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Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants.
mBio. 2021 08 31; 12(4):e0114021.MBIO

Abstract

The recent emergence of multiple variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a significant concern for public health worldwide. New variants have been classified either as variants of concern (VOCs) or variants of interest (VOIs) by the CDC (USA) and WHO. The VOCs include lineages such as B.1.1.7 (20I/501Y.V1 variant), P.1 (20J/501Y.V3 variant), B.1.351 (20H/501Y.V2 variant), and B.1.617.2. In contrast, the VOI category includes B.1.525, B.1.526, P.2, and B.1.427/B.1.429. The WHO provided the alert for last two variants (P.2 and B.1.427/B.1.429) and labeled them for further monitoring. As per the WHO, these variants can be reclassified due to their status at a particular time. At the same time, the CDC (USA) has marked these two variants as VOIs up through today. This article analyzes the evolutionary patterns of all these emerging variants, as well as their geographical distributions and transmission patterns, including the circulating frequency, entropy diversity, and mutational event diversity throughout the genomes of all SARS-CoV-2 lineages. The transmission pattern was observed highest in the B.1.1.7 lineage. Our frequency evaluation found that this lineage achieved 100% frequency in early October 2020. We also critically evaluated the above emerging variants mutational landscape and significant spike protein mutations (E484K, K417T/N, N501Y, and D614G) impacting public health. Finally, the effectiveness of vaccines against newly SARS-CoV-2 variants was also analyzed. IMPORTANCE Irrespective of the aggressive vaccination drive, the newly emerging multiple SARS-CoV-2 variants are causing havoc in several countries. As per the CDC (USA) and WHO, the VOCs include the B.1.1.7, P.1, B.1.351, and B.1.617.2 lineages, while the VOIs include the B.1.525, B.1.526, P.2, and B.1.427/B.1.429 lineages. This study analyzed the evolutionary patterns, geographical distributions and transmission patterns, circulating frequency, entropy diversity, and mutational event diversity throughout the genome of significant SARS-CoV-2 lineages. A higher transmission pattern was observed for the B.1.1.7 variant. The study also evaluated the mutational landscape and important spike protein mutations (E484K, K417T/N, N501Y, and D614G) of all of the above variants. Finally, a survey was performed on the efficacy of vaccines against these variants from the previously published literature. The results presented in this article will help design future countrywide pandemic planning strategies for the emerging variants, next-generation vaccine development using alternative wild-type antigens and significant viral antigens, and immediate planning for ongoing vaccination programs worldwide.

Authors+Show Affiliations

Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal, India.Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, Gangwon-do, Republic of Korea.Department of Zoology, Fakir Mohan Universitygrid.444315.3, Balasore, Odisha, India.College of Pharmacy and Health Care, Tajen Universitygrid.412902.c, Yanpu, Taiwan.Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, Gangwon-do, Republic of Korea.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

34465019

Citation

Chakraborty, Chiranjib, et al. "Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants." MBio, vol. 12, no. 4, 2021, pp. e0114021.
Chakraborty C, Sharma AR, Bhattacharya M, et al. Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. mBio. 2021;12(4):e0114021.
Chakraborty, C., Sharma, A. R., Bhattacharya, M., Agoramoorthy, G., & Lee, S. S. (2021). Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. MBio, 12(4), e0114021. https://doi.org/10.1128/mBio.01140-21
Chakraborty C, et al. Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. mBio. 2021 08 31;12(4):e0114021. PubMed PMID: 34465019.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. AU - Chakraborty,Chiranjib, AU - Sharma,Ashish Ranjan, AU - Bhattacharya,Manojit, AU - Agoramoorthy,Govindasamy, AU - Lee,Sang-Soo, Y1 - 2021/08/31/ PY - 2021/9/1/entrez PY - 2021/9/2/pubmed PY - 2021/9/15/medline KW - effect on vaccines KW - emerging variants KW - mutational landscape KW - transmission pattern SP - e0114021 EP - e0114021 JF - mBio JO - mBio VL - 12 IS - 4 N2 - The recent emergence of multiple variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a significant concern for public health worldwide. New variants have been classified either as variants of concern (VOCs) or variants of interest (VOIs) by the CDC (USA) and WHO. The VOCs include lineages such as B.1.1.7 (20I/501Y.V1 variant), P.1 (20J/501Y.V3 variant), B.1.351 (20H/501Y.V2 variant), and B.1.617.2. In contrast, the VOI category includes B.1.525, B.1.526, P.2, and B.1.427/B.1.429. The WHO provided the alert for last two variants (P.2 and B.1.427/B.1.429) and labeled them for further monitoring. As per the WHO, these variants can be reclassified due to their status at a particular time. At the same time, the CDC (USA) has marked these two variants as VOIs up through today. This article analyzes the evolutionary patterns of all these emerging variants, as well as their geographical distributions and transmission patterns, including the circulating frequency, entropy diversity, and mutational event diversity throughout the genomes of all SARS-CoV-2 lineages. The transmission pattern was observed highest in the B.1.1.7 lineage. Our frequency evaluation found that this lineage achieved 100% frequency in early October 2020. We also critically evaluated the above emerging variants mutational landscape and significant spike protein mutations (E484K, K417T/N, N501Y, and D614G) impacting public health. Finally, the effectiveness of vaccines against newly SARS-CoV-2 variants was also analyzed. IMPORTANCE Irrespective of the aggressive vaccination drive, the newly emerging multiple SARS-CoV-2 variants are causing havoc in several countries. As per the CDC (USA) and WHO, the VOCs include the B.1.1.7, P.1, B.1.351, and B.1.617.2 lineages, while the VOIs include the B.1.525, B.1.526, P.2, and B.1.427/B.1.429 lineages. This study analyzed the evolutionary patterns, geographical distributions and transmission patterns, circulating frequency, entropy diversity, and mutational event diversity throughout the genome of significant SARS-CoV-2 lineages. A higher transmission pattern was observed for the B.1.1.7 variant. The study also evaluated the mutational landscape and important spike protein mutations (E484K, K417T/N, N501Y, and D614G) of all of the above variants. Finally, a survey was performed on the efficacy of vaccines against these variants from the previously published literature. The results presented in this article will help design future countrywide pandemic planning strategies for the emerging variants, next-generation vaccine development using alternative wild-type antigens and significant viral antigens, and immediate planning for ongoing vaccination programs worldwide. SN - 2150-7511 UR - https://www.unboundmedicine.com/medline/citation/34465019/Evolution_Mode_of_Transmission_and_Mutational_Landscape_of_Newly_Emerging_SARS_CoV_2_Variants_ L2 - https://doi.org/10.1128/mBio.01140-21 DB - PRIME DP - Unbound Medicine ER -