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. 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,[1] has various subvariants, including BA.1 (the first subvariant of omicron), BA.2,[2] BA.4, and BA.5.[3] 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.[4] 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.[5] These two variants became dominant in the UK and the US in June 2022.[6] In the meantime, BA.2.12.1 and BA.2.75 were also spreading in the US and India respectively in May 2022.[7][8] 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.[9] After that, in October 2022, BQ.1, which is a subvariant of BA.5 starting to prevail in France, was found.[10]
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.[11] This mutation renders higher hACE2-binding affinity compared to its ancestor (XBB.1), that is likely responsible for its high growth.[12] We also noticed another leading mutation on the same site, F486I, which could be a dangerous mutation in the coming time.
References
- ↑ Gowrisankar, A., Priyanka, T. M. C. & Banerjee, S. Omicron: a mysterious variant of concern. Eur. Phys. J. Plus 137, (2022).
- ↑ Arora, P. et al. Comparable neutralisation evasion of SARS-CoV-2 omicron subvariants BA.1, BA.2, and BA.3. Lancet Infect. Dis. 22, 766–767 (2022).
- ↑ Mohapatra, R. K. et al. The recently emerged BA.4 and BA.5 lineages of Omicron and their global health concerns amid the ongoing wave of COVID-19 pandemic – Correspondence. Int. J. Surg. 103, 10–12 (2022).
- ↑ Yamasoba, D. et al. Virological characteristics of the SARS-CoV-2 Omicron BA.2 spike. Cell 185, 2103-2115.e19 (2022).
- ↑ Tegally, H. et al. Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa. Nat. Med. 28, 1785–1790 (2022).
- ↑ Callaway, E. What Omicron’s BA.4 and BA.5 variants mean for the pandemic. Nature 606, 848–849 (2022).
- ↑ Del Rio, C. & Malani, P. N. COVID-19 in 2022 - The Beginning of the End or the End of the Beginning? JAMA - J. Am. Med. Assoc. 327, 2389–2390 (2022).
- ↑ Shaheen, N. et al. Could the New BA.2.75 Sub-Variant Cause the Emergence of a Global Epidemic of COVID-19? A Scoping Review. Infect. Drug Resist. 15, 6317–6330 (2022).
- ↑ Wang, Q. et al. Alarming antibody evasion properties of rising SARS-CoV-2 BQ and XBB subvariants. Cell 1–8 (2022) doi:10.1016/j.cell.2022.12.018.
- ↑ European Centre for Disease Prevention and Control: Spread of the SARS-CoV-2 Omicron variant sub-lineage BQ.1 in the EU/EEA https://www.ecdc.europa.eu/sites/default/files/documents/Epi-update-BQ1.pdf (2022).
- ↑ 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).
