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Slack / Private Message Drop, pp.945-946 [SLACK_001159] · slack_pm:msg:09840

Date: 2021-06-19 10:35
Type: chat message · slack
recipient: Kristian G. Andersen, Robert F. Garry, Edward C. Holmes
speaker: Andrew Rambaut

Recipients on this medium are inferred from channel membership, not per-message addressing.

Amplicons - ```The study describes an approach to diagnose infection withSARS-CoV-2 and other respiratory viruses by nanopore sequenc-ing. This approach involved reverse-transcription of total RNAfrom swab samples, followed by PCR with specific primers togenerate amplicons covering portions of the viral genome. Theseamplicons were then sequenced on an Oxford Nanopore Grid-ION, and infection was diagnosed if the sequencing yieldedsufficient reads aligning to the viral genome. Importantly, thestudy notes that this approach yields information about thesequence ofthe virus as well enabling diagnosis of infection```At least 2 of the mutations talked about are in or immediately adjacent to ARTIC primer sites which always ring a fewalarm bells:```C18060TMN908947.3 18036 18062 nCoV-2019_59_RIGHT 60 -C28144TMN908947.3 28145 28172 nCoV-2019_92_RIGHT 60 -G28085TMN908947.3 28081 28104 nCoV-2019_93_LEFT 60 +```

In context

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2021-06-19 10:10 Robert F. Garry open

Bloom - please read !channel IMPORTANT [shared file(s): paper.pdf]
2021-06-19 10:15 Robert F. Garry open

"However, the current study suggests that at least in one case, the trusting structures of science have been abusedto obscure sequences relevant to the early spread of SARS-CoV-2 in Wuhan. A careful re-evaluation of otherarchived forms of scientific communication, reporting, and data could shed additional light on the early emergence ofthe virus."
2021-06-19 10:33 Andrew Rambaut open

Is it deep sequencing data? Or amplicons?
2021-06-19 10:35 Andrew Rambaut

Amplicons - ```The study describes an approach to diagnose infection withSARS-CoV-2 and other respiratory viruses by nanopore sequenc-ing. This approach involved reverse-transcription of total RNAfrom swab samples, followed by PCR with specific primers togenerate amplicons covering portions of the viral genome. Theseamplicons were then sequenced on an Oxford Nanopore Grid-ION, and infection was diagnosed if the sequencing yieldedsufficient reads aligning to the viral genome. Importantly, thestudy notes that this approach yields information about thesequence ofthe virus as well enabling diagnosis of infection```At least 2 of the mutations talked about are in or immediately adjacent to ARTIC primer sites which always ring a fewalarm bells:```C18060TMN908947.3 18036 18062 nCoV-2019_59_RIGHT 60 -C28144TMN908947.3 28145 28172 nCoV-2019_92_RIGHT 60 -G28085TMN908947.3 28081 28104 nCoV-2019_93_LEFT 60 +```
2021-06-19 10:35 Robert F. Garry open

Wang _et al._ (2020a) sequenced PCR amplicons covering nu- cleotide sites 21,563 to 29,674 of the SARS-CoV-2 genome, which spans from the start of the spike gene to the end of ORF10. They also sequenced a short amplicon generated by nested PCR that covered a fragment of ORF1ab spanning sites 15,080 to 15,550. In this paper, I only analyze the region from spike through ORF10 because this is a much longer contiguous sequence and theamplicons were generated by conventional rather than nested PCR. I slightly trimmed the region of interest to21,570 to 29,550 because many samples had poor coverage at the termini."
2021-06-19 10:36 Andrew Rambaut open

Ah - OK so not the ARTIC amplicons then
2021-06-19 10:39 Robert F. Garry open

WA1 is lineage A and has bat-like T8782 and C28144 plus another bat-like snp - what mutation is this?
2021-06-19 10:41 Robert F. Garry open

More top secret stuff - Tony and Francis have arranged a call with Jesse tomorrow - need to sort this out...

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