Genome sequencing and analysis of an emergent SARS-CoV-2 variant characterized by multiple spike protein mutations detected from the Central Visayas Region of the Philippines
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The emergence of SARS-CoV-2 variants of concern such as the B.1.1.7, B.1.351 and the P.1 have prompted calls for governments worldwide to increase their genomic biosurveillance efforts. Globally, quarantine and outbreak management measures have been implemented to stem the introduction of these variants and to monitor any emerging variants of potential clinical significance domestically. Here, we describe the emergence of a new SARS-CoV-2 lineage, mainly from the Central Visayas region of the Philippines. This emergent variant is characterized by 13 lineage-defining mutations, including the co-occurrence of the E484K, N501Y, and P681H mutations at the spike protein region, as well as three additional radical amino acid replacements towards the C-terminal end of the said protein. A three-amino acid deletion at positions 141 to 143 (LGV141_143del) in the spike protein was likewise seen in a region preceding the 144Y deletion found in the B.1.1.7 variant. A single amino acid replacement, K2Q, at the N-terminus of ORF8 was also shared by all 33 samples sequenced. The mutation profile of this new virus variant warrants closer investigation due to its potential public health implications. The current distribution of this emergent variant in the Philippines and its transmission are being monitored and addressed by relevant public health agencies to stem its spread in nearby islands and regions in the country.
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The Theta variant was first reported in March 2021 in the Philippines and contains 13 lineage-defining mutations including N501Y, E484K, P681H and the NTD deletion at positions 141-143.
“The Theta variant was first reported in March 2021 in the Philippines.It contains 13 lineage-defining mutations including N501Y, E484K, P681H and the NTD deletion at positions 141-143 (refs 155,156 ).”
From The biological and clinical significance of emerging SARS-CoV-2 variants (2021) · cites this paper as [156]
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- Authors
- Tablizo, F. A., Kim, K. M., Lapid, C. M., Castro, M. J. R., Yangzon, M. S. L., Maralit, B. A., Ayes, M. E. C., Cutiongco-de la Paz, E. M., De Guzman, A. R., Yap, J. M. C., Llames, J.-H. S., Araiza, S. M. M., Punayan, K. P., Asin, I. C. A., Tambaoan, C. F. B., Chong, A. L. U., Padilla, K. S. A. R., Cruz, R. P. S., Morado, E. K. D., Dizon, J. G. A., Hao, R. N. M., Zamora, A. A., Pacial, D. R., Magalang, J. A. R., Alejandria, M., Carlos, C., Ong-Lim, A., Salvaña, E. M., Wong, J. Q., Montoya, J. C., Singh-Vergeire, M. R., & Saloma, C. P.
- Affiliations
- University of the Philippines System (PH)
- Department of Health (PH)
- Corresponding author
- Saloma, Cynthia P.
- ORCID
- Venue
- medRxiv
- Publisher
- openRxiv
- Published
- 2021-03-05
- OpenAlex
- W3134822027
- Cited by
- 46
- References
- 19
- Citations by year
- 2024: 5 · 2023: 3 · 2022: 10 · 2021: 27 · 2020: 1
- Type
- posted content
- Language
- en
- Open access
- green
- doi.org
- Licence
- cc-by-nc-nd
- Locations
- medRxiv (acceptedVersion, cc-by-nc-nd)
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Health Sciences › Medicine › Infectious Diseases › COVID-19 Clinical Research Studies
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 detection and testing
- Keywords
- SARS-CoV-2, spike protein mutations, E484K, N501Y, genomic surveillance, Central Visayas, public health response
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