TWiV 416: Scattered seeds dormant

The multi-dimensional TWiV-brane brings you the entries in the haiku/limerick contest, and explain how a giant virus infects a host within another host (it has to do with predators!).

You can find TWiV #416 at, or listen below.

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Dugas was not AIDS Patient Zero

aids_index_case_graphThe 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.

TWiV 415: Ebola pipettors and the philosopher’s clone

Jeremy Luban, Aaron Lin, and Ted Diehl join the TWiV team to discuss their work on identifying a single amino acid change in the Ebola virus glycoprotein from the West African outbreak that increases infectivity in human cells.

You can find TWiV #415 at, or listen below.

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Zika virus in Nicaragua with Eva Harris

I spoke with Eva Harris of the University of California, Berkeley, on the state of Zika virus in Nicaragua.

Zika in the Guys

In this episode of Virus Watch, we explore the finding that Zika virus infects the testis of mice, causing damage to the organ, reduced sperm production, and less fertility. The important question: does the same happen in humans?

TWiV 414: Zika in the guys with Diamond

On episode #414 of the science show This Week in Virology, Michael Diamond visits the TWiV studio to talk about chikungunya virus and his laboratory’s work on a mouse model of Zika virus, including the recent finding of testicular damage caused by viral replication.

You can find TWiV #414 at, or listen below.

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Increased infectivity of Ebola virus glycoprotein from West Africa

filovirionWhen viruses cross species, serial transmission may lead to the selection for mutations that confer improved replication or transmission in the new host. Identifying such mutations in human viruses is extremely difficult: we cannot conduct the appropriate experiments in humans, and often do not have viral isolates spanning the time from spillover through prolonged circulation. The 2013-2016 outbreak of Ebola virus in West Africa is unique because viral genome sequences were obtained early and throughout the epidemic. The results of two new studies (link to paper one, link to paper two) suggest that some of the observed mutations increase infectivity for human cells. The impact of these mutations on infection of humans, and their role in the West African outbreak, remain unknown.

Many mutations have been identified among the many hundreds of genome sequences obtained during the recent Ebola virus epidemic. One stands out: a mutation that leads to a single amino acid change in the viral glycoprotein, from alanine to valine at position 82 (A82V). This change arose early in the outbreak (it was first observed in Guinea in March 2014) and was subsequently found in most of the isolates. It has never been observed in previous Ebolavirus outbreaks.

The effect of the A82V change on viral infectivity was determined by building pseudotyped viral particles – in this case, HIV particles with the Ebola virus glycoprotein. Human cells in culture were infected with pseudotyped viruses with the Ebola virus glycoprotein with either alanine or valine at position 82. Infectivity was measured by quantifying the production of a protein from the HIV genome. The results show that A82V increases infectivity by twofold. The effect is also observed in cells from non-human primates, but not from rodents, dogs, or cats. However, the A82V change decreased infectivity in bat cells.

The A82V change is located at the binding site of the Ebola virus glycoprotein with the cell fusion receptor, NPC1. It appears to increase the fusion activity of the viral glycoprotein.

Other amino acid changes in the Ebola virus glycoprotein were also observed to increase infectivity in human cells, and decrease infectivity in bat cells.

The pattern of increased infectivity in primate cells, and decreased infectivity in bats, is consistent with the hypothesis that the outbreak virus came from bats, and after circulation of the virus in humans, it lost some ability to infect bat cells while becoming better at infecting human cells. However there is still no solid proof that bats are a reservoir of Ebolaviruses.

What does increased infectivity have to do with infection of humans? The idea is that the mutation increases the efficiency of virus entry into cells, and hence increased viral gene expression is observed. Fewer viruses needed to infect a cell, the better chance of initiating an infection. But is the two-fold increase observed in cells enough to impact infection in humans?

The assays used in these papers measure protein production from an HIV genome. The experiments need to be repeated using bona fide Ebola virus, to make sure that the mutations have the same effect. The changes might have impacts on other stages of viral replication. Furthermore, the impact of the changes in the viral glycoprotein should be assessed in animal models, to determine if improved infectivity has any impact on pathogenesis and transmission. Ultimately, we can’t prove that these mutations have any effect in humans – the needed experiments cannot be done.

I’m curious about why the A82V change was not seen in previous Ebola virus outbreaks. Those were in different parts of Africa – could the changes be driven by population genetics, ecology, or other factors? It will be important to determine if the same change is selected in future outbreaks.

The authors are sufficiently cautious in their conclusions. From paper #2:

Despite the experimental data provided here, it is impossible to clearly establish whether the adaptive mutations observed were in part responsible for the extended duration of the 2013–2016 epidemic. Indeed, it seems likely that the prolonged nature of the outbreak in West Africa was primarily due to epide- miological factors, such as an increased circulation in urban areas that in turn led to larger chains of transmission.

From paper #1:

Our findings raise the possibility that this mutation contributed directly to greater transmission and thus to the severity of the outbreak. It is difficult to draw any conclusions from this hypothesis, though…

As I feared, press coverage of these findings has been inaccurate. For example, a BBC headline proclaims “Ebola adapted to easily infect people”. Even the journal Cell, which published both papers, made an incorrect conlcusion: see the screen capture below from the journal website.key mutations ebola virusBoth Cell and the BBC might have taken too literally the unfortunate title of one of the papers,  “Human adaptation of Ebola virus during the West African Outbreak.” The results suggest adaptation to human cells, not to humans. The title of the second paper is sufficiently careful: “Ebola virus glycoprotein with increased infectivity dominated the 2013-2016 epidemic”. But that’s not a BBC headline.

TWiV 413: Partnerships not parachutes

From the EIDA2Z conference at Boston University, Vincent, Alan and Paul meet up with Ralph Baric, Felix Drexler, Marion Koopmans, and Stacey Schultz-Cherry to talk about discovering, understanding, protecting, and collaborating on emerging infectious diseases.

You can find TWiV #413 at, or watch or listen here.

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Genome recombination across viral families

coronavirus and reovirus A novel coronavirus isolated from bats in China is unusual because the genome contains a gene from a virus in a completely different family, the Reoviridae (link to paper). The finding suggests that recombination occurred between a (+) strand RNA virus and a virus with a segmented, double-stranded RNA genome.

The unusual recombinant virus was identified in rectal swabs from Rousettus leschenaulti bats in Yunnan Province, China. Sequence analysis revealed a typical coronavirus genome with the exception of a small region near the 3′-end of the viral RNA with homology to a bat reovirus. This sequence, called p10, was also detected in viral mRNAs from infected bats, further demonstrating the presence of the reovirus-like gene in the coronavirus genome.

In bat reoviruses, the p10 gene is known to encode a protein that causes cell fusion. When the p10 gene from the bat coronavirus was expressed in cells, formation of syncytia (fused cells) was observed. Furthemore, the p10 protein was detected by western blot analysis of feces from infected bats. These results indicate that the p10 protein is produced from the viral genome and that the protein is functional.

This report is not the first suggesting recombination between viruses of different families – we discussed one example here previously (link to article), and there are a handful of other examples. The important question is how such inter-family recombinants arise. It must begin with co-infection of a host with two different viruses – in this case, likely a bat – but the precise molecular events are unknown. It might be useful to attempt to isolate such recombinants in cell culture to understand the underlying mechanisms.

TWiV 412: WO, open the borders and rig the infection

The TWiVome reveal the first eukaryotic genes found in a bacteriophage of Wolbachia, and how DNA tumor virus oncogenes antagonize sensing of cytoplasmic DNA by the cell.

You can find TWiV #412 at, or listen below.

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