0
$\begingroup$

RFI reports:

"You have to remember -- these labs are still open inside of China these labs that contain complex pathogens that were being studied. It's not just the Wuhan Institute of Virology," Pompeo told reporters.

"It's important that those materials are being handled in a safe and secure way such that there isn't accidental release," Pompeo told reporters.

Pompeo cited the example of nuclear facilities, pointing to the rigorous global inspections to ensure safety.

He renewed concerns that China has not shared a sample of the initially detected virus, known scientifically as SARS-CoV-2.

"We still do not have a sample of the virus, nor has the world had access to the facilities or other locations where this virus may have originally originated inside of Wuhan," Pompeo said.

(China has now rejected this US call as being "politically motivated" but they weren't terribly specific beyond that.)

Would China [physically] sharing "a sample of the initially detected virus" (which of course begets the question which sample is that precisely--but let's assume they share all 40 or so initial samples they reported/discovered back in Jan) have any scientific value? E.g. is [physically] sharing those samples (more broadly) likely to shed any additional light on the virus' origins? (In that regard, have Western scientists asked for those [physical] samples, or said they are important for China to [physically] share them, independently/before the US political leadership's involvement in the matter?)

For more context, a Yale med page from January says:

Two weeks ago, we didn't even know what the nCOV2019 virus was. Today, thanks to China’s quick public release of the initial nCOV2019 virus genome [...] To go from unknown pathogen to diagnostic tests so quickly is incredible! The scientists at the Fudan University, China CDC, Chinese Academy of Medical Sciences, Chinese Academy of Sciences, Zhejiang Provincial CDC, and the Thai National Institute of Health should be highly praised for making their data rapidly available to the public.

A bit later, Chinese researchers published a paper on 10 genomes from the initial outbreak in Wuhan. The (FASTA) data for those seems publicly available, although behind a registration page.

So, per comments below, if Pompeo means something else by "sample of the virus" (not physical sample[s]), what is that?

$\endgroup$
  • $\begingroup$ You interpolate [physical(ly)] throughout - does that mean that you are asking about physical sharing only, as opposed (e.g.) to sharing complete genome sequences of all the samples? $\endgroup$ – Ben Bolker Apr 25 at 0:27
  • $\begingroup$ @BenBolker: I'm willing to be corrected that Pompeo meant something else, as you suggest. (E.g. if non-Chinese experts said that such extra sequences would help.) I know China shared some genome sequences, do you think if they shared more that would elucidate the kind questions that Pompeo is interested in, like the origin of the virus? $\endgroup$ – SX welcomes ageist gossip Apr 25 at 0:36
  • $\begingroup$ @BenBolker: thelancet.com/article/S0140-6736(20)30251-8/abstract "We did next-generation sequencing of samples from bronchoalveolar lavage fluid and cultured isolates from nine inpatients, eight of whom had visited the Huanan seafood market in Wuhan. Complete and partial 2019-nCoV genome sequences were obtained from these individuals. [...] The ten genome sequences of 2019-nCoV obtained from the nine patients were extremely similar, exhibiting more than 99·98% sequence identity. " $\endgroup$ – SX welcomes ageist gossip Apr 25 at 0:41
  • $\begingroup$ @BenBolker: "These data have been deposited in the China National Microbiological Data Center (accession number NMDC10013002 and genome accession numbers NMDC60013002-01 to NMDC60013002-10) and the data from BGI have been deposited in the China National GeneBank (accession numbers CNA0007332–35). " And the data seems available on nmdc.cn/nCov/en although it seems to require a login to download the actual fasta files. (They have a registration page, alas the latter seems to only be in Chinese, and I haven't tried to use it.) $\endgroup$ – SX welcomes ageist gossip Apr 25 at 0:51
  • $\begingroup$ The premise of this question presupposes the veracity of a Trump agent, whose behavior is political, in the least. $\endgroup$ – Alex Reynolds Apr 26 at 9:36
1
$\begingroup$

I'll take a shot at this. It's my impression that most of this is political rather than scientifically grounded. There are reasons to want physical samples of viruses (rather than just genomic sequences), e.g. if you want to do experimental (in vitro or in vivo) studies on a particular virus strain. (It might be theoretically possible to edit the genome or reconstruct the genome of an earlier strain, but it's much easier if you have the desired viral strain in hand.)

Based on this Financial Times article (which may or may not be accessible without a subscription/accepting cookies)

Mr Pompeo added the Chinese Communist party had still not shared virus samples with anyone outside China, impeding efforts to understand how it emerged.

A researcher at Wuhan Institute of Virology, who declined to be named, told the Financial Times earlier this month that China had not shared samples of the live virus with the WHO as the country “had already published plenty of information” such as the genetic code of coronavirus.

It does seem that almost all of the research on the origins of SARS-COV-2 is based on genome sequences rather than on phenotypic studies (i.e., in vitro and in vivo studies of actual viruses).

I don't think viral samples would actually be very useful (that's why I said at the beginning that I think most of this argument is political rather than scientific). In principle I guess you could use the viral samples from an early stage do experimental infections in different animal species, but I don't know that any researchers actually want to do that, and I don't think there's been enough phenotypic evolution in the last few months that the early-epidemic viral samples would behave that differently from current samples ... it's also likely that researchers could study the effects of particular mutations (observed in genomic sequence) by modifying viral samples they had in hand.

To take an example from an earlier pandemic, researchers have done experimental studies in mice to show how particular mutations influenced the virulence of earlier flu strains. This is an example where it's useful to have an actual virus rather than just the genome - but in this case the virus was actually reconstructed from knowledge of the genome ("two isogenic recombinant chimeric viruses were created with an influenza A/WSN/33 virus background containing the PB1 segment from the HK/156/97").

| improve this answer | |
$\endgroup$
  • $\begingroup$ Thanks for that clarification. So. as I suspected, the Chinese rejected the US request interpreted as a request for live virus samples because they though/said the genetic info they have published suffices. But besides validating my q to some extent, this isn't really answering it. Why are domestic live samples not enough? Why are live samples from China in particular necessary in the US? $\endgroup$ – SX welcomes ageist gossip Apr 25 at 16:25
  • $\begingroup$ More precisely, in re your last para, when have "phenotypic studies" elucidated the origin of an outbreak? Are there [past] examples? $\endgroup$ – SX welcomes ageist gossip Apr 25 at 16:31
  • $\begingroup$ Thanks for the update. (+1) $\endgroup$ – SX welcomes ageist gossip Apr 25 at 18:02
  • 4
    $\begingroup$ Ralph Baric already cloned the virus from Chinese sequence data. This is just politics. $\endgroup$ – iayork Apr 26 at 1:29
  • $\begingroup$ @layork feel free to post your own answer, or edit my question (if I don't do it first) $\endgroup$ – Ben Bolker Apr 26 at 14:18

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.