I spoke with Jonna Mazet, PhD, UC Davis School of Veterinary Medicine, about emerging pathogen surveillance and public health. Dr. Mazet is the Principal Investigator and Global Director of the novel viral emergence early warning project, PREDICT, that has been developed with the US Agency for International Development’s (USAID) Emerging Pandemic Threats Program. Recorded at the Emerging Infectious Diseases A to Z (EIDA2Z) conference hosted by the National Emerging Infectious Diseases Laboratories (NEIDL).
deep sequencing
Dugas was not AIDS Patient Zero
The popular history of HIV/AIDS describes a man known as Patient Zero, a sexually active flight attendant who traveled the globe and initiated the AIDS epidemic in North America. A new analysis of the viral genome recovered from his serum and that of other patients in the 1970s proves beyond a doubt that he was not Patient Zero (link to paper).
In a heroic effort, thousands of archived serum samples originally collected from cohorts of men who have sex with men in the 1970s in New York and San Francisco, were examined for the presence of HIV by western blot analysis. A total of 83 samples were found to be HIV positive and subjected to deep sequencing, but the viral RNA was degraded and present only in short pieces. To overcome this problem, many DNA primers were used to amplify short RNA fragments by PCR in a procedure colorfully called ‘jackhammering’. The impressive result is that complete HIV-1 coding sequences were obtained from 8 samples: 3 from San Francisco and 5 from New York City.
Analysis of the HIV genome sequences, and comparison with earlier and later data revealed that the virus likely traveled from Africa to the Caribbean around 1967, and from there to New York City in 1971. These results disprove previous ideas that HIV arrived in the Caribbean from the US.
Sequence analysis also reveals that New York City was a hub of early diversification of HIV, and that the epidemic was already mature and genetically diverse by the late 1970s. There appears to have been a single introduction of HIV into San Francisco from New York City in 1976. From those two cities the virus spread elsewhere in the US and overseas.
It has been suggested that a sexually active flight attendant, identified as Gaetan Dugas by Randy Shilts in his book And the Band Played On, was the source of the North American AIDS epidemic. Although at least one study years ago concluded that he was not the first case, this belief persists. Sequencing of HIV from this patient’s serum revealed that he was certainly not the first person in North America infected with this line of HIV-1 (Group M, subtype B) .
A historical reconstruction of the early days of AIDS in the US reveals how Dugas earned the label ‘Patient Zero’. CDC investigators who were studying a sexual network of 40 gay men placed one man at its center, whom they called ‘Patient O’, standing for ‘outside of California’ because he was Canadian (pictured; image credit). Upon publication of this work, the ‘O’ was misinterpreted as a zero and so began the belief that he was the origin of the AIDS outbreak in North America.
An RNA virus that infects Archaea?
Every different life form on earth can probably be infected with at least one type of virus, if not many more. Most of these viruses have not yet been discovered: just over 2,000 viral species are recognized. While the majority of the known viruses infect bacteria and eukaryotes, there are only about 50 known viruses of the Archaea, and these all have DNA genomes. The first archaeal RNA viruses might have been recently discovered in a hot, acidic spring in Yellowstone National Park.
Archaea are single-cell organisms that are similar in size and shape to bacteria, but are evolutionarily and biochemically quite distinct. They inhabit a broad range of environments including those with extreme conditions such as high temperature, acidity, and salinity. Identification of archaeal RNA viruses is important because their study could provide information about the ancestors of RNA viruses that infect eukaryotes. Direct sequencing of viral communities from the environment, known as viral metagenomics, is one approach being taken to discover archaeal viruses.
The acidic (pH <4) and hot (>80°C) springs in Yellowstone National Park were examined for the presence of archaeal RNA viruses because these bodies of water contain mainly Archaea. Samples were obtained from 28 different sites and extracted nucleic acids were treated with DNAase (to remove DNA genomes) and then reverse transcriptase (to copy RNA to DNA). If reverse transcription was reduced by treatment with RNAse, it was concluded that the sample contained mostly RNA. The results narrowed the sample size to three, all from Nymph Lake. New samples obtained twelve months later also showed a predominance of RNA and were used for metagenomic analysis by deep sequencing.
Analysis of the RNA viral sequences revealed coding regions for a predicted RNA dependent RNA polymerase (RdRp), a hallmark of RNA viruses. One assembled sequence of 5,662 nucleotides, believed to be a complete viral genome, encodes a single open reading frame containing a RdRp and a putative capsid protein similar to that of the positive-strand RNA containing nodaviruses, tetraviruses, and birnaviruses. Another viral sequence encoded a protein with 70% amino acid homology to the predicted RdRp. The sequences are from a novel virus which does not belong to any known virus family.
These results clearly show that at least two related but distinct RNA viruses are present in Nymph Lake. However whether or not the hosts of these viruses are Archaea or Bacteria cannot be determined by these metagenomic analyses. What is needed to resolve this question is old-fashioned virology: isolating RNA virus particles that can infect an archaeal host and produce new infectious viruses.
B Bolduc, DP Shaughnessy, YI Wolf, EV Koonin, FF Roberto and M Young J. Virol. 2012, 86(10):5562. DOI: 10.1128/JVI.07196-11.
TWiV 90: Guano happens
Hosts: Vincent Racaniello, Alan Dove, Rich Condit, and Eric F. Donaldson
On episode #90 of the podcast This Week in Virology, Vincent, Alan, Rich and Eric discuss identification of viruses in Northeastern American bats, vaccinia virus infection after sexual contact with a military vaccinee, and identification of a new flavivirus from an Old World bat in Bangladesh.
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Click the arrow above to play, or right-click to download TWiV #90 (64 MB .mp3, 89 minutes)
Subscribe to TWiV (free) in iTunes , at the Zune Marketplace, by the RSS feed, or by email, or listen on your mobile device with Stitcher Radio.
Links for this episode:
- Vaccinia virus infection after sexual contact with vaccinee
- Smallpox vaccination overview
- Smallpox vaccine lesions (jpg)
- Smallpox hospital, Roosevelt Island, NY (photo 1, photo 2)
- Isolation of a flavivirus from bats in Bangladesh (PLoS Pathogens)
- Review on hepatitis G virus
- Dickson has been teaching at Singularity University and fishing in Bozeman MT (jpg)
- Letters read on TWiV 90
Weekly Science Picks
Eric – Year of Darwin by Sean Carroll
Rich – March of the Penguins
Alan – Standing-height desks
Vincent – DengueWatch (thanks Richard!)
Send your virology questions and comments (email or mp3 file) to twiv@microbe.tv or leave voicemail at Skype: twivpodcast. You can also post articles that you would like us to discuss at microbeworld.org and tag them with twiv.
TWiV 86: Dark matter with Dr. Eric Delwart
Hosts: Vincent Racaniello, Rich Condit, and Eric Delwart
In episode #86 of the podcast This Week in Virology, Vincent and Rich travel to the Blood Systems Research Institute in San Francisco to speak with Eric Delwart about his work on virus discovery.
This episode is sponsored by Data Robotics Inc. Use the promotion code TWIVPOD to receive $75-$500 off a Drobo.
To enter a drawing to receive 50% off the manufacturers suggested retail price of a Drobo S or FS at drobostore.com, fill out the questionnaire here.
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Subscribe to TWiV (free) in iTunes , at the Zune Marketplace, by the RSS feed, or by email, or listen on your mobile device with Stitcher Radio.
Links for this episode:
- List of Dr. Delwart’s open-access journal articles (pdf) – to find each one, type PMID # into PubMed
- CDC says don’t give rotavirus vaccines to infants with SCID
- The Brighton Collaboration
- Product sheet for RotaTeq (pdf – thanks, Sheldon!)
- Letters read on TWiV 86
Weekly Science Picks
Rich – Google Crisis Response – Gulf of Mexico Oil Spill
Vincent – HHMI resources for teachers and students (thanks, Jim!)
Eric – Vaccine by Arthur Allen
Send your virology questions and comments (email or mp3 file) to twiv@microbe.tv or leave voicemail at Skype: twivpodcast. You can also post articles that you would like us to discuss at microbeworld.org and tag them with twiv.