deLemus
Update (30/12/2022)
Summary
The deLemus website provides information about the leading mutations in spikes glycoprotein of SARS-CoV-2. From the leading mutations, we can investigate the mutation patterns of the virus, allowing further research on their functions and possibly prediction of new variants in the future. Omicron, the latest SARS-CoV-2 lineage designated as a VOC by the WHO after being reported in South Africa in November 2021, has various subvariants, including BA.1 (the first subvariant of omicron), BA.2, BA.4, and BA.5. Omicron was spreading very quickly to many countries after its first report. Soon after the discovery of BA.1, BA.2 was detected and spread across the globe. In April 2022, BA.4 and BA.5 were monitored by the WHO after being found in multiple countries, and they showed a significant increase in growth advantage when compared to BA.2. These two variants became dominant in the UK, the US, and Germany in June 2022. In the meantime, BA.2.12.1 and BA.2.75 were also spreading in the US and India respectively in May 2022. In August 2022, XBB, a recombinant of BA.2.10.1 and BA.2.75, was found to have a small outbreak in various countries such as Singapore and Bangladesh. After that, in October 2022, BQ.1, which is a subvariant of BA.5 prevalent in France, was found.
Since the outbreak of COVID-19, there have been new variants emerging. Omicron, the latest lineage designated as a VOC by the WHO after being reported in South Africa in November 2021,Cite error: Invalid <ref> tag; name cannot be a simple integer. Use a descriptive title has various subvariants, including BA.1 (the first subvariant of omicron), BA.2,Cite error: Invalid <ref> tag; name cannot be a simple integer. Use a descriptive title BA.4, and BA.5.Cite error: Invalid <ref> tag; name cannot be a simple integer. Use a descriptive title Omicron was spreading very quickly to many countries after its first report. Soon after the discovery of BA.1, BA.2 was detected and spread across the globe.Cite error: Invalid <ref> tag; name cannot be a simple integer. Use a descriptive title In April 2022, BA.4 and BA.5 were monitored by the WHO after being found in multiple countries, and they showed a significant increase in growth advantage when compared to BA.2.Cite error: Invalid <ref> tag; name cannot be a simple integer. Use a descriptive title These two variants became dominant in the UK and the US in June 2022.Cite error: Invalid <ref> tag; name cannot be a simple integer. Use a descriptive title In the meantime, BA.2.12.1 and BA.2.75 were also spreading in the US and India respectively in May 2022.Cite error: Invalid <ref> tag; name cannot be a simple integer. Use a descriptive title,Cite error: Invalid <ref> tag; name cannot be a simple integer. Use a descriptive title In August 2022, XBB, which is a recombinant of BA.2.10.1 and BA.2.75, was found to have a small outbreak in various countries such as Singapore.Cite error: Invalid <ref> tag; name cannot be a simple integer. Use a descriptive title After that, in October 2022, BQ.1, which is a subvariant of BA.5 starting to prevail in France, was found.Cite error: Invalid <ref> tag; name cannot be a simple integer. Use a descriptive title
Confirmed Mutations
As explained above, deLemus can outline potential mutations in the coming time. In this section, we provide the outlined mutations that are currently confirmed in the emerging variant (EV).
K356T
Among all the detected mutations in spikes protein, this site is worthy to be monitored due to its persistent signal since April 2022. The mutation from Lysin(K) to Threonine(T) at site 356 enables N-X-T sequon, which is crucial for glycosylation, a defense mechanism for the virus to hide from immune surveillance, e.g., antibodies. Moreover, the emerging variant provided by GISAID also reveals that the R356T mutation shows up in the top 5 accelerating variants, the BN.1.4 variant.
F486P/I
The next mutation is F486P/I. Mutation from Phenylalanine (F) to Proline (P) at site 486 shows up in the recent accelerated variant, XBB.1.5, which is currently showing substantial growth in the US.[1] This mutation renders higher hACE2-binding affinity compared to its ancestor (XBB.1), that is likely responsible for its high growth.[2] We also noticed another leading mutation on the same site, F486I, which could be a dangerous mutation in the coming time.
References
- ↑ Highly immune evasive omicron XBB.1.5 variant is quickly becoming dominant in U.S. as it doubles weekly https://www.cnbc.com/2022/12/30/covid-news-omicron-xbbpoint1point5-is-highly-immune-evasive-and-binds-better-to-cells.html (2023).
- ↑ Yue, C. et al. Enhanced transmissibility of XBB.1.5 is contributed by both strong ACE2 binding and antibody evasion. bioRxiv https://www.biorxiv.org/content/10.1101/2023.01.03.522427v1 (2023).
Cite error: Invalid <ref> tag; name cannot be a simple integer. Use a descriptive title
Cite error: Invalid <ref> tag; name cannot be a simple integer. Use a descriptive title
Cite error: Invalid <ref> tag; name cannot be a simple integer. Use a descriptive title
Cite error: Invalid <ref> tag; name cannot be a simple integer. Use a descriptive title
Cite error: Invalid <ref> tag; name cannot be a simple integer. Use a descriptive title
Cite error: Invalid <ref> tag; name cannot be a simple integer. Use a descriptive title
Cite error: Invalid <ref> tag; name cannot be a simple integer. Use a descriptive title
Cite error: Invalid <ref> tag; name cannot be a simple integer. Use a descriptive title
Cite error: Invalid <ref> tag; name cannot be a simple integer. Use a descriptive title
Cite error: Invalid <ref> tag; name cannot be a simple integer. Use a descriptive title
