CME INDIA Presentation by Dr. H.D. Sharan, Ex Chairman CSI, Jharkhand, Ranchi.
16 Best Tips:
1. Mutation of the virus is a natural process which occurs due to error in copying mechanism of the biological systems when the virus multiples.
2. This leads to a minor change in genetic sequence which is called mutation.
3. Not all mutations are beneficial to the virus. In fact, some mutations may result in regression of a pandemic.
4. Mutations are rare in DNA viruses as compared to RNA virus like SARS CoV 2.
5. The only way to diagnose a mutant is to do genome sequencing. RT PCR cannot diagnose it. But absence of S gene in the report may be strong indication. The Kasturba viral lab in Mumbai has started sifting through positive RT PCR reports with S gene target failure for doing Genome sequencing.
6. The UK and South African strains arrived at the same time but are different.
7. The nomenclature of Virus and mutants is very interesting. The UK mutant has been given the name, SARS CoV 2 VUI 202012/1. VUI is variant under investigation, year 2020, month 12, variant 1. This was officially reported by UK on 14th December although it was first detected in September. No finger raised. White race?
8. This variant is a result of mutation in the spike called N501Y which again just means that in position 501 N amino acid is replaced with Y amino acid.
9. Dr Emma Hodcroft from Switzerland says that both UK and South African strains share this mutation but they have several other mutations that make them different.
10. Prof. Ravindra Gupta from Cambridge University says that ONE OF THE REASONS FOR THESE MUTATIONS IS USING CONVALESCENT PLASMA IN PATIENTS WITH POOR IMMUNE FUNCTION.
11. Infected persons with weakened immune system that is unable to beat the virus are the breeding grounds for mutations.
12. This new variant can spread 70 percent faster but there is no evidence as of now that it is deadlier too.
13. Around 60 percent of fresh infections in UK is caused by the new variant.
14. What effect this variant will have on response to vaccines? The m RNA vaccines produced by the Pfizer and Moderna target the spike protein. The companies say that the mutation is so small that it will not affect the response to vaccine. In the same breath, they also say that if needed they can tweak their vaccines in 3 weeks. The sum total is that they do not know as of now and their confidence may be misplaced.
15. Covishield is a whole virus vaccine but it is a vector. The adenovirus from Chimpanzees have been genetically tweaked to target the spike protein. Better than mRNA vaccines but there is a theoretical possibility that the mutation may cause a problem.
16. Covaxin from Bharat Biotec appears to be best bet against the variant as it is an attenuated whole virus vaccine with several targets available.
CME INDIA Learning Alert
The solid black line shows the proportion of positive tests with S dropout at the Milton Keynes Lighthouse lab, the dashed red line shows the proportion of all Lighthouse sequences that are B.1.1.7, and the blue dashed line shows the proportion of sequences that are other variants with Δ69-70.
Source: (https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/947048/Technical_Briefing_VOC_SH_NJL2_SH2.pdf)
- The UK has a high throughput national testing system for community cases based in a small number of large laboratories.
- Three of these laboratories use a three-target assay (N, ORF1ab, S).
- S gene target failures (in otherwise positive samples) began to increase dramatically from late November.
- And this epidemiological observation was beginning of New Strain SarsCoV2 new epidemic.
- Such Epidemiological observations have proved History changing impact in past too.
CME INDIA Tail Piece
Is it possible to diagnose UK strain by existing RT PCR test?
- Just use three-target assay (N, ORF1ab, S).
- Look for S gene target failures (positive N, ORF and negative S gene).
- The VOC (Variant of Concern) includes a deletion of six nucleotides in the S gene,causing loss of two amino acids at positions 69 and 70 (Δ69-70) and has been previously reported by another group to result in S gene dropout in commercial assays (Bal A, et al. medRxiv, 2020).
- Δ69-70 is present in over 99% of sequenced S gene dropouts, but less than 0.1% of sequenced S gene positives.
- This is termed as S-gene target failure (SGTF). Spike gene target failure (SGTF) can serve as a proxy for carriage of the VOC
- Further confirmation was provided by molecular analysis: sequencing of diagnostic PCR amplicon products from S gene dropout samples showed that the S gene target contains the Δ69-70 deletion in the middle of the amplicon. Researchers inferred that because the S gene is successfully amplified that the S gene dropout must be due to a failure of the qPCR probe to bind as a result of the Δ69-70 deletion.
- Only a small fraction of all new cases of VOC 202012/01 are identified using whole genome sequencing, and this data typically lags test date by about two weeks. A proxy SGTF is, therefore, used to indicate VOC carriage.
- There was a high correlation between S-gene target failure (SGTF) during COVID-19 PCR testing and frequency of the variant, thus suggesting that S-gene target failure could be a biomarker to detect the variant in the community.
- From monitoring patterns in which genes are found to be present in the PCR test, it can be identified where cases of the new variant are likely to be increasing. The new variant has genetic changes in the S gene, hence, it is no longer detected by the current test. Samples that would previously have been positive on all three genes are now found positive only on the ORF1ab and N genes.
What is “a shift in age composition?”
- The new SARS-CoV-2 variant, first detected in southern England, has a transmission advantage of 0.4 to 0.7 points higher in reproduction number, or R0, in comparison with the initial strain, reported British researchers.
- This variant has a considerable transmission advantage, and its reproduction numbers could range from 1.4 to 1.8, suggest researchers at Imperial College London (ICL).
- Researchers noted a larger proportion of individuals below 20 years of age among reported cases of the variant versus non-variant cases, calling it ‘a shift in age composition.’ The variants R0 is estimated to be 40%-80% higher than for the wild-type virus.
How UK is testing new strain?
- The UK has a high throughput national testing system for community cases based in a small number of large laboratories.
- Three of these laboratories employ a three-target assay (N, ORF1ab, S).
- S gene target failures (in otherwise positive samples) started escalating considerably from late November.
- Epidemiologically it was observed: Currently more than 97% of pillar 2 PCR tests which test negative on the S-gene target and positive on other targets are due to the VOC. They used the frequency of S-gene target negatives among PCR positives as a proxy for frequency of the VOC. This proxy has a limited time window.The VOC has a deletion of six nucleotides in the S gene,with loss of two amino acids at positions 69 and 70 (Δ69-70).
- Researchers found Δ69-70 in >99% of sequenced S gene dropouts, but less than 0.1% of sequenced S gene positives from the same labs. This is S-gene target failure (SGTF). Further confirmation came from molecular analysis. Sequencing of diagnostic PCR amplicon products from S gene dropout samples revealed S gene target to contain the Δ69-70 deletion in the middle of the amplicon. Since S gene is successfully amplified, the S gene dropout must be due to a failure of the qPCR probe to bind as a result of the Δ69-70 deletion. Some other variants also have Δ69-70, but as of late November, the VOC represents nearly all observed sequences with that mutation.
Weekly number of cases tested by laboratories using Thermofisher TaqPath, by S-gene detection
Source: https://www.gov.uk/government/publications/investigation-of-novel-sars-cov-2-variant-variant-of-concern-20201201
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