Sailing the Seven Viro-seas

--A photo that the French Consulate took of the Tara, a research vessel dedicated to studying the diversity of oceanic plankton and their viruses, from (http://www.sciencetimes.com/articles/6613/20150523/sampling-the-world-s-oceans-on-a-global-scale-reveals-the-complex-relationship-between-viruses-and-microbes.htm)

            In March 2011, the Tara, a 36-meter research ship, started a series of expeditions that would form part of a multi-year journey-- about 180,000 miles of sailing. One of the scientists on board, Melissa Duhaime, spent most of the voyage not looking at open ocean animals, but at the diversity of oceanic plankton and… and viruses?  

Duhaime and her colleagues set out on a quest to quantify the diversity of viruses in the oceans. Through thousands of genetic screens of microorganisms in seawater, over 35,000 species of plankton. most of which were previously undescribed. Oceanic viruses have only been studied since the 1980’s, but no study has even been this ambitious. This study was truly vast in its scope, as it sampled the microbiota between the surface and 6,561 feet deep. The study (http://www.sciencemag.org/content/348/6237/1261498) used quantitative double-stranded DNA and protein analysis to screen for pelagic DNA and RNA viruses. The team found 5,476 species of viruses; only 39 of these were previously known to science. Because of plankton’s importance in global carbon cycles (and therefore importance to the regulation of Earth’s climate), understanding the pathogens of plankton is an important part of understanding marine ecosystems.

            They also found that viral communities varied based on the physical conditions and organisms that lived in a given region. They concluded that viruses are passively transported on oceanic currents and locally structured by environmental conditions that affect host community structure. Their findings suggested that a “seed-bank” hypothesis (i.e. high local genetic diversity can exist when individual communities diverge from a common and relatively limited global “common” gene pool) could be used to describe the variations in viral communities across the world’s oceans. 

The ocean is a huge place, though. There are undoubtedly even more discoveries to be made about the virology of the oceans. 

Paper: http://www.sciencemag.org/content/348/6237/1261498

More references:

https://www.quantamagazine.org/20150521-ocean-viruses/

http://oceans.taraexpeditions.org/en/m/science/news/first-scientific-results-from-the-tara-oceans-expedition/  

http://www.hngn.com/articles/94586/20150522/marine-microbe-diversitys-influence-environment-revealed-breakthrough-study.htm

http://www.sciencetimes.com/articles/6613/20150523/sampling-the-world-s-oceans-on-a-global-scale-reveals-the-complex-relationship-between-viruses-and-microbes.htm 

--Joe

MERS on the Move

--Camel selfie--They're really A-MERS-ing animals

This week, MERS has popped up in Bahrain, Quatar, Saudi Arabia, and … Korea?

Korean patient zero is thought to be a 68-year old male who traveled to Bahrain on a business trip between April 18^th and May 3^rd. He visited a hospital before it was known that he was infected, and he infected a 76-year old man. As a result, the hospital quarantined 64 workers. The public health authorities of nearby countries, including Taiwan and Thailand, are on high alert for the virus, although they have not found any cases yet.

True to its name, MERS (Middle Eastern Respiratory Syndrome) primarily resides in the Middle East, but back in 2012, it has a massive outbreak that killed about 400 people in Europe, the Middle East, and in East Asia (it spread to North America but nobody there died).  (http://www.who.int/csr/disease/coronavirus_infections/MERSCov_WHO_KSA_Mission_Jun13_.pdf). The first recorded case in this current outbreak occurred in a 29-year old man in Qatar who transported camels in his truck for a living (which makes sense since camels are a known reservoir of MERS). The camels he was transporting at the time he was diagnosed all tested positive for MERS-CoV. Most of the other cases in Saudi Arabia have been in middle-aged or older individuals. Currently, 9 individuals are receiving treatment for MERS, and another is in home quarantine.

The true origin of this outbreak may have been as early as February, when 3 middle-aged men and one middle-aged woman were infected, and the WHO called the country out for not doing a better job of containing the virus. While these numbers don’t seem like much of an outbreak, MERS has a mortality rate of about 27% (http://www.who.int/csr/disease/coronavirus_infections/faq/en/).

http://www.wantchinatimes.com/news-subclass-cnt.aspx?id=20150523000098&cid=1103

http://bangkokpost.com/news/health/407538/ministry-goes-on-alert-for-mers-virus

http://www.wantchinatimes.com/news-subclass-cnt.aspx?id=20150523000098&cid=1103

http://www.cidrap.umn.edu/news-perspective/2015/05/more-mers-cases-south-korea-qatar-saudi-arabia

http://www.cdc.gov/coronavirus/mers/about/index.html

http://news.yahoo.com/south-korea-confirms-second-case-mers-virus-third-022536212.html

http://news.yahoo.com/south-korea-confirms-second-case-mers-virus-third-022536212.html

http://www.newsweek.com/critical-gaps-knowledge-remain-mers-infects-50-saudi-arabia-308829

--Joe

Norovirus outbreak on ship departing from San Francisco

An outbreak of norovirus occurred last week on a Princess Cruise ship departing from nearby San Francisco en route to Hawaii.  Of the 3,681 people on board, over 150 passengers and crewmembers were infected with the virus aboard the Star Princess.  Norovirus was detected in preliminary tests collected onboard the ship, and  stool samples have been collected and sent to the CDC for further testing.

After detection, sanitation procedures were ramped up to prevent further transmission of the virus. Passengers were also advised of ways to minimize transmission and their risk of infection, including washing their hands thoroughly, and using only restrooms in their cabin.  Furthermore, passengers were not allowed to disembark the ship, due to the possible risk of transmission.  Upon its return to San Francisco, the ship was thoroughly cleansed in preparation for its next cruise.

This latest outbreak has further affirmed the reputation of cruise ships as a breeding ground for extremely contagious pathogens such as Norovirus.  In fact, this incident represents the sixth time in 2015 that a cruise ship has reported a Norovirus outbreak en route to a US port.  The Princess Cruise line is no stranger to Norovirus outbreaks; in 2014 alone, outbreaks operated by Princess Cruises accounted for seven of the sixteen documented outbreaks on cruise ships in 2012.

http://sfbay.ca/2015/05/15/virus-sickens-150-on-star-princess-cruise-ship/

--Andrew Duong

Rabies in Brain Imaging

We spent a bit of time talking about rabies in Humans and Viruses. A scary zoonotic infection that kills if untreated, rabies has been a scourge of humanity since ancient times. Over the past few years however, Ed Callaway of the Salk institute has been working with a deletion mutant strain of rabies with a GFP gene added. Rabies infects neurons through axon terminals and spreads backward (i.e. in a retrograde direction). This mutant strain replicates within host cells, but cannot spread beyond the first neuron they infect. Thus, the vector is not only safe, but it also doesn’t lead to any background fluorescence other than that which comes from the cells it infects.

http://www.newyorker.com/tech/elements/the-brighter-side-of-rabies
http://www.nature.com/nmeth/journal/v4/n1/full/nmeth999.html

--Joe

Rift Valley Fever Virus Helps Understand Viral Replication

A group in Montreal, Canada is attempting to understand hemorrgaic fever viruses through the lens of basic research. By understanding the mechinism by which the viruses replicate adn mutate, they hope to create possible drug targets for future therapeutics which may be a more economically viable solution to such diease than a vaccine (vaccines have been difficult to finance becasue many of these viruses occur in poor countries where there is not a large enough financial incentive for large scale produciton).

Using Rift Valley Fever Virus, researches attempted to characterize the method of replication of the virus. Using nuclear magnetic imaging (NMR), the researches attempting to characterize what each of the viral proteins were responsible for  replication. They discovered that a non-structural protein (NSs) of the virus binds to Transcription Factor II in the cell and creates nuclear filaments. The viral protein that does this looks similar to the human DNA repair proteins (sharing similar structural motifs) and may be a potential candidate for drug-targeting, since inhibiting the protein's action reduces virulence.

Paper:http://www.pnas.org/content/early/2015/04/22/1503688112
---Lauren

Mutagenesis Induction in Viruses

Viruses - particularly retroviruses like HIV - are notorious for their ability to mutate.  The rapid replication of viruses paired with their high mutation rate allow viruses to adapt to their host quickly. However, mutations are only beneficial to a certain extent, and most mutations are likely maladaptive.  Using this information, scientists at the University of Chicago and MIT have been able to induce mutagenesis in viruses, increasing their rate of mutation to a point where the virus can no longer function effectively.  Moreover, these scientists have developed a spectroscopy method that further elucidates the mechanism behind nucleotide analogs.

The researchers used an anti-HIV agent called KP1212 that evades viral detection and infiltrates a viruses genome.  KP1212 functions essentially as a nucleotide analog that mimic DNA bases and result in mismatching of the normal adenosine-thymine, and cytosine-guanine base pairings in DNA. KP1212 is believed to work by repositioning hydrogen atoms in DNA, and resulting in faulty hydrogen bonding.

The use of two-dimensional infrared microscopy by the scientists to examine the structure of mutated viral DNA is novel, as scientists typically use nuclear magnetic resonance.  The benefit of infrared microscopy is that scientists can examine the quickly changing structures of mutagenic viral DNA in aqueous solution (the natural environment of cells) as opposed to organic solvents.  The ability of infrared microscopy to detect different mutagenic viral DNA structures, which quickly change shape and are keenly sensitive to time-changes, has resulted in the discovery of many different tautomers invoked by the KP1212 molecule.

Source: http://news.uchicago.edu/article/2015/04/14/shape-shifting-molecule-tricks-viruses-mutating-themselves-death

--Andrew Duong

Ebola found in the eye of "cured" patient

Following up on last week's post about the alleged sexual transmission of Ebola through a previously infected man's sperm, a new report this week has found a new potential reservoir for Ebola: the inside of a person's eye.  The eye is a prime place for a virus to reside because the inside of the eye (alongside the testicles) exhibit immune privilege, a phenomenon wherein certain immune molecules and compounds are found at lower concentrations in these areas.  Ebola was found in the eye of Dr. Ian Crozier, an American doctor who was infected with Ebola, and "recovered" from the virus in October.   However, months later, high pressure in his eye developed, resulting in blurred vision and discomfort for Dr. Crozier.  Knowing that Dr. Crozier was once infected with Ebola just a few months ago, opthalmologists at Emory University drew fluid from the inside of his eye to test if Ebola was responsible for the pressure build-up inside his eye.

Surprisingly, laboratory tests revealed the presence of Ebola in the inside of the Dr. Crozier's eyes, but not in his tears or surface film, meaning that while Ebola persisted in his system, his potential to infect others was very low.  With no approved treatments for Ebola, Dr. Crozier's condition deteriorated rapidly.  In a particularly gruesome incident, Dr. Crozier's eye changed color from blue to green for several weeks.  Eye color change is extremely rare for viral infections, and usually indicate a severe infection.  Scientists are preliminarily dubbing the new eye condition post-Ebola syndrome, as reports from West Africa suggest that other recovered patients have experienced similar eye problems.

Luckily for Dr. Crozier, an experimental treatment consisting of steroids and an antiviral has resulted in his gradual recovery, showing promise for treatments currently in development against the virus. His eye color, for example, reverted back to its natural blue color, and parts of his vision are returning.  However, it is still too early to tell what the long-term effects of Ebola are, and if Dr. Crozier will ever fully recover from the disease.  Future research is critically needed to study the chronic effects of Ebola, especially given that there have been relatively few infections and even fewer survivors prior to the 2014 West African Ebola outbreak.

Source: http://www.nytimes.com/2015/05/08/health/weeks-after-his-recovery-ebola-lurked-in-a-doctors-eye.html

--Andrew Duong