Genome-wide mutational analysis of Chikungunya strains from 2016 to 2017 outbreak of central India: An attempt to elucidate the immunological basis for outbreak
Chikungunya re-emerged in India in 2016–2017, as the first major outbreak since 2006. In our previous study, we undertook partial E1 gene sequencing and phylogenetic/mutational analysis of strains from the 2016–2017 outbreak of Chikungunya in central India and reported important mutations associated...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2022-11-01
|
| Series: | Heliyon |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2405844022026883 |
| _version_ | 1811321683105021952 |
|---|---|
| author | Sudheer Gupta Ashvini Yadav Sam Stubbs Simon Frost Kudsia Ansari Ram Kumar Nema Shashwati Nema Debasis Biswas |
| author_facet | Sudheer Gupta Ashvini Yadav Sam Stubbs Simon Frost Kudsia Ansari Ram Kumar Nema Shashwati Nema Debasis Biswas |
| author_sort | Sudheer Gupta |
| collection | DOAJ |
| description | Chikungunya re-emerged in India in 2016–2017, as the first major outbreak since 2006. In our previous study, we undertook partial E1 gene sequencing and phylogenetic/mutational analysis of strains from the 2016–2017 outbreak of Chikungunya in central India and reported important mutations associated with the outbreak. This study was performed to validate the previous findings and to identify key mutations that had emerged throughout the entire genome of Chikungunya virus that could be driving the enormity of this outbreak. The phylogenetic analysis revealed the closeness of our isolates with ECSA genotype, specifically with the Singapore 2015 strain. We found 2 mutations in C and E2 genes, which were present in our isolates but were non-existent during the period of 2010–2016. Furthermore, re-emergence of Arg amino acid in place of stop codon in nsP3 gene and Thr at E2:312 positions was observed after 2011. We also used computational tools to assess the effect of the identified mutations on the T cell and B cell epitopes that could influence the protective immune response against this infection. |
| first_indexed | 2024-04-13T13:22:01Z |
| format | Article |
| id | doaj.art-a4c8686450844d8a9f9a46644a80f448 |
| institution | Directory Open Access Journal |
| issn | 2405-8440 |
| language | English |
| last_indexed | 2024-04-13T13:22:01Z |
| publishDate | 2022-11-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Heliyon |
| spelling | doaj.art-a4c8686450844d8a9f9a46644a80f4482022-12-22T02:45:17ZengElsevierHeliyon2405-84402022-11-01811e11400Genome-wide mutational analysis of Chikungunya strains from 2016 to 2017 outbreak of central India: An attempt to elucidate the immunological basis for outbreakSudheer Gupta0Ashvini Yadav1Sam Stubbs2Simon Frost3Kudsia Ansari4Ram Kumar Nema5Shashwati Nema6Debasis Biswas7Regional Virology Laboratory, All India Institute of Medical Sciences, Bhopal, IndiaRegional Virology Laboratory, All India Institute of Medical Sciences, Bhopal, IndiaDepartment of Veterinary Medicine, University of Cambridge, UKDepartment of Veterinary Medicine, University of Cambridge, UKRegional Virology Laboratory, All India Institute of Medical Sciences, Bhopal, IndiaRegional Virology Laboratory, All India Institute of Medical Sciences, Bhopal, IndiaRegional Virology Laboratory, All India Institute of Medical Sciences, Bhopal, India; Department of Microbiology, All India Institute of Medical Sciences, Bhopal, IndiaRegional Virology Laboratory, All India Institute of Medical Sciences, Bhopal, India; Department of Microbiology, All India Institute of Medical Sciences, Bhopal, India; Corresponding author.Chikungunya re-emerged in India in 2016–2017, as the first major outbreak since 2006. In our previous study, we undertook partial E1 gene sequencing and phylogenetic/mutational analysis of strains from the 2016–2017 outbreak of Chikungunya in central India and reported important mutations associated with the outbreak. This study was performed to validate the previous findings and to identify key mutations that had emerged throughout the entire genome of Chikungunya virus that could be driving the enormity of this outbreak. The phylogenetic analysis revealed the closeness of our isolates with ECSA genotype, specifically with the Singapore 2015 strain. We found 2 mutations in C and E2 genes, which were present in our isolates but were non-existent during the period of 2010–2016. Furthermore, re-emergence of Arg amino acid in place of stop codon in nsP3 gene and Thr at E2:312 positions was observed after 2011. We also used computational tools to assess the effect of the identified mutations on the T cell and B cell epitopes that could influence the protective immune response against this infection.http://www.sciencedirect.com/science/article/pii/S2405844022026883ChikungunyaPhylogeneticsOutbreakGenome sequencingNanopore |
| spellingShingle | Sudheer Gupta Ashvini Yadav Sam Stubbs Simon Frost Kudsia Ansari Ram Kumar Nema Shashwati Nema Debasis Biswas Genome-wide mutational analysis of Chikungunya strains from 2016 to 2017 outbreak of central India: An attempt to elucidate the immunological basis for outbreak Heliyon Chikungunya Phylogenetics Outbreak Genome sequencing Nanopore |
| title | Genome-wide mutational analysis of Chikungunya strains from 2016 to 2017 outbreak of central India: An attempt to elucidate the immunological basis for outbreak |
| title_full | Genome-wide mutational analysis of Chikungunya strains from 2016 to 2017 outbreak of central India: An attempt to elucidate the immunological basis for outbreak |
| title_fullStr | Genome-wide mutational analysis of Chikungunya strains from 2016 to 2017 outbreak of central India: An attempt to elucidate the immunological basis for outbreak |
| title_full_unstemmed | Genome-wide mutational analysis of Chikungunya strains from 2016 to 2017 outbreak of central India: An attempt to elucidate the immunological basis for outbreak |
| title_short | Genome-wide mutational analysis of Chikungunya strains from 2016 to 2017 outbreak of central India: An attempt to elucidate the immunological basis for outbreak |
| title_sort | genome wide mutational analysis of chikungunya strains from 2016 to 2017 outbreak of central india an attempt to elucidate the immunological basis for outbreak |
| topic | Chikungunya Phylogenetics Outbreak Genome sequencing Nanopore |
| url | http://www.sciencedirect.com/science/article/pii/S2405844022026883 |
| work_keys_str_mv | AT sudheergupta genomewidemutationalanalysisofchikungunyastrainsfrom2016to2017outbreakofcentralindiaanattempttoelucidatetheimmunologicalbasisforoutbreak AT ashviniyadav genomewidemutationalanalysisofchikungunyastrainsfrom2016to2017outbreakofcentralindiaanattempttoelucidatetheimmunologicalbasisforoutbreak AT samstubbs genomewidemutationalanalysisofchikungunyastrainsfrom2016to2017outbreakofcentralindiaanattempttoelucidatetheimmunologicalbasisforoutbreak AT simonfrost genomewidemutationalanalysisofchikungunyastrainsfrom2016to2017outbreakofcentralindiaanattempttoelucidatetheimmunologicalbasisforoutbreak AT kudsiaansari genomewidemutationalanalysisofchikungunyastrainsfrom2016to2017outbreakofcentralindiaanattempttoelucidatetheimmunologicalbasisforoutbreak AT ramkumarnema genomewidemutationalanalysisofchikungunyastrainsfrom2016to2017outbreakofcentralindiaanattempttoelucidatetheimmunologicalbasisforoutbreak AT shashwatinema genomewidemutationalanalysisofchikungunyastrainsfrom2016to2017outbreakofcentralindiaanattempttoelucidatetheimmunologicalbasisforoutbreak AT debasisbiswas genomewidemutationalanalysisofchikungunyastrainsfrom2016to2017outbreakofcentralindiaanattempttoelucidatetheimmunologicalbasisforoutbreak |