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Evolution of monkeypox virus from 2017 to 2022: In the light of point mutations

Monkeypox virus (MPXV) causing multi-country outbreak-2022 is related to viruses caused outbreak-2017–2018 in West Africa. Still not fully understood which proteins of the MPXV discovered in Nigeria in 2017 have mutated through different lineages to the extent that it could cause a multi-country out...

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Autores principales: Desingu, Perumal Arumugam, Rubeni, T. P., Sundaresan, Nagalingam R.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9795006/
https://www.ncbi.nlm.nih.gov/pubmed/36590408
http://dx.doi.org/10.3389/fmicb.2022.1037598
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author Desingu, Perumal Arumugam
Rubeni, T. P.
Sundaresan, Nagalingam R.
author_facet Desingu, Perumal Arumugam
Rubeni, T. P.
Sundaresan, Nagalingam R.
author_sort Desingu, Perumal Arumugam
collection PubMed
description Monkeypox virus (MPXV) causing multi-country outbreak-2022 is related to viruses caused outbreak-2017–2018 in West Africa. Still not fully understood which proteins of the MPXV discovered in Nigeria in 2017 have mutated through different lineages to the extent that it could cause a multi-country outbreak in 2022; similarly, codon usage bias, host adaptation indices, and the role of selection or mutation pressure in the mutated genes are also not fully studied. Here we report that according to the available sequence data this monkeypox virus acquires point mutations in multiple proteins in each period, and these point mutations accumulate and become a virus that can root outbreak-2022. Viruses exported from Nigeria to Singapore, Israel, and the United Kingdom in 2018–2019 were developed as evolutionary ancestors to B.1 viruses (MPXVs causing multi-country outbreak-2022) through MPXV/United States/2021/MD virus. Although these exported viruses have different amino acid mutations in different proteins, amino acid mutations in 10 proteins are common among them. The MPXV-United Kingdom-P2 virus evolved with only mutations in these 10 proteins and further evolved into MPXV/United States/2021/MD with amino acid mutations in 26 (including amino acid mutations in 10 proteins of the MPXV-United States-P2) proteins. It is noteworthy that specific amino acid mutations in these 22/26 (presence in MPXV/United States/2021/MD) proteins are present in B.1 viruses. Further, analysis of Relative Synonymous Codon Usage (RSCU), Synonymous Codon Usage Fraction (SCUF), and Effective Number of Codons (ENc) revealed codon usage bias in genes that exhibited nucleotide mutations in lineage B.1. Also, host adaptation indices analyzes such as Codon Adaptation Index (CAI), Expected-CAI (eCAI), Relative Codon Deoptimization Index (RCDI) and Expected value for the RCDI (eRCDI) analyzes reveal that the genes that demonstrated nucleotide mutations in lineage B.1 are favorable for human adaptation. Similarly, ENc-GC3s plot, Neutrality plot, and Parity Rule 2 (PR2)-bias plot analyzes suggest a major role of selection pressure than mutation pressure in the evolution of genes displaying nucleotide mutations in lineage B.1. Overall, from 2017 to 2022, MPXV’s mutation and spread suggests that this virus continues to evolve through point mutation in the genes according to the available sequence data.
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spelling pubmed-97950062022-12-29 Evolution of monkeypox virus from 2017 to 2022: In the light of point mutations Desingu, Perumal Arumugam Rubeni, T. P. Sundaresan, Nagalingam R. Front Microbiol Microbiology Monkeypox virus (MPXV) causing multi-country outbreak-2022 is related to viruses caused outbreak-2017–2018 in West Africa. Still not fully understood which proteins of the MPXV discovered in Nigeria in 2017 have mutated through different lineages to the extent that it could cause a multi-country outbreak in 2022; similarly, codon usage bias, host adaptation indices, and the role of selection or mutation pressure in the mutated genes are also not fully studied. Here we report that according to the available sequence data this monkeypox virus acquires point mutations in multiple proteins in each period, and these point mutations accumulate and become a virus that can root outbreak-2022. Viruses exported from Nigeria to Singapore, Israel, and the United Kingdom in 2018–2019 were developed as evolutionary ancestors to B.1 viruses (MPXVs causing multi-country outbreak-2022) through MPXV/United States/2021/MD virus. Although these exported viruses have different amino acid mutations in different proteins, amino acid mutations in 10 proteins are common among them. The MPXV-United Kingdom-P2 virus evolved with only mutations in these 10 proteins and further evolved into MPXV/United States/2021/MD with amino acid mutations in 26 (including amino acid mutations in 10 proteins of the MPXV-United States-P2) proteins. It is noteworthy that specific amino acid mutations in these 22/26 (presence in MPXV/United States/2021/MD) proteins are present in B.1 viruses. Further, analysis of Relative Synonymous Codon Usage (RSCU), Synonymous Codon Usage Fraction (SCUF), and Effective Number of Codons (ENc) revealed codon usage bias in genes that exhibited nucleotide mutations in lineage B.1. Also, host adaptation indices analyzes such as Codon Adaptation Index (CAI), Expected-CAI (eCAI), Relative Codon Deoptimization Index (RCDI) and Expected value for the RCDI (eRCDI) analyzes reveal that the genes that demonstrated nucleotide mutations in lineage B.1 are favorable for human adaptation. Similarly, ENc-GC3s plot, Neutrality plot, and Parity Rule 2 (PR2)-bias plot analyzes suggest a major role of selection pressure than mutation pressure in the evolution of genes displaying nucleotide mutations in lineage B.1. Overall, from 2017 to 2022, MPXV’s mutation and spread suggests that this virus continues to evolve through point mutation in the genes according to the available sequence data. Frontiers Media S.A. 2022-12-14 /pmc/articles/PMC9795006/ /pubmed/36590408 http://dx.doi.org/10.3389/fmicb.2022.1037598 Text en Copyright © 2022 Desingu, Rubeni and Sundaresan. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Desingu, Perumal Arumugam
Rubeni, T. P.
Sundaresan, Nagalingam R.
Evolution of monkeypox virus from 2017 to 2022: In the light of point mutations
title Evolution of monkeypox virus from 2017 to 2022: In the light of point mutations
title_full Evolution of monkeypox virus from 2017 to 2022: In the light of point mutations
title_fullStr Evolution of monkeypox virus from 2017 to 2022: In the light of point mutations
title_full_unstemmed Evolution of monkeypox virus from 2017 to 2022: In the light of point mutations
title_short Evolution of monkeypox virus from 2017 to 2022: In the light of point mutations
title_sort evolution of monkeypox virus from 2017 to 2022: in the light of point mutations
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9795006/
https://www.ncbi.nlm.nih.gov/pubmed/36590408
http://dx.doi.org/10.3389/fmicb.2022.1037598
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