2022-02-03 General


This is really strange. This article says that in New York City and also in some places in California, they have been seeing strange variants in their wastewater surveillance for the past year — variants they haven’t seen in any people. It wasn’t clear, but I think there are three main lineages (classed as WNY 3, WNY 10, and WNY 11, which I think are the most common substrains in each lineage). The lineages have strong geographical association: WHY 3 and WNY 10, for example, have always been in the their “home” sewersheds. WNY11 sometimes was seen in its home sewershed and also occasionally in adjacent sewersheds.

There is a particular mutation which shows up regularly in spike location 498, which is really really rare in the catalog of human variants, but which has been seen in rodents.

When the case counts in NYC go down, then the level of COVID-19 in the wastewater goes down — and the percentage of the cryptic sequences goes up.

The theories for where they are coming from are:

  • people who have had a persistent infection, e.g. a few immunocompromised patients;
  • random New Yorkers who just never happened to get their strains sequenced (less than 3% of samples in NYC get sequenced);
  • unusual places in the body (e.g. the gut, instead of the nose or throat);
  • an animal population (like perhaps rats or cats).

If it were from humans, you would expect each strains to show up in multiple sewersheds, as humans move around. If it was from invalid humans who were confined to bed, you wouldn’t expect WNY11 to move around to neighbouring sewersheds.

If it’s an animal, it needs to be one which doesn’t move around that much. They came up with a list of candidate animals (bats, cats, dogs, squirrels, mice, opossums, rabbits, raccoons, rats, and skunks), then looked for RNA from those animals in the sewershed. They only found RNA from humans, cats, dogs, and rats in the sewersheds that showed the cryptic variants.

They found a very low level of rat RNA in WNY 10’s sewershed. It is a residential area which has a pretty low density of rats, and has separate wastewater and storm drain systems. By contrast, there was lots of rat RNA in WNY 3’s sewershed — second only to human RNA and comprising over 1% of the RNA found. In WNY 11, they found very little cat RNA. So if it’s in an animal reservoir, it’s probably not just one type animal.

Plant Health Inspection Service at the U.S. Department of Agriculture has been looking hard for evidence of the variants in blood/stool of local rats, and have not been able to find any.

And bad news: WNY 3 and WNY 4 are completely resistant to all of the monoclonal antibodies which have been approved.


This article reports that a South African biotech company has made (a very small amount of) a copy of the Moderna vaccine! (Moderna has agreed not to enforce its patents during the pandemic, so it’s not actively helping but also not actively impeding progress.)

This paper says that a long interval between doses (8-16 weeks) gives better antibody protection than a short interval (3-6 weeks). T cell protection, however, was about the same for long and short intervals. Histograms of level vs. # of subjects:


This article says that there is a pathway for Molnupiravir to mutate a cell’s DNA, and hence it is theoretically dangerous.


This preprint says that using rapid tests was useful for triaging patients in the ER, and that the accuracy of the rapid tests was significantly higher in high-risk patients (100%) than in low-risk patients (75%).

Mitigation Measures

This article reports that Canadian Armed Forces has kicked out 58 service members for refusing a vaccine, with another 66 resigning voluntarily and 256 starting the process of getting kicked out.

This article reports on a meta-study (led by a libertarian) which found that lockdowns and border closures were pretty worthless for reducing death rates, but that masking and closing non-essential businesses (probably mostly closing bars) was effective.

Research Practice

During the pandemic, a massive amount of research has been published via preprints instead of via the traditional journal review process. This article reports that publishing preprints has not caused a degradation in research.