympics in Tokyo. Other European leagues have adopted similar “no fans” policies for their recent matches. American basketball star LeBron James stated he would not play if the NBA decided to go a similar route. American sports have made some changes in response to the outbreak. The NBA, NHL, MLB, and MLS all released a joint statement announcing that all locker rooms would be closed saved for the team and essential personnel. This decision mostly impacts TV and newspaper reporters who would interview players postgame. Now, all postgame comments will go through the traditional press conference. With March Madness, Opening Day, NBA, and NHL playoffs all on the sports calendar in the next few months, things are certainly going to be interesting.

Patrick Moynahan

Saturday, March 7, 2020

Flu Season 2019-2020

While Coronavirus continues to wreak havoc in the media and around the world, a recent report on the flu indicate at least 32 million cases in the US this flu season. It is difficult to know whether the peak of the season has been reached, but the rate of outpatient visits for flu-like illness has decreased for the last two weeks in a row and the percentage of specimens testing positive for influenza A or B have decreased in the last week. Key indicators have been high this year, with 18000 flu associated deaths and highest recorded hospitalization rates in younger populations since influenza reporting began in 2004-05 season. The report estimates so far that this year's vaccine is 45% effective overall and is 55% effective in children.

-Micah

Source:
https://www.contagionlive.com/news/us-flu-cases-reach-32-million-pediatric-hospitalization-rates-hit-record-high 

Obesity promotes change in Influenza Virus

Researchers have noted that obesity may act as a risk factor for increased severity of influenza A infection, high levels of viral titers, and prolonged length of viral shedding. Thus, it is important to understand whether a factor such as obesity might also impact the diversity of the Influenza virus.

Using genetically obese mice to conduct experimental models, researchers studied the effects of the obese microenvironment on the evolution of the virus in vivo. Next-generation sequencing showed that obese host-passaged viruses was correlated with higher mortality in the following WT host. This implies that viral (instead of host) determine virulence. Human primary respiratory epithelial cells were studied, and increased viral replication along with blunted interferon response occurred in obese donors. 

-Micah


Sources:

Tuesday, March 3, 2020

Covid-19: Italy’s accurate count of Covid-19 patients has damaged its international position.

Italy has had a bad week. As reported in a New York Times article on February 27, 2020 [1], Italy leapt to the top ranks of the world’s coronavirus “centers of global concern”—joining China and South Korea with alarming alacrity—as it reported 650 infections and 17 deaths related to the virus. The newly reported infections have been concentrated in the Lombardy region (northern Italy), which claimed 403 of the newly reported cases. (According to the Times article, Lombardy has strong trading ties with China.) These reported cases included asymptomatic infections and counting those infections helped to rapidly increase Italy’s numbers [2]. Political issues, as well as national 2 and international health policy concerns, are swirling over the number of Italian cases identified so quickly. Lombardy immediately faced strong criticism both internally and internationally for its comprehensive testing effort.

Lombardy, as distinct from even the rest of Italy and certainly the balance of the world, is trying to identify asymptomatic carriers of the virus in addition to cases where the patient is already exhibiting signs of infection. To that end, Lombardy’s health officials have been swabbing and testing individuals who are not coughing, wheezing or feverish. As a result of this more comprehensive approach, Lombardy is obtaining a more accurate understanding of both the scope of infection and  human response (or nonresponse) to the virus. That effort to better understand has left wealthy Lombardy in a world of hurt.

Following on its reports of a significant number of infections outside of China, Italy has been internationally branded as a “hotspot,” and travel to and relationships with the country have been immediately and materially impacted. Around the world, people are speculating on how and why Italy developed so many and so many infections so quickly. The speculation is all negative for Italy. Interestingly, though its protocols in this regard are under review, the World Health Organization does not recommend testing asymptomatic carriers of the virus because it does not see asymptomatic carriers as a source of virus spread [1]. The U.S. Centers for Disease Control have taken a similar approach; in the U.S. testing is limited to symptomatic patients.

Lombardy has bowed to national and international pressure and has suspended asymptomatic testing. While recognizing the impact that their “accurate” reporting of actual infections has had on Italy’s international reputation, Lombardy health officials continue to insist that comprehensive testing—identifying both asymptomatic and symptomatic carriers of the virus—is essential to understanding the virus and its spread.

~~ David M. Walsh

[1] - Horowitz, Jason. “Italy, Mired in Politics Over Virus, Asks How Much Testing Is Too Much”. New York Times. New York, New York. February 27, 2020. https://www.nytimes.com/2020/02/27/world/europe/italy-coronavirus.html.

[2] - In addition, infections which may have originated in Lombardy have been reported in Austria, Switzerland and the Canary Islands. 

Vietnam vs South Korea: 0 to 28 death, 16 to 5,186 cases, 16 to 30 recovered

On Friday, February 26, Vietnam declared all sixteen Covid-19 patients in the country have recovered; and there had been no new cases (1). How did Vietnam achieve such remarkable result while South Korea continues to report new cases after new cases? According to the Vietnamese government, it is all due to early action. In Vietnam’s case, stopping mass gathering early on also helped.

When Wuhan began to experience the outbreak, Vietnam took action to limit New Year celebrations. On February 4, Vietnam closed its border by suspending passengers train service and denying entre to Chinese travelers. In addition, the labor ministry has asked businesses to track down their employees, and ordered those who have recently traveled to China and other infected areas to be quarantined and monitored. When six cases came to light on February 12, lock down was ordered and everyone in the commune and the communes nearby were locked down for 20 days (2).

The story is very different in South Korea. South Korea’s population is less than Vietnam (51 million to 95 million), both borders China, one in the south, the other in the northeast. But incidents of Covid-19 in South Korea ballooned. For a month after the first incident, South Korea only had single-digit day-over-day increase of incidents. But things changed on February 19, when 20 new cases were reported, the next day, 53 new cases. Since then, the number of incidents has been going up in triple digits each day (3). It turns out, Patient 31 was a member of a church that regularly hold meetings attended by large groups. Patient 31 infected others. The spread of Covid-19 became hard to contain.

~~ You Jia Zhu

1. Sen Nguyen, “Coronavirus miracle? Vietnam says all its infected patients cured”, Al Jazeera, February 28, 2020.

2. Denzan Shira & Associates, “Vietnam Business Operations and the Coronavirus: Updates”, VietnamBriefing, March 3, 2020.

3. 2020 coronavirus outbreak in South Korea, WikiPedia. Last accessed on March 3, 2020.

4. Kelly Kasulis, 'Patient 31' and South Korea's sudden spike in coronavirus cases,” Al Jazeera, March 3, 2020.

Japan Shocks Parents by Moving to Close All Schools Over Coronavirus

Motoko Rich, Ben Dooley and Makiko Inoue’s article titled, Japan Shocks Parents by Moving to Close All Schools Over Coronavirus, reveals that Japan’s Prime Minister has decided to close all schools (elementary, middle and high schools) for a month because of the coronavirus. Japan has also canceled “large sports and cultural events” throughout the country as well. The country has had 210 cases of the coronavirus and four deaths. The government believes it must take “aggressive” measures to minimize infection and slow down the spreading of the coronavirus. However, doctors believe the closures are not “medically warranted” because children are not easily infected from the virus. They also point out that public transportation is still open where many people encounter each other. With this belief some think that the school closings were a political move because Japan is hosting the Olympics in Tokyo this July. The school closings will make the life of parents very difficult because they might be forced to stay home to take care of their children or send them to live with other members of the family so they can work. Some parents are relieved that the schools will be closed so their children will be at a lower risk to get infected.

This article relates directly to our “Virus in the News” class because it focuses on the response to the never-ending coronavirus. More specifically, the governments response to the coronavirus outbreak. The decision to shut down school makes sense to me because I learned in our class that viruses attack the weakest immune systems, which are the elderly and children. However, this belief was conflicted by Japanese doctors who were interviewed for this article. The doctors stated that children are not easily infected by the coronavirus. I look forward to bringing this topic up in our class on Tuesday night.

~~ John Sikora

https://www.nytimes.com/2020/02/27/world/asia/japan-schools coronavirus.htmlaction=click&module=Top%20Stories&pgtype=Homepage

Economic Analysis of Covid19 – When will the Third Shoe Drop?

Today the Federal Reserve cut rates by 50 Basis Points in an attempt to blunt the economic impact of Covid19, also known as SARS II. The rate cut came sharply on the heels of bullying by the President, who tweeted yesterday that the Fed “Should ease and cut rate big. Jerome Powell led Federal Reserve has called it wrong from day one. Sad!” After the rate cut today, the President tweeted, “The Federal Reserve is cutting but must further ease and, most importantly, come into line with other countries/competitors.” Of course this kind of interaction between the President and the Federal Reserve is entirely unprecedented, as the Federal Reserve is supposed to be independent of political influence. It is has been widely reported that the President is obsessed with the stock market, and has been upset that the market suffered heavy losses last week, including the largest single day drop (measured in point totals) in history. One could interpret the President’s bullying of the Fed, and the rate cut that followed as a response to the stock market, and not to the pandemic that appears to be upon us. The stock markets gyrated wildly after the rate cut today, but by mid afternoon the DOW was down almost 900 points.

The stock market’s decline, regardless of rate cuts by the Federal Reserve should come as no surprise. Rate cuts by the Fed are an appropriate tool to stimulate aggregate demand in the economy. The concern about aggregate demand was the first economic shoe to drop in the Covid19 crisis. The measures taken by the Chinese government in response to the outbreak resulted in stores closing and the Chinese consumer all but disappearing during and since the Lunar New Year holiday. Since China is the world’s second largest economy, taking that much demand out of the global economy was sure to impact global GDP growth. The stock market had a fairly modest reaction to that demand shock about three weeks ago, but seemed to regain its footing after a couple days of volatility. Then last week the second shoe dropped, and the market began to price in the more important impact of the conditions in China, specifically the fact that Chinese factory product did not resume after the Lunar New Year, and still has not reached anything close to full capacity. It is unclear when the factories in China will come back on line. Most companies manufacture in China, so this means that firms like Apple don’t have product to sell. The cratering global supply chain is what has led to the dramatic stock market sell-off over the last 8 trading days. No rate cut will address this issue. Regardless of how much central banks act to provide liquidity and stimulate demand, there simply are no products to sell. While some technology firms may not raise prices, ultimately prices will rise across the board for a wide variety of products. Basic economics tells us that when Supply is reduced and demand is constant or rising, the result is higher prices, otherwise known as inflation. It would have been more prudent for the Fed to hold off on the rate cut until supply came back on line, and then cut rates to goose demand as supply increased.

But there remains still at least one more shoe to drop: the cash-flow shoe. Many firms finance manufacturing, and service their revolving debt through subsequent sales into their distribution channels. The constant turn-over of sales and manufacturing, and ideally growth of those volumes, sustains the firms’ business model. Invariably when growth slows, some unprepared firms drop out of the market, or are consolidated into their competitors. The global supply shock we are currently experiencing will be like a recession on steroids with regard to how it impacts cash-flow industries, like the PC business for example. The impact will be made worse by the fact that the economy was relatively healthy to begin with. With full employment and relatively low costs of capital, firms were not anticipating a global slow down so they will be even less prepared for the complete interruption in the cash-flow cycle. So we should anticipate a wider swath of firms failing than we would see in a traditional recession. I predict this will be the next shoe to drop, and we can expect it to happen within the next 3 to 6 weeks.

~~ Pete Dailey

HIV Vaccines — Fact or Fiction?

Dorothy Crawford’s excellent book Viruses, A Very Short Introduction has an intriguing section about why, 30 years after HIV was first identified, there is still no effective HIV vaccine.

It has not been for lack of effort. Huge amounts of money and scientific effort have been expended.  Crawford outlines three main problems.  First, because HIV mutates at a high rate, there are no, after 30 years, many different varieties of of HIV circulating in the human “herd.”   Second, because the human immune system cannot clear an HIV infection, this tells us that it’s very hard to clear HIV… it’s a high hurdle any vaccine has to exceed.   Third, because HIV transmission is usually via the genital tract, that is where the antibodies and immune T cells that are stimulated by a vaccine must reach.  Lastly, because HIV can transmit inside of cells as well as as a free virus, it greatly complicates the job a vaccine must do.

In sum, it’s a tall order across these four difficulties, and Crawford is not optimistic that a vaccine can be developed.  However, there are effective measures that can be taken to help someone from getting infected.   If an HIV-infected person has a sexual partner who is un-infected, then that partner can be largely protected by giving them antiretroviral drugs.

We don’t want to end on a completely negative note, even though HIV mutates rapidly and has unique ways of evading the immune system, some vaccine trials have shown partial sucess. The RV144 clinical trial in Thailand, reported in 2009, demonstrated a 31% reduction in HIV infection. It’s not ready or enough to deploy beyond testing, but it’s a start.

~~ Robert Carr

Sources:

Crawford, Dorothy H.   VIRUSES, A Very Short Introduction.  Oxford. 2018.

https://www.niaid.nih.gov/sites/default/files/hivvaccineinfographic.pdf

Two Op-Eds on SARS: Then and Now

This week two op-eds caught my attention. The first, “Preventing the Next SARS” was written in 2003 by Ezekiel Emanuel, the American oncologist and bioethicist. The second, “Living in Hell,” is a personal essay from a resident of Wuhan published today, March 3rd, 2020. While separated by 17 years and two continents, the juxtaposition of the two articles illustrates the dire urgency and need to learn all we can from one outbreak in order to prevent or minimize the human impact of future infectious epidemics, particularly as COVID-19 continues to wreak havoc across the globe.

Originating in the Guangdong province of China, the 2003 SARS outbreak began as a “mysterious illness” characterized by severe respiratory symptoms. The outbreak lasted for six months, from February-July. When Emanuel wrote his op-ed in May 2003, the SARS crisis had begun to stabilize. Yet, he cautiously warns that it would be a “huge mistake” after containment to “move on, to focus on the next issue.”

According to Emanuel, virologists explain that China is the source of viruses that cause respiratory infections due to the close proximity of people and animals in cohabitation. Without specifying zoonosis, he provides the example of birds shedding the influenza virus in their stools where pigs eating from the ground can absorb the bird virus. Moreover, “pigs can harbor both both human and bird viruses, creating an environment in which genes can be exchanged, leading to new strains of old viruses or new viruses that can infect and kill humans” (Emanuel). He also mentions the “staggering” financial resources required “to improve the millions of small farms, slaughterhouses and housing and sanitation in China.” Emanuel states, “Traditions surrounding cuisine and food preparation can be barriers to better hygiene, but concerns for health should prevail.”

In contrast to Emanual’s op-ed written after the original SARS outbreak reached its peak, the second article is a personal essay written during the current outbreak of COVID-19.The author, a resident of Wuhan, writes anonymously in fear of reprisals from the Chinese government. He describes what it is like during the lock-down, as well as the gap that exists between government propaganda and reality. Questions and inconsistencies haunt the writer, particularly the fact that the government announced the lockdown of Wuhan at 2AM on the second to last morning before the Lunar New Year. He explains that his childhood ambition was to become a journalist, but as he became an adult and realized that he lived in a regime in which truth could not be told, he needed to find another career.

The anonymous writer tells how others around him have had to reckon with reality…that infected patients were first treated at the beginning of December, but the government did not inform the public until much later, missing the window of prevention. He describes the mad rush to gather food and other necessities after the lockdown was announced. How residents were asked to provide rides to medical workers, despite a ban imposed on residents preventing them from riding. How medical workers were not given adequate medical supplies leading to their exposure to the virus. How the government locked down the internet, further preventing residents from obtaining supplies such as masks. How dormitories of medicine students have become appropriated for quarantined patients. And how younger residents (born after 1995) who grew up during a time of prosperity and have had a more positive view of the government, now face the reality that overcrowded hospitals turn away their  family members infected by the coronavirus.

~~ Janette Canare

Emanuel, Ezekiel J. “Opinion | Preventing the Next SARS.” The New York Times, May 12, 2003, sec. Opinion. https://www.nytimes.com/2003/05/12/opinion/preventing-the-next-sars.html.


NPR.org. “Personal Essay From Wuhan: ‘Living In Hell.’” Accessed March 3, 2020. https://www.npr.org/sections/goatsandsoda/2020/03/03/809965742/personal-essay-from-wuhan-living-in-hell.

Kyasanur Forest disease (KFD) in Karnataka, India

Kyasanur Forest disease (KFD) -- also known as monkey fever -- has claimed its 2nd victim in the Indian state of Karnataka, a 64 year old who died on 29 February.

The death comes almost a month after a woman in the Shivamogga district of Karnataka state, died due to the disease. She died while being moved to a hospital in Manipal from Shivamogga.

According to Dr. Ashok Kumar, "Two cases of KFD have been confirmed in Siddapura.  Samples from the carcass of the monkey also revealed the presence of the virus. We have enough vaccine and are creating awareness among the public about vaccination. KFD surfaces from March to May but has appeared as early as January this year."

In Shivamogga alone, 55 people have tested positive for the KFD virus. "Of 55 positive cases, 22 people were vaccinated with 2 and 3 rounds of vaccination," a medical officer said.

KFD is an acute febrile illness caused by Kyasanur Forest disease virus (KFDV), a member of the family Flaviviridae, characterized by severe muscle pain, gastrointestinal symptoms, and bleeding. The virus was 1st identified in 1957 after it was isolated from a sick monkey from the Kyasanur Forest in Karnataka State. The disease is transmitted to humans following a tick bite or contact with an infected animal, especially a sick or recently dead monkey. There is no evidence of person-to-person transmission.

KFD typically occurs during the dry season from November through May and is related to the increased activity of the nymphs of ticks. Exposure to adult ticks and nymphs in rural areas increases the risk of infection; herders, forest workers, farmers, and hunters are particularly at risk.

~~ Steve Blasberg

Epidemics as Tests of Rationality

One of the fascinating angles that a health epidemic such as the current Corona outbreak brings to the forth is the degree to which humans can (or cannot) be approximated as rational agents. We would like to think of ourselves as rational beings, but as the growing field of behavioral economics has shown, reality is far from it. A real human made of flesh and blood is far from the rational contemplating platonic agent we hope it to be. To put it differently, it looks like our brains have certain bugs (or features, depending on how one look at it) which become especially noticeable under certain new conditions.

As an example, it seems like our rationality is particularly vulnerable whenever we are faced with situations that involve probabilities. Most people have no problem handling judgments that require basic mathematical operations like addition or multiplication or even more complex operations such as solving equations. However, the same people often cannot make rational conclusions when faced even with the simplest situations that involve probabilities or statistics. There has been many excellent works that have shown these deficiencies in detail. For example, Daniel Kahneman's Thinking Fast and Slow is a classic and detailed study of the subject.1

One of these shortcomings that helps us understand the reactions to the current Corona outbreak better is what Kahneman calls the "availability" heuristics. This is the case where people make decisions or judgments about the probability of an event based on examples or instances of that event that they can access most easily. In the current context, this means judging the severity of the situation based on the most readily available examples or images. And because for most people the news outlets are their window to the reality, and because those outlets are saturated with news about the Corona outbreak, the natural conclusion is to associate a very high risk with the corona virus. In other words, the public perception of the risk associated with the virus is almost independent of the actual statistics and data. That there is a higher risk of dying from the flu than from Covid19 (at least as of now) does not seem to matter.

This non-rational response has profound effects as it tends to be amplified in situations involving closed positive feedback loops, leading to unstable behavior. As a result, we have witnessed the biggest drop in the financial markets in the past few days since the depression of 2008. In other words, we panic not because of some real world reality, but because others have panicked. And our panic causes more panics in others, which in turn causes more panic in us, etc. Clearly, this outbreak is far more than an infectious disease outbreak. It is also a laboratory for studying the nature of human behavior.

~~ Moe Azadeh

1. Daniel Kahneman, Thinking Fast and Slow, Farrar, Straus and Giroux, 2011.

Coronavirus Patient at UC-Davis Hospital Was Not Tested For Days

I have been telling my family and friends to not panic about coronavirus, but an article published two hours ago in The New York Times has me a bit rattled. NYT reporters Roni Caryn Rabin and Sheri Fink document that a patient in California – later revealed to be in Davis – had to wait days to be tested for coronavirus, even though doctors requested the test. This patient, who has now tested positive, may be the first person in the United States to be infected through community spread, the CDC reported yesterday.

While it is possible that the patient was exposed to a traveler returning from an outbreak zone, the source of the infection is unknown, and may very well be a case of local, community transmission. 

The delay in the patient’s testing – which delayed the diagnosis and thus presumably delayed appropriate containment measures - was due to federal restrictions limiting testing to patients who have recently traveled to China or know they have had contact with someone with coronavirus.

In the midst of criticism of the federal government’s slow response to the epidemic, President Trump named Vice President Mike Pence to coordinate the government’s response, deemphasizing the seriousness of the threat. “The risk to the American people remains very low,” said Mr. Trump. “We have the greatest experts, really in the world, right here.” 

Meanwhile, the actual experts, doctors at the Universtiy of California, Davis Medical Center, considered coronavirus as a possible diagnosis when the patient was first admitted last week, but were unable to obtain appropriate testing procedures because of the stringent restrictions of the federal agency that conducts such testing.

The patient was moved to the medical center from another hospital in Northern California (where??) with a suspected viral infection, and was already in bad shape and using a ventilator upon arrival, UC Davis wrote in a letter yesterday. “Upon admission, our team asked public health officials if this case could be Covid-19,” the letter said. The medical center requested testing from the C.D.C. “Since the patient did not fit the existing C.D.C. criteria for Covid-19, a test was not immediately administered. U.C. Davis Health does not control the testing process.”

Previous to this case, public health officials have traced the source of all the infections in the U.S. to a trip abroad or a known patient. If this patient has had no contact with anyone coming from an affected country, then that means there are already undiagnosed cases of coronavirus in the community, here in Northern California. 

To be honest, I would still recommend to family and friends that they not panic. As has been pointed out repeatedly in class, this virus will certainly make its way through the human population, and the best thing we can do is wash our hands, get enough sleep, and not suppress our immune systems by stressing about it. 

At the same time, my 13-year-old daughter just came downstairs and said “my throat hurt” and my husband teased, “is it coronavirus?” We laughed, but if my daughter did happen to contract a respiratory illness that put her on a ventilator and her doctors suspected coronavirus, I would be furious if she was unable to be tested. 

~~ Amy Allebest
https://www.nytimes.com/2020/02/27/health/coronavirus-testing-california.html

United States 2019-NCOVID Testing Ramps Up

AS 2019-NCOVID continues to spread throughout the United States so too does urgency for significantly increasing testing capacity for the virus. “The Trump administration said on Monday that nearly a million tests could be administered for the coronavirus in the United States by the end of this week, a significant escalation of screening as the American death toll reached six and U.S. infections topped 100.” Both public and private sector entities are being leveraged to increase the United States testing capacity in a short amount of time. It is widely expected that as testing capacity expands so too will the number of confirmed cases.

Getting enough testing supplies distributed throughout the country for such a new virus has proven difficult. Last Tuesday and Wednesday only 337 additional testing kits were made available with each kit being capable of testing approximately 350 people. As the virus moves closer to pandemic proportions, it is clear that capacity to address it will have to increase in similar proportion. In addition to increasing testing capacity, the White House is also looking to take steps that could potentially decrease the number of new cases entering the country through an expansion of the existing 2019-NCOVID related travel ban. While details of what countries may be included are still unknown, Italy, South Korea, and Iran seem to be likely candidates due to the scope of their outbreaks.

While work on a vaccine is still moving ahead as quickly as possible it looks as though getting something to market is at a minimum one year away. Additionally, some have been critical of the pace at which testing has occurred. A variety of factors including a focus on keeping the virus out of the country, poor leadership, and faulty test kits have been cited as the cause of delays.

Citation: Weiland, Noah and Emily Cochrane. “Close to a Million Could Be Tested for the Coronavirus This Week, Health Official Says.” The New York Times, 2 March 2020. https://www.nytimes.com/2020/03/02/us/politics/coronavirus-testing.html. Accessed 3 March 2020.

Post by Richard Hackmann

Cranberry vs Noro: A New Approach to Treating Produce for Norovirus

With all the craze around COVID-19, it’s hard to even imagine that any other virus poses any risk to human health. But you can rest assured, scientists are still looking for ways to combat our greatest microscopic foes such as the infamous norovirus. Norovirus - a member of the caliciviridae family - ravages dorms, cruise ships and any communities in close quarters, and they take refuge in foods to disperse gastroenteritis to unsuspecting victims worldwide. Noro is also hardy for a virus as they are resistant to cold pasteurization such as irradiation that is used to kill other microbes. In order to kill the virus, the produce would need to be treated with high dose X-rays that destroy the chemical properties of the plants. Recently, researchers found that organic acids and polyphenol in cranberry juice and citrus extract alters the viral protein structure in norovirus and makes them susceptible to normal pasteurization treatments. The technique is an exciting new approach to safely and naturally eliminate the dangerous Norovirus using ingredients that will not harm the consumer or strip nutrients that make fresh fruits and vegetables worth eating. 
~Avi Kaye

Article: Gobeil et al. Radiosensitivity increase in FCV‐F9 virus using combined treatments with natural antimicrobials and γ‐irradiation. Journal of Applied Microbiology, 2020. https://doi.org/10.1111/jam.14596

Monday, March 2, 2020

The glaring loophole in U.S. virus response: Human error


This broad, far reaching Politico piece summarizes the way in which even the best laid pandemic plans can go awry through the simple reason that people mess up. The article then contrasts the money being devoted towards fighting the coronavirus with mistakes made by agencies and local health workers. The CDC’s test had serious flaws, and their testing guidelines proved too narrow. A California man was in the hospital for a week undiagnosed because of these strict guidelines, exposing himself to staffers. In general, there exists a lack of protection for health care workers. Long term care facilities appear especially vulnerable, considering their elderly population has compromised immune systems. For a pandemic plan to work, everything must go exactly as planned; oftentimes small mistakes have lasting, outsized consequences. In this way the current COVID19 response mirrors the Ebola outbreak in 2014. In that situation, a Dallas hospital misdiagnosed an Ebola patient, leading to widespread panic. The most encouraging part of the article came when the author quotes Tom Frieden who explained that so long as officials prove adaptable to changing conditions and are transparent with the public, confidence ought to be maintained. In addition, so long as decisions continue to be made based on the science, the public has no cause for alarm.

Patrick Moynahan