Thread by @stevenemassey

A leak of polio from a research facility is indicated by a poliovirus genome sequence generated from a sample collected in 2014 in China by the Wuhan Institute of Virology

The sequence is 99 % identical to that of a polio strain from 1954 🧵
academic.oup.com/ve/article/10/…

2/ Chesnais et al sequenced 3 poliovirus genomes recovered from 60 year old historic samples generated by Albert Sabin at the Pasteur Institute, Paris

Sabin is the father of the oral polio vaccine, created from attenuated polio strains

3/ Poliovirus is a single stranded positive sense RNA virus, that only naturally infects humans (no other natural hosts are known)

There are 3 poliovirus serotypes: PV-1, PV-2 and PV-3

4/ The 3 genome sequences were from strains Glenn (PV-3), cold variant P2149 (PV-1) and cold variant P712 (PV-2)

Glenn was a cold adapted strain isolated before 1956 from a child in Cincinnati

5/ The P712 cold variant was a serially passaged derivative of strain P712. P712 is a constituent of the oral polio vaccine

The P2149 cold variant is likewise a serially passaged derivative of strain P2149

Both cold variants are able to grow at 25C

6/ Surprisingly, the Glenn genome showed 95 % identity to WIV14, generated from a sample collected in Dec 2014 by the Wuhan Institute of Virology (WIV)

WIV14 (accession KY703697) was isolated in Vero cells. from a child in Anhui, China, described 👇
sciencedirect.com/science/articl…

7/ As Glenn is related to Saukett A (PV-3), which is used to produce inactivated polio vaccine (IPV), the group also sequenced the Saukett A genome

They obtained a sample from the British National Institute for Biological Standards and Control (NIBSC)

8/ Saukett A was first obtained from a child, James Sarkett (the name of the strain was misspelled), in California prior to 1954 by medical pioneer Jonas Salk, creator of the IPV

Salk never received a Nobel for his work, but perhaps should have done

archive.triblive.com/news/a-lasting…

9/ The Saukett A genome showed a 99% match to the WIV14 genome, providing a closer match than Glenn

This can be seen on the tree below (genetic distance is indicated by branch lengths)

10/ The high sequence identity, with only 70 nucleotide differences, indicates a recent common ancestor between Saukett A and WIV14

However, Saukett A was isolated < 1954. Given the high mutation rate of polioviruses, the high sequence identity is anomalous

11/ WIV14 should be more divergent at the sequence level if it had been in circulation for 60 years after splitting from Saukett A

The most plausible explanation is that its progenitor was in storage for a substantial amount of time, and then released into the population

12/ This would be reflected in WIV14's retarded sequence evolution in comparison to Saukett A

The most likely reason for storing its likely progenitor, Saukett A, would be for vaccine development, given Saukett A's role in the IPV

13/ Could the WIV14 sequence be the result of contamination from a WIV source during the sequencing process ?

I think this is unlikely as contaminating genome sequences often have low sequencing depth, and the sequence was described as coming from a poliovirus live isolate

14/ In addition, the sequence was generated using Sanger sequencing, which is not as prone to contamination as next generation sequencing

However, PCR amplification was used to generate the sequence fragments, and this can amplify contaminating sequences

15/ Given the widespread use of the IPV, and consequently Saukett A, then it is more difficult to identify a potential originating facility

There should be a paper trail, however, regarding those facilities doing that type of work

16/ Given that WIV14 was isolated from a child in Anhui, China it implies the originating facility was in China

WIV14 had apparently been in circulation somewhat before isolation given the sequence divergence from Saukett A, molecular clock analyses can give an approximate date

17/ Of interest are the 10 nonsynoymous mutations in the capsid protein which suggest immune pressure, consistent with circulation in the human population, or serial passage in a lab animal (rather than a cell line)

18/ Given that there are mouse adapted polio PV-3 strains then passaging in a lab mouse cannot be ruled out

Vincent Racaniello @profvrr for example has worked on a mouse adapted PV-3 strain, it would be interesting to hear his opinion

journals.asm.org/doi/10.1128/jv…

19/ In principle, examination of the mutations in WIV14 might provide evidence for mouse adaptation (as would infectivity studies in mice)

20/ Chesnais et al note the possibility that WIV14 had undergone serial passage in a lab before release into the population, and that this would result in accelerated evolution (from a Saukett A progenitor)

21/ While WIV14 was isolated by the WIV14 in Vero cells, only 6 passages were reported, which is insufficient to generate the nucleotide differences observed with Saukett A

22/ To conclude, it appears highly likely that WIV14 was the result of a leak from a scientific facility

Its 'frozen' sequence is reminiscent of the Russian H1N1 flu genome, which was also likely released from a scientific facility

onlinelibrary.wiley.com/doi/full/10.11…

23/ Another example of 'frozen' sequences is that of hand, foot and mouth disease (HMFD) strains sampled in 2007-2009 from China, which bear high identity to the BrCr prototype strain sampled in 1970 USA, indicating a likely lab leak origin

journals.plos.org/plosone/articl…

24/ Venezuelan equine encephalitis virus (VEEV) strains isolated in 1995 also have 'frozen' sequences, showing striking genome identities to strains isolated 1962-64

The 1995 strains likely derived from a leaked 1962-64 strain used for vaccine production
journals.asm.org/doi/full/10.11…

25/ Finally, another intriguing example of a 'frozen' sequence is that of the 2021 Ebola outbreak in Guinea. The genome sequence was little different from 2014 sequences from the same region

nature.com/articles/s4158…

26/ Is there a connection with research facilities in the region ? Collaborators of the West African Emerging Infectious Disease Research Center, Drs Kristian Andersen and Robert Garry, no doubt would have an enlightening take

@COVIDSelect

scripps.edu/news-and-event…

27/ It appears a new paradigm for pathogen emergence has crystallized

@threadreaderapp unroll