Coronavirus - Taiwan 2021

They just did.

It’s a testing merry go round. See the woman who just returned from the US and tested negative three times in the US but tested positive here.

As the bear indicated, I think you must understand the drill by now.

A worker from Vietnam goes home and tests positive upon arrival. Vietnam dutifully reports this to the Taiwan authorities. Taiwan authorities dutifully trace and test the contacts this worker had in her final days in Taiwan (in this latest case, seven people). Results then released (as per the Focus Taiwan article linked above, one of the seven contacts so far has tested negative).

Guy

You forget the final step which is @SuperS54 posting “weak positive!” :joy:

No, there is no final step here, as Belgian Pie will of course step up and ask: “If it’s not in Taiwan how can she export it?”

Then we start all over again!

Guy

So is the current thinking that she caught it in Taiwan, or she caught it abroad a whole ago and is still testing positive because it is still in her system? How long was she in Taiwan before leaving to go to Vietnam?

She’d been here four years. There’s been many of these cases. Never has a single contact been found to also have the virus. Hence the false positive meme.

It could be dodgy testing or exposure en route home.

If she was exposed on her flight home, everyone on the flight would also have been in Taiwan during at least the previous two weeks, so either way Taiwan has more cases in the wild than we think. Unless of course it is a false positive. How does Taiwan CDC explain it?

Does the 250,000 represent TW Citizens arriving from the USA after a lengthy absence from Taiwan, or something else?

False positive rate is what…1 in a hundred ?
Multiply by number of migrant workers going both ways
Also can get infected enroute.

Do a few close contact tests and don’t worry much more about it unless something pops up in the close contacts.

I think so. It’s a repatriation figure.

A lot of labs are using high Ct values when doing PCR testing. Some experts say that anything above 30 is questionable, and anything above 35 is downright dubious.

In the US, I believe the default being used in many places is 37-40. Might partly explain why there are so many asymptomatic “cases”.

Yes, it is likely that some of the higher Ct values represent past infection with remaining viral fragments, especially more than a few weeks after symptoms. Labs do often use a cutoff of 40, but the tests are not technically quantitative so it is hard to give exact numbers. But if people getting tested for symptoms, you would expect more of that group to be truly positive than when you screen asymptomatic people.

Yes, it could be that the test is picking up remnants of a past infection.

I also wonder about the RNA fragments being used for testing. Each testing kit producer can use different fragments. How do we really know that SARS-CoV-2 is the only virus with those fragments? We’re talking about really short sequences of RNA here.

Already, there are some theories that parts of Asia, including Taiwan, have been less hard hit because SARS-like viruses have been spreading undetected for years without causing major illness. If that’s the case, it’s within the realm of possibility that there are other viruses that share the RNA the tests are looking for.

Most of them use spike and another target. Sequence variations can throw the primers and cause false negatives in theory. They do test for cross reactivity with other viruses and very little has been found. Some tests may show limited cross reactivity with the previous SARS, but that is not in circulation.

Apparently the government is now considering whether or not to allow Chinese students to enter Taiwan

Well there are good genomes available of the four endemic human coronaviruses . I’m guessing they do the usual blast search against all known genomes and exclude as many common sequence as possible. Then there are tecnqhiues to improve selectivity such as nested PCR.
Latest one being promoted is isothermal amplification I’m interested to know how it’s working in reality.

If I recall rightly the closest genome to SARS2 detected was actually identified and sequenced at WIV lab a few years ago .
It has 96% homology and it’s a bat coronavirus from Yunnan thousands of KM away.

And one asks how come SARS2 then somehow popped up in Wuhan first. Maybe it’s a massive coincidence and other labs haven’t really been looking A very very big maybe.

https://www.nature.com/articles/d41586-020-03217-0

Only a handful of known coronaviruses are closely related to SARS-CoV-2, including its closest known relative, RaTG13. That was discovered in intermediate horseshoe bats ( Rhinolophus affinis ) in the Chinese province of Yunnan in 2013, and was published2 only earlier this year. There are also several other coronaviruses, found in other Rhinolophus bats and pangolins captured between 2015 and 2019, that scientists now know to be closely related to SARS-CoV-2.

“SARS-CoV-2 probably wasn’t a brand new virus that popped up all of a sudden. Viruses in this group existed before we became aware of them in 2019,” says Tracey Goldstein, associate director of the One Health Institute at the University of California, Davis, who is involved with the Cambodian team.

Latinne says the discoveries confirm that Rhinolophus bats are the reservoir of these viruses.

Horseshoe bats are almost certainly the reservoir species.

More background on similarity from their Feb paper.
Takeaway from this is that there are no similar coronaviruses in circulation that could reasonably present a false positive as long as the PCR test is calibrated correctly. Covid19 is quite distinct even from other SARS-Coronaviruses.

We then found that a short region of RNA-dependent RNA polymerase (RdRp) from a bat coronavirus (BatCoV RaTG13)—which was previously detected in Rhinolophus affinis from Yunnan province—showed high sequence identity to 2019-nCoV. We carried out full-length sequencing on this RNA sample (GISAID accession number EPI_ISL_402131). Simplot analysis showed that 2019-nCoV was highly similar throughout the genome to RaTG13 (Fig. 1c), with an overall genome sequence identity of 96.2%. Using the aligned genome sequences of 2019-nCoV, RaTG13, SARS-CoV and previously reported bat SARSr-CoVs, no evidence for recombination events was detected in the genome of 2019-nCoV. Phylogenetic analysis of the full-length genome and the gene sequences of RdRp and spike ( S ) showed that—for all sequences—RaTG13 is the closest relative of 2019-nCoV and they form a distinct lineage from other SARSr-CoVs (Fig. 1d and Extended Data Fig. 2). The receptor-binding spike protein encoded by the S gene was highly divergent from other CoVs (Extended Data Fig. 2), with less than 75% nucleotide sequence identity to all previously described SARSr-CoVs, except for a 93.1% nucleotide identity to RaTG13 (Extended Data Table 3). The S genes of 2019-nCoV and RaTG13 are longer than other SARSr-CoVs. The major differences in the sequence of the S gene of 2019-nCoV are the three short insertions in the N-terminal domain as well as changes in four out of five of the key residues in the receptor-binding motif compared with the sequence of SARS-CoV (Extended Data Fig. 3).

PS - It seems they never published any data from RaTF13 previously even though it was first identified in 2013. They say it’s because they never sequenced it fully, only had a sub sequence…Maybe…

I suspect a bit of both. We got the champion, the woman who had stayed away from Taiwan nearly 40 years …and lo and behold, was found to be sick on arrival.

Then we have the last two cases. One arrived there in September and hit jackpot.

We got students whose schools went virtual. We got students and workers and residents who got spooked. We got workers who were stranded and had to wait for repatriation flights. Others risked it for business sake. All came back here because it is safer… unless you ask my neighbors.

I actually wonder how many came voluntarily and how many were,vehem, coersed?