🔴 A lot of discussions have come up on the BA.2.75 variant of #SARSCOV2. A continuously updated 🧵on emerging evidence on this variant.
This variant was highlighted for designation recently. Majority of genomes have come from India 🇮🇳, apart from many other countries. github.com/cov-lineages/p…
Why is this lineage interesting?
⚪ Interesting because it has 9 unique changes in the spike protein incl. a reversion compared to the BA.4 and BA.5 subvariants of omicron now spreading widely across the globe.
Schema @mercy_rophina
If you map the mutations to the spike protein, this becomes a bit clear. G446S is in the RBD which binds to the human receptor and also associated with major immune (Ab) escape
Plot @mercy_rophina
🔴 Immune Escape
G446S can possibly influence both immune escape and ACE2 binding. Given data at hand, it is very likely that while this might decrease the binding efficiency, could contribute to significant immune(ab) escape based on data from @jbloom_lab jbloomlab.github.io/SARS-CoV-2-RBD…
This could mean Reinfections vaccine breakthrough infections could drive the spread of BA.2.75. @jbloom_lab has an extensive thread on this 👇
⚪ Growth advantage
While the number of genomes from India in public domain for the variant is quite small to preclude assessments, the rapid increase in recent weeks (albeit small numbers in very small number of genomes) suggest it might have a growth advantage ...
compared to BA.2 and sublineages.
⚪ Point to note here is BA.2 and sublineages are the ones prevalent in India presently and BA.4 and BA.5 has not caught up significantly in Maharashtra where most of the BA.2.75 has come up. So essentially it is competing with other BA.2.x now.
🔴 Is there a need to panic now ?
NO, as the variant is NOT YET suggested to cause severe disease or increased mortality.
Point to keep in mind is that the variant is continuously evolving and accumulating more mutations and it is too early to jump into conclusions
⚪ a much broader & stronger genomic surveillance, epidemiology and more importantly, availability of data for analysis is key to understand the picture in a better way.
🔴 How can you protect yourself and your near and dear ?
😷 better masks , more masks
☁️ better ventilation
💉 complete the vaccine schedule for all.
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Briefly, the variants were identified - thanks to the researchers in South Africa 🇿🇦 who have been using genomic surveillance quite efficiently. We knew about these two variants as early as April 2022 as cases were slowly increasing in SA just after the omicron wave.
A lot of discussion about B.1.640.2 reported from Southern France 🇫🇷 and a preprint on the variant medrxiv.org/content/10.110…
This 🧵is to summarize what we know. 👇
🔴14 changes including N501Y and E484K, & 9 deletions in Spike
🔵B.1.640 (now renamed B.1.640.1) had been in the @WHO watchlist for quite some time (Nov 2021)
🔵Index case seemingly was from Cameroon (doesn't mean it originated there)
🔴Many of the mutations are shared with VoCs
🟢Though predates omicron, sequences have not grown rapidly
🟢 Mutation specific qPCR assays can screen and differentiate from Delta and Omicron
🔴We don't know whether the increasing cases in South France 🇫🇷 are associated with the new variant
🔴Transmissibility or Virulence : What should really worry us ?
Since these two have been widely discussed, given #omicron is around. A short explainer 👇.
3 plots below - from ~2x of Rt value and 1/2 of hospitalization rates (less virulent) to basal value (~ Delta wave)
Rt is the effective reproductive no.
One could clearly see why 2x Rt would create a sharper and ⏫rate of hospitalizations.
For a less virulent and highly transmissible variant, assuming 1/2x hospitalization rate, this would still create a significant wave of hospitalizations.
A much detailed mathematical basis to this was discussed in the past by @AdamJKucharski
SARS-CoV-2 Variants and RT-PCR
Can RT-PCR Detect Omicron ?
A short thread on the topic. 👇
RT-PCR is a sensitive molecular method widely used for the detection of SARS-CoV-2 in biological samples. This is based on the principle that short pieces of DNA (aka primers) can specifically target DNA/RNA and amplify them using a polymerase protein
Typically COVID-19 RT-PCR kits use 2 or more sets of primers which target the virus nucleic acid at 2 or more genes/sites in the genome. This is to improve the specificity of the detection. Combinations between N, E, RdRP and S genes are typically used.
What do we know about the B.1.1.529 variant of SARS-CoV-2 with a very large number of mutations
An updated thread on emerging evidence.
B.1.1.529 is a newly designated variant of SARS-CoV-2 github.com/cov-lineages/p…
This would not have been possible without the exemplary work of researchers in Africa who have sequenced and deposited the genomes in public domain which forms the basis of this variant designation.