Resistant variable, Kentucky nursing home

[url]https://www.cdc.gov/mmwr/volumes/70/wr/mm7017e2.htm[/url] or https://www.cdc.gov/mmwr/volumes/70/wr/mm7017e2.htm CDC report from april this year on this outbreak; 

The SNF conducted vaccination clinics using Pfizer-BioNTech mRNA vaccine on January 10, January 31, and February 21, 2021. Among 83 residents and 116 HCP, 75 (90.4%) and 61 (52.6%), respectively, received two vaccine doses. All vaccinated residents and HCP were vaccinated on-site, the majority on January 10 and 31. Four residents and five HCP received their second dose during the third clinic, which was <14 days before the outbreak onset.

Before and during the outbreak, SARS-CoV-2 testing was used for evaluating symptomatic illness in residents and HCP. Symptom screening of residents and HCP had been ongoing since March 2020, and twice-weekly screening testing of all HCP had been occurring since November 2020. A COVID-19 case was defined as a positive SARS-CoV-2 antigen or reverse transcription–polymerase chain reaction (RT-PCR) test result. Possible reinfection was defined as a positive SARS-CoV-2 test result >90 days after a previous laboratory-confirmed infection.

The outbreak was identified during routine HCP antigen testing on March 1.* This was 8 days after the third vaccination clinic. The index case occurred in an unvaccinated, symptomatic HCP. Once the outbreak was identified, daily rapid point-of-care antigen testing of all residents, regardless of symptoms, was added to the twice-weekly HCP testing. Additional specimens were collected the same day for RT-PCR confirmation of positive antigen test results. One week after the outbreak was identified, resident antigen testing was reduced to three times weekly, then to twice weekly after no additional cases were identified for 1 week.

DJ The forbes article is from september 20-so "new" ; The R.1 variant shares a common origin with all variants of interest or concern. They are marked by what I call the Triad, three mutations, one the 5’ untranslated region: C241U, a second in the viral polymerase NSP12: P323L, and the third D614G in the exterior S1 domain of the spike protein. The D614G mutation increases the infectivity. The contribution of the other two members of the Triad remains a mystery. Together these three mutations characterize the first major variant first observed in early 2020. 

-

R.1 is a variant to watch. It has established a foothold in both Japan and the United States. In addition to several mutations notably in the spike and nucleocapsid protein in common with variants of concern, R.1 has a set of unique mutations that may confer an additional advantage in transmission, replication, and immune suppression.

DJ I would expect more at [url]https://www.gisaid.org/help/search/[/url] or https://www.gisaid.org/help/search/ ...

See also [url]https://deadline.com/2021/09/r-1-new-covid-variant-u-s-japan-1234841685/[/url] or https://deadline.com/2021/09/r-1-new-covid-variant-u-s-japan-1234841685/ ; According to a CDC report, among 83 residents and 116 healthcare workers, 26 residents and 20 workers tested positive for Covid. Twenty eight specimens were subjected to whole genome sequencing and, on March 1, found to have mutations that aligned with the R.1 lineage. (The outbreak reportedly began with an infected staffer.) “Attack rates were three to four times as high among unvaccinated residents and [workers] as among those who were vaccinated,” according to the findings.

-

Roughly 90% of the facility’s residents and and 52% of the staff had received 2 vaccine doses. Among those, 25.4% of the residents and 7.1% of the workers were infected. That, according the CDC analyses, raises concerns about reduced protective immunity to R.1 from vaccines.

What’s more, four possible reinfections were identified, “providing some evidence of limited or waning natural immunity to this variant,” per the report. All of those people experienced symptomatic illness. One of them died.

-

R.1 was first identified in Japan in January 2021 among three members of one family. One of those infected was in their 40s and the other two were under 10 years old. “These three patients were living in Japan and had no history of traveling abroad,” according to an NIH report.

As of April 22, 2021, the NIH analysis states that “the percentage of SARS-CoV-2 isolates belonging to the R.1 lineage in Japan increased more rapidly” than it did in the U.S.

DJ "Japan-variant"?  Immunity still doing a good-but far from perfect-job.

The history of Kentucky is notorious for tuberculosis cases. Haseltine’s article claims that the R.1 variant mutation, G769V, is unique. Unique to what? Without mutating, it is G769 in porcine TGEV (subsistence on metal surfaces for up to 28 days and remaining viable), porcine PRCoV, feline FCoV and canine CCoV. Furthermore, the Chinese communist virus infecting Kentuckians thinks its in a mink: R.1 mutation R203K, in mink alphacoronavvirus 1/2016 China, without mutating is R203. R.1 variant mutation F28L, in a different strain of mink coronavirus, without mutating, is L28. R.1 variant mutation P412H is, without mutating, H412 in feline infectious peritonitis virus (FIPV), traditionally fatal in the cat host. R.1 variant mutation, P323L is, without mutating, P323 in human HCoV-NL63, porcine TGEV and PRCoV, feline FCoV and FIPV, and canine CCoV.

Badger2, are you a fan of Bucky the Badger ?