Phylogenetic analysis of 17271 Indian SARS-CoV-2 genomes to identify temporal and spatial hotspot mutations.
PLoS One
; 17(3): e0265579, 2022.
Artículo
en Inglés
| MEDLINE | ID: covidwho-1765536
ABSTRACT
The second wave of SARS-CoV-2 has hit India hard and though the vaccination drive has started, moderate number of COVID affected patients is still present in the country, thereby leading to the analysis of the evolving virus strains. In this regard, multiple sequence alignment of 17271 Indian SARS-CoV-2 sequences is performed using MAFFT followed by their phylogenetic analysis using Nextstrain. Subsequently, mutation points as SNPs are identified by Nextstrain. Thereafter, from the aligned sequences temporal and spatial analysis are carried out to identify top 10 hotspot mutations in the coding regions based on entropy. Finally, to judge the functional characteristics of all the non-synonymous hotspot mutations, their changes in proteins are evaluated as biological functions considering the sequences by using PolyPhen-2 while I-Mutant 2.0 evaluates their structural stability. For both temporal and spatial analysis, there are 21 non-synonymous hotspot mutations which are unstable and damaging.
Texto completo:
Disponible
Colección:
Bases de datos internacionales
Base de datos:
MEDLINE
Asunto principal:
Genoma Viral
/
Punto Alto de Contagio de Enfermedades
/
SARS-CoV-2
/
COVID-19
/
Mutación
Tipo de estudio:
Estudio experimental
/
Estudio observacional
/
Ensayo controlado aleatorizado
Tópicos:
Vacunas
Límite:
Humanos
País/Región como asunto:
Asia
Idioma:
Inglés
Revista:
PLoS One
Asunto de la revista:
Ciencia
/
Medicina
Año:
2022
Tipo del documento:
Artículo
País de afiliación:
Journal.pone.0265579
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