"finally, the time has slip and slid its slimy course through to us - and we're the vicious bastards of the new generation. we do not relent, and we should not be held to account for our ancestral faults"
He considers that the extremely long branch (>1 year) indicates continual evolution in a chronically infected individual before spilling back into the population.
He highlights the striking accumulation of mutations in the S1 domain of the spike protein.
He concludes that the presence of host derived RNA insertion from TMEM245 gene points to evolution within humans rather than spillback from animal population
"Looks like the new strain was either incubated in an immunocompromized person for months or serially passaged in a lab in the presence of convalescent plasma"
As COVID-19 collides with HIV/AIDS, the pandemic may be taking an ominous turn
https://t.co/RMZ2y9i23I
18. Rumours abound - Molnupiravir (1)
@veryvirology and @marc_g_wathelet point to a possible connection to recent trials with Merck and Ridgeback’s Investigational Oral Antiviral "Molnupiravir" in South Africa
For some, these mutations support lab leak theory (Wuhan), for example @zhiyanle
"the mutations again proves SARS-2 is lab-made. Natural Cov needs 50 years for 1100BP mutation; but lab-made nCov can have 5 times more mutation just in a year"
1. The argument that the 681 Proline was somehow "suboptimal" relies on misunderstanding about the conditionality its presence given the rest of the Spike protein structure
"The mutations in Omicron which seem to wipe out the majority of neutralizing antibody epitopes are very worrisome. Combined with the apparent fitness of the virus, this could be a problem"
36. From a storm in a teacup to a blessing?
via @DMoffin
"Wouldn't artificially creating a highly infectious virus with very low pathogenicity, & therefore outcompeting more deadly variants, be most genius thing researchers could do to end the pandemic?
"there may be an increased risk of reinfection with Omicron (ie, people who have previously had COVID-19 could become reinfected more easily with Omicron), as compared to other variants of concern"
"Previous infection used to protect against Delta but now with Omicron that doesn't seem to be the case," said Anne von Gottberg, microbiologist at South Africa's National Institute for Communicable Diseases.
"We monitored these reinfections for Beta & Delta wave & we didn't see increase in reinfections above what we expect when the force of infection changes - when the wave stops. However, we are seeing an increase for Omicron"
Now as is well known, HIV cannot infect mice, rats..
BUT
Humanized mouse models currently available are capable of replicating both HIV-1 & 2 exclusively in human immune cells that are present both in the periphery & in tissues ncbi.nlm.nih.gov/labs/pmc/artic…
Update 21 - Humanised Mouse Models (2)
Humanized mouse models like the T cell only mouse or the myeloid only mouse permit the analysis of HIV biology in individual cell types.
systemic reconstitution of humanized mice with human cells permit in vivo analysis of HIV persistence
Update 22 - Sample HIV Mouse papers
1. A mouse model for study of systemic HIV-1 infection, antiviral immune responses, and neuroinvasiveness (USA 2005) pnas.org/content/102/10…
Update 23 - Sample HIV Mouse papers
2. Rectal Transmission of Transmitted/Founder HIV-1 Is Efficiently Prevented by Topical 1% Tenofovir in BLT Humanized Mice (UNC, 2013)
"now scientists have shown that a genetically engineered rat is susceptible enough to HIV infection that it may be able to help evaluate some AIDS drugs"
Department of Pathology, Faculty of Health Sciences, University of Cape Town
Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town
"One hypothesis for emergence of this lineage, given the many mutations relative to background mutation rate of SARS-CoV-2, is that it arose via intra-host evolution in 1 or more people with prolonged viral replication"
"If evolution within long-term infections were the explanation for the evolution of this lineage then it supposes a transmission chain that passes through multiple individuals"
Update 31 - Garry & Gallaher - Rodent Mutations
"7 (mutations) are associated with rodent adaptation — changes that allow the virus to infect mice, rats & related species. All 7 of those mutations are in Omicron"
"in an otherwise deserted lab. Cele & de Oliviera chanced their luck on using human saline to infect monkey cells, which until then had proved unresponsive to weeks of experimentation. The outcome was best Christmas gift ever"
Experiments using plasma from donors with 1st wave variant B.1.351 (501Y.V2 VOC)
Update 55 - Suart Neil's Opinión
I don't usually RT Threads by @stuartjdneil but will make an exception this time as his thread presents some quite valid counter arguments against certain recent leaking suggestions,
Same genetic sequence appears in HCoV-229E and in the human immunodeficiency virus (HIV)
Update 62 - Deja Vu
B.1.1.7 variant first detected in UK had 12 + mutations that appeared suddenly. Recombination may merge mutations from different variants that arose spontaneously within same person over time or that co-infected someone simultaneously
Party in UK where 14 of 18 guests tested positive for the new variant despite everyone being double jabbed & some with booster, all guests had taken a lateral flow test 24 hours beforehand that was negative!
"There are B.1.1.529 lineages that do not have the N440K & K417N mutation (336 GISAID entries) & form a separate clade when analysed with other sequences that do contain these mutations"
"Either an intermediate that didn't acquire all defining mutations or it is consensus of a mixture of 2 lineages"
"If chronic infection hypothesis is true, no reason to believe patient zero would only have transmitted to one other"
Update 89 - One BIG uncertainty
Omicron’s less severe cases prompt cautious optimism in South Africa
"However, potential for Omicron to result in less severe symptoms may be more a consequence of immunity than the virus evolving to become less virulent"
Good luck using your critical thinking skills to seperate wheat from chaff so that you can decide what is propaganda & what is fact.
Of course the easy options are to dismiss everything as lies or to swallow everything as fact.
2. What I recommend
If you are interested in a balanced analysis of the Russian claims and all the detailed evidence presented by Kirillov before his assassination in Moscow, as well as relted topics, then I highly recommend you plough through those threads at your leisure.
1. "DOJ subpoenaed EcoHealth’s communications (inlcuding WeChat) with, at least, Dr. Shi. This subpoena included both Dr. Shi’s official WIV email address & her Hotmail"
2. “DoJ subpoena for genetic sequences, docs — almost complete”
Yi Gang Tong confrimed again the 2017 isolation date for MpCov-GX.
He experimented with it, but did not write a paper, and they did not upload the sequence until 8th Feb 2022, just after the beginning of the SARS-COV-2 pandemic