🔴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
The present sustained human-human transmission of the MPX virus is believed to have happened via superspreader events in Europe with 16000+ cases now spread across 70+ countries,
The initial cases seemingly were predominantly among gays/bisexuals and msm networks
A detailed publication on the initial 528 infections from 16 countries is summarised in the recent paper in @NEJMnejm.org/doi/full/10.10…
Many geomes from across the world sort of support this observation. This largely is represented as the B.1 lineage of the virus and encompass the predominant lineage for genomes in 2022.
However a very small no of genomes belong to a distinct cluster A.2
The A.2 cluster is peculiar in many aspects.
1⃣ Only a very few genomes belong to this cluster
2⃣The earliest genomes are from 2021
3⃣The genomes are from USA (Florida, Texas & Virginia) and Thailand
4⃣Cluster does not show polytomy suggestive of a superspreader event.
There is a detailed article on this distinct cluster by @HelenBranswell
Incidentally the two genomes from #Kerala map to this small distinct cluster A.2
This would mean
1⃣ These cases are not possibly linked to the european superspreader events.
2⃣ We might be looking at a distinct cluster of human-human transmission and possibly unrecognised for yrs
Incidentally the two cases from Kerala have a travel history to the Middle East, and so do some other cases in this cluster have travel history to Middle East / East Africa
The tMRCA for the cluster (time to most recent common ancestor) is mid 2021 (caveat-small no of samples).
The earliest sample in the cluster from USA is indeed from 2021 suggesting the virus has been in circulation for quite some time, and earlier than the European events.
In conclusion
1⃣ Kerala MPX genomes belong to A.2 in contrast to majority of the genomes across the world which belongs to B.1 lineage
2⃣ Genomes can uncover many interesting facts & leads. Epidemiologists need to follow up leads
3⃣ Genome surveillance is invaluable in outbreaks
Taking forward,
🔹We should be looking forward to more genomes as cases emerge and possibly sequence every single case.
🔹Public Health measures and communication needs to take these new insights into consideration
🔹Wide testing and awareness could uncover many more cases.
To reiterate facts, and give credits where it is due, the sequences were deposited by @icmr_niv in @GISAID and the cases were worked up by clinicians in @KeralaHealth
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🔴 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
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.