Thread by @SolidEvidence

Ohio cryptic lineage clarification/rant.

1. Washington Court House is a town of about 15,000 people. It is not an actual court house.

2. There are about 700 people that commute from Franklin county (Columbus) to Fayette county (WCH) and about 900 people that commute the other way. This is not nearly enough information to identify them.
Thanks to the person that pointed out census info.
onthemap.ces.census.gov

3. The Columbus Southerly sewershed processes about 125 million gallons of wastewater/day. That’s the volume of 189 olympic swimming pools.

The sample used for sequencing usually represents about a teaspoon.

Think about it. It’s only in absolutely EXTREME situations where we can discern something from a single individual from wastewater.

4. Absolutely everything I have posted about the Ohio cryptic lineage came from public databases.
ncbi.nlm.nih.gov/sra/
coronavirus.ohio.gov/dashboards/oth…

Here are most of the accession numbers if anyone wants to look them up themselves. Happy to share my analyses too. The lineage is pretty obvious.

5. When we tracked the lineage in Wisconsin we did not know that we were looking for an individual; I was convinced we were looking for an animal reservoir.
medrxiv.org/content/10.110…

Once we realized that the lineage was coming from a person, the health department communicated the information to the relevant individuals, but the research STOPPED while we sought approval to continue.

It was frustrating that the investigation had to stop, but it was reassuring that the individuals were at least notified. A few months later the signal disappeared.

Maybe the person got appropriate treatment once they knew what was going on.

We’ll probably never know.

6. How do I know this is coming from one person? It’s the only logical explanation. Here is why:

In the first positive samples last summer both sewersheds had core RBD sequence of:
K417T-L455M-E484V-F490Y-Q493K-S494P-Q498H/Y-N501T

Then on the same day in November, sequences in both sewersheds picked up the change P499S.

Then around new year’s, during the same week sequences in both sewersheds switched to from P499S to P499T, and also picked up F486H.

Then in February, during the same week sequences in both sewersheds switched from Q493K to Q493T.

How can you explain this synchronicity other than the lineages came from the same source?

7. There is almost zero chance the patient in Ohio knew about their infection.

There is almost zero chance their doctor would figure it out.

It is very likely the infection is causing long term damage.

I’m glad that there is a chance now that they might get appropriate care.

8. If people want write to ask me questions I will try to answer them, but I can’t give medical advice. I can only point you to an appropriate physician. I don’t have approval to test patient samples.

9. There is no ‘manhunt’ to track this lineage through wastewater, but it would not be hard at all given the massive amount that is shed.

The question is whether that is the correct thing to do.

I think it is, but this decision can only be made by public health officials.