In about 5 hours, we’ll be gathering for a conversation about, oh boy, the pandemic. Expect different perspectives, but none of them crazy.
Speaking of perspectives, we also have a guest this month: Dr Tara Smith. She’ll be providing the extremely well informed perspective.
Watching recent TWiV. Daniel Griffin is painting a less rosy picture of Omicron:
https://youtu.be/DTysKBBRL_Y
Plus explains some of rationale behind changes in CDC guidance, like not having things come to a grinding halt.
Reposting Larry Moran on the mouse angle (which is an intriguing angle on what was this variant/strain doing since mid-2020):
https://sandwalk.blogspot.com/2022/01/the-effect-of-spike-protein-mutations.html
And a hefty article that gets into differences with Omicron per endocytosis (versus entry of other variants), less lung targeting, and lack of spike based cell-cell fusion leading to syncytia:
https://www.gla.ac.uk/media/Media_829360_smxx.pdf
“…we demonstrate a shift in the SARS-CoV-2 entry pathway from cell surface fusion, triggered by TMPRSS2, to cathepsin-dependent fusion within the endosome. This fundamental biological shift may affect the pathogenesis and severity of disease and requires further evaluation in population-based studies.”
Larry has posted on hospitalization in Ontario:
https://sandwalk.blogspot.com/2022/01/ontario-canada-hospitals-are-filling-up.html
“Given the high levels of vaccination, you might suspect that most of the people in hospital will have been fully vaccinated and that’s exactly what we see. 71% of the COVID-19 patients in the hospitals have been fully vaccinated but this number is slightly misleading since it includes patients who were admitted for other reasons and subsequently tested positive for COVID-19. Those people aren’t necessarily being treated for severe COVID symptoms.”
[…]
“However, it’s worth noting that 51% of the patients in the ICUs are either fully or partially vaccinated. You can still get a serious case of COVID-19 if you are fully vaccinated.”
Way back in the early days so long ago in the Omicron era there was speculation that Omicron had perhaps borrowed from an hCoV neighbor during coinfection in a person. This Reuters article gives a digested version of the narrative and links the actual article:
https://www.reuters.com/business/healthcare-pharmaceuticals/omicron-variant-may-have-picked-up-piece-common-cold-virus-2021-12-03/
“Cells in the lungs and in the gastrointestinal system can harbor SARS-CoV-2 and common-cold coronaviruses simultaneously, according to earlier studies. Such co-infection sets the scene for viral recombination, a process in which two different viruses in the same host cell interact while making copies of themselves, generating new copies that have some genetic material from both “parents.”
This new mutation could have first occurred in a person infected with both pathogens when a version of SARS-CoV-2 picked up the genetic sequence from the other virus, Soundararajan and colleagues said in the study, which has not yet been peer-reviewed.”
The mouse origin paper addresses that idea suggesting an alternative explanation:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8702434/
“…it was noted that Omicron harbored a nine-nucleotide insertion (GAGCCAGAA, encoding the peptide EPE) after residue 214 in the spike protein. This insertion is identical to the sequence of TMEM245 in the human genome or that of ORF S in the human coronavirus hCoV-229E, which was used as evidence to support a human origin for Omicron (Venkatakrishnan et al., 2021). However, we provide a simpler explanation for this insertion, namely that it was derived from an RNA fragment of ORF N in the SARS-CoV-2 genome (Fig. S7) because the RNA abundance of ORF N is much higher than that of mRNA encoded by the human genome (Wei et al., 2021). And this is especially so for ORF N due to the nested nature of the coronavirus genome and subgenomes (Kim et al., 2020).”
Also as a trivial aside in the mouse origin paper they use “hSCV2 spectrum” as a shorthand way of referring to “molecular spectrum for SARS-CoV-2 variants known to have evolved strictly in humans”. I’ve been looking for less unwieldy way to refer to SARS-CoV-2. Would SCV2 be acceptable or too unfamiliar and confuse people? I’m lazy.
OT sciency stuff (happy news to prevent depression)
The JWST mirrors have started unfolding.
Researchers in Minnesota have made the first 3D-printed flexible OLED display.
Covid: Governor Ron De Santis has been missing for weeks. Now he showed up för a speech and clearly was sick, the voice was unsteady. But he is never going to offer clarification, having invested så much in “Covid is no big deal”.
This is discouraging. Correct me if I’m wrong but this sounds like you’re still just as likely to end up in the ICU whether you’re vaccinated or not.