SARS-CoV-2 and other human coronaviruses: Mapping of protease recognition sites, antigenic variation of spike protein and their grouping through molecular phylogenetics

Chakraborty, Chiranjib; Sharma, Ashish Ranjan; Bhattacharya, Manojit; Saha, Rudra P.; Ghosh, Sanmitra; Biswas, Soham; Samanta, Saikat; Sharma, Garima; Agoramoorthy, Govindasamy; Lee, Sang Soo

doi:10.1016/j.meegid.2021.104729

Cited by 5 publications

(7 citation statements)

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“…4b). We found Europe to show the highest number of confirmed cases (20,625), and the Western Pacific showed the lowest number of confirmed cases (121). North and South America also revealed several infected cases (20,436 cases), and the cases are more compared to Africa (404 cases)..…”

Section: Epidemiology Of Mpxv and Hmpxv1mentioning

confidence: 67%

“…If we calculate in terms of nucleotide changes, it should be related to approximately 1-2 nucleotide changes per year. However, the evolution study of this dsDNA virus is slow compared to the other pandemic ssRNA virus (SARS-CoV-2) [20,86,87].…”

Section: Discussionmentioning

confidence: 99%

“…Several researchers have done the evolutionary analysis of pathogens from time to time. Recently, researchers analyzed the evolution of SARS-CoV-2 to understand how quickly the pandemic virus is evolving and the status of the variants creation [19][20][21][22]. It illustrated genomic diversity, genetic changes, and the evolutionary epidemiology of this virus.…”

Section: Introductionmentioning

confidence: 99%

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Evolution, epidemiology, geographical distribution, and mutational landscape of newly emerging monkeypox virus

et al. 2022

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Recent monkeypox (MPX) outbreaks are major ones in non-endemic countries. The present study analyzed molecular phylogenetics, divergence, epidemiology, the geographical distribution, entropy diversity of genome, mutational landscape, and evolution of the monkeypox virus (MPXV) genome and the current MPXV is entitled “hMPXV1.” We used different in-silico and statistical methods to study our objectives. The developed phylogram from molecular phylogenetics describes the origin and evolution of hMPXV1 of A, A.1, A.1.1, A.2, and B.1 lineages. The microevolution of B.1 lineage shows its evolution from May to August 2022. B.1 lineage is further adapting and showing more mutation and sub-lineages. The scatter plot of all lineages shows the clustering pattern of lineages and the divergence. We also developed two statistical models of confirmed cases and a diagram of the age-related pattern of infected cases to illustrate the epidemiology of the MPX outbreaks. The entropy diversity and mutational landscape of the hMPXV1 genome were analyzed in nucleotide and codon contexts. Our study has shown the in-depth evolution pattern of different lineages of the hMPXV1. We found B.1 lineage is associated with the current outbreaks. The mutational landscape informs about the slow mutation of the virus. Finally, the study might assists the new therapeutic development considering all the above points and would help the researcher to set up their future research directions.

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Section: Epidemiology Of Mpxv and Hmpxv1mentioning

confidence: 67%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Evolution, epidemiology, geographical distribution, and mutational landscape of newly emerging monkeypox virus

et al. 2022

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“…5 ). The amino acid change P681R near the protease cleavage site might relate with the spike protein stability ( Chakraborty et al, 2021 ), and the mutations L452RT and 478 K could alter B-cell epitopes of the spike protein to weaken the binding ability of serum or convalescent patients' antibodies and even the transmission ( Bhattacharya et al, 2020 ; Greaney et al, 2021 ; Li et al, 2020 ). Notably, sub-haplotype 2C_3 also showed a novel mutation G671S in nsp12 (RNA-dependent RNA polymerase, RdRp) that was the target for the antiviral drug in treatment such as remdesivir in many countries ( Kupferschmidt and Cohen, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021

Bui

Lin

Huang

et al. 2022

Infection, Genetics and Evolution

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“…SARS-CoV-2 enters the host cell through an interaction between its surface spike protein (S protein) and the angiotensin-converting enzyme 2 (ACE2) receptor. 5 , 6 The S protein is a large trimeric protein comprising three non-covalently joined subunits. Any mutation in SARS-CoV-2 S protein is of interest given its direct involvement in viral infectivity and pathogenicity.…”

mentioning

confidence: 99%

Natural selection of the D614G mutation in SARS-CoV-2 Omicron (B.1.1.529) variant and its subvariants

Chakraborty¹,

Saha²,

Bhattacharya³

et al. 2023

Molecular Therapy - Nucleic Acids

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SARS-CoV-2 and other human coronaviruses: Mapping of protease recognition sites, antigenic variation of spike protein and their grouping through molecular phylogenetics

Cited by 5 publications

References 70 publications

Evolution, epidemiology, geographical distribution, and mutational landscape of newly emerging monkeypox virus

Evolution, epidemiology, geographical distribution, and mutational landscape of newly emerging monkeypox virus

Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021

Natural selection of the D614G mutation in SARS-CoV-2 Omicron (B.1.1.529) variant and its subvariants

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