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. Image
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.
The lineage (variant) is characterized by 32 conserved spike mutations A67V Δ69-70 T95I G142D/Δ143-145, Δ211/L212I ins214EPE G339D S371L S373P S375F K417N N440K G446S S477N T478K E484A Q493K G496S Q498R N501Y Y505H T547K D614G H655Y N679K P681H N764K D796Y N856K Q954H N969K L981F
Many of the spike mutations independently predict immune (Antibody) escape and transmissiblity.

Some of the mutations suggest possibility of S-gene droput, which means some primers targeting the Spike gene locus might not work, and could be used to detect the variant quickly.
3 mutations are in the S1/S2 furin cleavage site possibly suggesting better cell entry (and may be transmissibility)

Point to keep in mind: Properties of single mutations don't always add up when they occur in combination. Nevertheless they give potential directions to explore.
The sequences currently available in public domain are from South Africa, Hong Kong (South African traveler) and Botswana. Large nos of sequences are from Gauteng in South Africa.
For a quick update, there is this press statement
Gauteng saw a rapid increase in test positivity last week.
Notwithstanding the potential for bias in sequencing, the B.1.1.529 variant seemingly is becoming dominant (almost 0 to 75% in 2 weeks) in South Africa. More sequences and data is awaited over the coming days. Image
@rid1tweets has a wonderful plot mapping the waves of COVID-19 infection in South Africa, including the present outbreak.
Eagerly awaiting more details as they emerge, especially the NICD SA and UKHSA reports on the emerging evidence
A useful map of literature on functional mutations in B.1.1.529 has been made available by @YYCist
people.ucalgary.ca/~gordonp/linea… also suggesting increase in B cell epitope mismatch residues compared to Delta
@jbloom_lab has a wonderful thread on immune escape mutations in B.1.1.529 variant.
The B.1.1.529 variants seemed to be spreading rapidly in South Africa, much faster than other VoCs we have seen in the past. Image
@FT has a wonderful plot putting the variants and waves of infection in South Africa. The previous waves has been dominated by Beta and Delta VoCs Image
@nextstrain has named the B.1.1.529 lineage as 21K to enable.easy comparison between the lineage nomenclature systems.
#Israel confirms its first case of B.1.1.529 in a traveller from Malawi
2 other suspected travellers being investigated as per the news report.
Statement from #Botswana on the four cases of B.1.1.529 #COVID19 variant suggests all four were vaccinated. The same applies to 2 cases from #HongKong
This suggest the B.1.1.529 variant can indeed cause #vaccine #breakthrough infections. Image
At least one case of B.1.1.529 in #Israel seems to have received a #COVID19 vaccine #booster suggesting the variant can cause #vaccine breakthrough infections. The disease severity is yet to be known, which is the most important point to consider.

#Belgium reports two suspected cases infected with B.1.1.529 variant of #SARSCoV2
🔴 While vaccine breakthrough infections per se is not the major concern (delta also caused V-BTs), transmissibility and clinical outcomes (severity and mortality) are the key points.
ECDC has designated B.1.1.529 as a variant of concern
ecdc.europa.eu/en/covid-19/va… Image
🔴 UKHSA designates B.1.1.529 as a Variant Under Investigation VUI-21NOV-01
No cases in 🇬🇧 yet. Image
🔴 @WHO designates variant B.1.1.529 as a Variant of Concern #VoC. Names it #Omicron
who.int/news/item/26-1… Image
🔴 @WHO statement on #Omicron #VOC designation for B.1.1.529
@trvrb on #Omicron B.1.1.529
The extremely long branch (>1 year) indicates an extended period of circulation or continual evolution in a chronically infected individual before spilling back into the population. Image
The identification of the #Omicron / B.1.1.529 variant would not have been possible without the tireless efforts of clinicians and researchers in Africa who have provided timely alerts

@nicd_sa @Tuliodna @BWGovernment @discoverhk

Sequencing coverage issues with #Omicron on Midnight assay on @nanopore and how to work around
The structural context of the immune escape mutations in omicron / B.1.1.529 variant compiled by @mercy_rophina and colleagues in the ESC database. For accessing the database, please visit clingen.igib.res.in/esc

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More from @vinodscaria

24 Nov
Real-world data on effectiveness of BBV152 / Covaxin whole inactivated #COVID19 vaccine against symptomatic infection
👥Healthcare Workers at @aiims_newdelhi
🗓 Coincided with the 2nd wave in #Delhi majorly driven by VoCs

#MedTwitter #vaccines #India
Adjusted effectiveness of BBV152 against symptomatic COVID-19 after 2 doses adm at least
🔸️14d before testing was 50% (95% CI 33–62; p<0·0001).
🔸️28d before testing was 46% (95% CI 22–62) 
🔸️after excluding previous COVID19 cases, 14d before testing was 47% (95% CI 29–61)
In summary
🔸️Vaccine effectiveness requires at least 2 doses and 14 days after 2nd dose

What this means for #PublicHealth
🔸️ Underscores the need for completing vaccine schedule of 2doses
🔸️ Continued non-pharmacological measures in the face of a wave of infections
Read 4 tweets
3 Nov
Insights on the recent wave of COVID-19 infections in @Singapore
The present wave in Singapore is of interest since a significant large proportion (82.7%) of population has received 2 doses of #COVID19 #vaccines but nevertheless have a wave of infections and deaths.
With respect to COVID-19 variants and VoCs, clearly Delta (and 2 prominent sublineages AY.23 and AY.23.1) dominate the present wave of infections.
Data: @DiseaseOutbreak
There are some interesting insights, thanks to the data made available at data.gov.sg
While on first look there is a significant number of cases spread across all age-groups.
The community cases are largely dominated by the younger age-groups (59 years and above)
Read 8 tweets
20 Oct
What do we know and don't about the Delta sub-lineage AY.4.2
ℹ️ AY.4.2 is a sub-lineage Delta (B.1.617.2) in the UK which has shown consistent increase over the past few months and has caught attention.
Plot: Sanger COVID-19 Genomic Surveillance Dashboard covid19.sanger.ac.uk/lineages/ Image
The background:
Delta had significant advantage over other lineages, in almost all regions, practically eliminating all other lineages as they spread widely.
The continued evolution of delta provided a number of sublineages
There are now ~55 sublineages (AY.1 - AY.41) of Delta
Some of the AY.x sublineages have geographical preponderance, due to mutations present at the time of introductions. For example, UK has a AY.4 sublineage. More about the lineages and distribution is available at cov-lineages.org/lineage_list.h… Image
Read 9 tweets
24 Jul
Closely tracking the delta+ lineages now across the world, one of the lineages AY.3 seems to be emerging in the United States of America. This tweetorial is to summarise the observations. I will be updating this thread as new evidence emerges.
Thanks Image
The interest in looking at this lineage closely comes from the fact that this lineage has been on the rise in USA in recent weeks.
Thanks @Unusual_Times for pointing this. Image
AY.3 seems to be localized to some states, like #Mississippi and #Missouri with nearby states slowly picking up. Image
Read 15 tweets
13 Jul
The recent outbreaks of #Zika Virus in #Kerala has renewed interest in this virus. This tweetorial explains some key aspects about the virus and why we should be actively using #genomics for #GeneticEpidemiology Image
The disease in most people is mild. Majority of people infected with Zika virus DO NOT develop symptoms. Symptoms are generally mild including fever, rash, conjunctivitis, muscle and joint pain, malaise, and headache, and usually last for 2–7 days.
Source: @CDCgov Image
Death is RARE
Infection during pregnancy can cause microcephaly & congential malformations.
Neurological complications like Guillain-Barré syndrome, neuropathy and myelitis are seen in some.
Read 13 tweets
8 Jul
Why are numbers in Kerala an anomaly ?
Here is my take on these numbers
No. of cases are not directly comparable across states, due to the large disparity in testing capacities. It is most likely that the high nos are just representative of the testing nos. Here is a comparison of some states. Data from covid19india.org
So are the COVID-19 deaths for the states. Of note and contrast would be Kerala and Bihar - see closely the no of tests and deaths
Read 8 tweets

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