🔴 #Mpox aka #Monkeypox is spreading .
But not where you think it is.
A short 🧵 The latest situation report on the multi-country outbreak of #mpox from @WHO has come out . In Summary:
▶️ 87,929 cases and 146 deaths from Jan 2022
▶️ 111 countries / territories affected as of date

🔴 Characterisation of #Influenza A #H3N8 with hallmarks of continued evolution, spread in poultry and occasional spillover to humans from #China 🇨🇳

journals.asm.org/doi/10.1128/jv… ▶️ Continued infection of poultry and spillover into humans could potentially accelerate evolution and adaptation to human to human tranmission
▶️ Adaptation to other mammals noted in the past, through evolutionary processes.

#COVID19 in #China.
What we know and what we don't.
A long thread, summarizing my thoughts, which I hope to keep updated over the coming weeks. To give a brief background:
The aggressive approach by #China to contain the virus following initial cases in Wuhan, has been seen with awe and admiration by man.
This included:
🔴Strict quarantine & lockdown
🔴Massive testing & surveillance
🔴Early vaccines
🔴Health Infra

🔘Recombinant variants of SARS-CoV-2 and XBB/XBB.1 the recent and emerging recombinant variants with large immune evasive potential.
A short 🧵on emerging evidence. Recombinant variants of viruses are generated when two or more viruses co-infect a cell at the same time. Chances for co-infection is rare, but nevertheless they occur.
Genomic surveillance can efficiently pick up such recombinant isolates.

🔴The curious case of Indian #Monkeypox Genomes
Wonderful effort by clinicians in @KeralaHealth who diagnosed the disease and researchers at @icmr_niv, we now have sequences of MPX isolates in @GISAID .

This short 🧵is on what the early genomes say.
Analysis @bani_jolly Briefly 4⃣ genome sequences have been deposited for two samples (EPI_ISL_13953610 and EPI_ISL_13953611) along with 2 re-sequenced genomes from isolates of one of the sample.
▶️Both the isolates were from early cases reported from Kerala
▶️Both cases have a travel history

🔴 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…

While #SARSCoV2 infections surge once again across the world, a short and continuously updated 🧵 on the BA.4 /BA.5 variants. Have written in quite detail about the variants in the past. thehindu.com/sci-tech/will-…

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

🔴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.

and now this !
bbc.com/news/world-eur… Scotland outbreak cases had no apparent travel history to Southern Africa.
theguardian.com/uk-news/2021/n…

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

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.

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
thelancet.com/journals/lanin…

#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)

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

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/ 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

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 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.

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 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

Why are numbers in Kerala an anomaly ?
Here is my take on these numbers

https://twitter.com/NewsBytesApp/status/1412738394547908610

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

As delta continues to evolve acquiring new mutations, there is a lot if interest in understanding these mutations. This tweetorial summarizes the emerging lineages of delta, otherwise named delta+

Data and analysis : @bani_jolly and @mercy_rophina Understanding this continued evolution is of great importance in mapping the evolutionary landscape of emerging variants. Largely the virus has tried to optmise for transmission and immune escape by step-wise acquisition of new mutations.

Interesting preprint on the antibody response after ChAdOx1-nCOV (Covishield) and BBV-152 (Covaxin) among Health Care Workers. (N=552 Covishield =456; Covaxin=96)
Both vaccines elicited👍immune response after 2nd dose. Seropositivity Covishield >Covaxin
medrxiv.org/content/10.110… A number of factors include Age, Sex. Comorbidity including T2DM and Hypertension influence the antibody titres (Day 21-36 after 2nd dose)

B.1.618 - a new lineage of SARS-CoV-2 predominnatly found in India and characterized by a distinct set of genetic variants including E484K , a major immune escape variant. Initial sequences in the B.1.618 lineage were found in West Bengal, India.

Members of this lineage is also found in other parts of the world, cov-lineages.org/lineages/linea… but do not have the full complement of variants as found in India