Tulio de Oliveira

We detected evidence of positive selection on six genes since the ancestral BA.1/Omicron and BA.2 lineage split: S-gene, exonuclease, nsp6, M-gene, N-gene, and E-gene. In all six genes, this selection was strong (dN/dS > 10) - details on Extended Table 2 https://krisp.org.za/manuscripts/ZHTOWa-MEDRXIV-2021-268028v1-deOliveira.pdf …

The growth advantage of Omicron is likely to be mediated by (i) an increase relative to other variants of its intrinsic transmissibility, (ii) an increase relative in its capacity to infect & be transmitted from, previously infected & vaccinated individuals; or both.

The predicted combination of transmissibility and immune evasion for Omicron depends on the assumed level of current population immunity against infection by, and transmission of, the competing variant Delta, by prior infections with other strains, and/or vaccination

The results of seroprevalence studies and vaccination coverage (40%) in South Africa suggest that the proportion of the population with potential immunity against Delta and earlier variants is likely to be above 60%. x

The notion of immune evasion is supported by findings that show increased risk of SARS-CoV-2 reinfection associated with the emergence of Omicron in South Africa (See reference 48) and initial results from neutralization assays (see references 26,27) https://krisp.org.za/manuscripts/ZHTOWa-MEDRXIV-2021-268028v1-deOliveira.pdf …

Conclusions: Strong genomic surveillance systems in SA & Botswana enabled identification of Omicron within a week of observing a resurgence in cases in Gauteng Province. Immediate notification of the WHO and early designation as a VOC has stimulated global scientific efforts.

Early identification has given other countries time to prepare their response. Omicron is now driving a fourth wave of the SARS-CoV-2 epidemic in southern Africa and is spreading rapidly in several other countries.

Genotypic and phenotypic data suggest that Omicron has the capacity for substantial evasion of neutralizing antibody responses, and modelling suggests that immune evasion could be a major driver of the observed transmission dynamics

Close monitoring of the spread of Omicron in countries outside southern Africa will be necessary to better understand its transmissibility and the capacity of this variant to evade post-infection and vaccine-elicited immunity.

Neutralizing antibodies are only one component of the immune protection from vaccines and prior infection, and the cellular immune response is predicted to be less affected by the mutations in Omicron.

Vaccination, therefore, remains critical to protect those at highest risk of severe disease and death. The emergence and rapid spread of Omicron poses a threat to the world and a particular threat in Africa, where fewer than one in ten people is fully vaccinated

The quick identification and characterization of #Omicron is an example of regional and global collaboration. This manuscript has close to 100 authors that work day and night to make the world a safer place!

Would like to thank and acknowledge the hard work #Omicron of @drSikhulileMoyo @houzhou @CathrineSch07 @C_Althaus @maciekboni @rmcolq @KoenDef @deelansd @susanen2 @Jenn_Giandhari @Mittenavoig @viralverity @HsiaoMarvin @sergeilkp @MOUGK @rjlessells

Would like to thank and acknowledge the hard work #Omicron of @ShahinLockman @aglucaci @ArishaMaharaj30 @TongaiMaponga @Nokuzola_Mbhele @zolkol @moir_monika @NokukhanyaMsomi @YeshneeN @SureshneePillay @YajnaRamphal @Upasana_16 @JSAN4CHRIST @DKTshiabuila

Would like to thank and acknowledge the hard work on #Omicron of @GeneJockey15 @EduanWilkinson @WP87738523 @Carolyn86563982 @EvolveDotZoo @BhimanJinal @DarrenM98230782 @arambaut and many other authors that are not on Twitter!