Genomic epidemiology of novel coronavirus (HCoV-19)

Post by nostromo » Mon, Mar 02, 2020, 4:31 PM UTC

throwanem wrote: post #8

rjtavares wrote: post #6

Earlier quoted context omitted.

We know the virus is widespread in Iran. We don't know if it is widespread in Africa or New Zealand.

No more so in Africa or in New Zealand [1] than in Finland, which is represented in this dataset. I'm not really seeing the basis for whatever conspiracy theory the original parent comment seems like it wants to point toward, is what I'm getting at here. These are the early stages of what looks to be a pandemic of a disease at least an order of magnitude, possibly several orders of magnitude [2], more lethal than sea…

Post by jfoster » Mon, Mar 02, 2020, 4:45 PM UTC

nostromo wrote: post #11

throwanem wrote: post #8

Earlier quoted context omitted.

No more so in Africa or in New Zealand [1] than in Finland, which is represented in this dataset. I'm not really seeing the basis for whatever conspiracy theory the original parent comment seems like it wants to point toward, is what I'm getting at here. These are the early stages of what looks to be a pandemic of a disease at least an order of magnitude, possibly several orders of magnitude [2], more lethal than sea…

Estimates are dropping down from 2% as we discover lots of cases that were mild or asymptomatic. The New England Journal of Medicine says it may likely be considerably less than 1%: https://www.nejm.org/doi/full/10.1056/NEJMe2002387 People should remember the context of a respiratory disease in China. 2/3rds of men smoke, and air pollution is common. Things also spread faster there as it’s densely populated with lowe…

Post by kire2345 » Mon, Mar 02, 2020, 5:15 PM UTC

Post by consp » Mon, Mar 02, 2020, 5:42 PM UTC

cstejerean wrote: post #16

kire2345 wrote: post #15

So am I reading this correctly that for example the strain in Lombardy Italy/CDG1/2020 (GISAID EPI ISL 412973) from 20.02.2020, has its origin in the strain collected in Bavaria Germany/BavPat1/2020 (GISAID EPI ISL 406862) from 28.01.2020. So the outbreak in Bavaria that was thought be contained somehow made its way to Italy? Or do these kind of interpretations not make any sense?

That seems like the right interpretation. The second case in Washington State appears to be a descendant of the first case on January 19, so we’ve also had about 6 weeks of undetected spread here from a case that was believed to be contained. It goes to show that “contained” doesn’t mean much when you only test people with symptoms but you know that the virus can spread asymptomatically. Early on the official guidanc…

Post by all_blue_chucks » Mon, Mar 02, 2020, 5:53 PM UTC

consp wrote: post #17

cstejerean wrote: post #16

Earlier quoted context omitted.

That seems like the right interpretation. The second case in Washington State appears to be a descendant of the first case on January 19, so we’ve also had about 6 weeks of undetected spread here from a case that was believed to be contained. It goes to show that “contained” doesn’t mean much when you only test people with symptoms but you know that the virus can spread asymptomatically. Early on the official guidanc…

Or people having just a mild variant which does not cause fever and airway problems. If they think it is something else, or don't care, it is just as well a transfer risk as asymptomatic individuals and in my opinion at least as likely.