Emergence of Recombinant Subclade D3/Y in Coxsackievirus A6 Strains in Hand-Foot-and-Mouth Disease (HFMD) Outbreak in India, 2022
Coxsackievirus-A6 (CV-A6) is responsible for more severe dermatological manifestations compared to other enteroviruses such as CV-A10, CV-A16, and EV-A71, causing HFMD in children and adults. Between 2005 and 2007, the recombinant subclade D3/RF-A started to expand globally, and a CV-A6 pandemic sta...
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MDPI AG
2024-02-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/12/3/490 |
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| author | Sanjaykumar Tikute Pratik Deshmukh Nutan Chavan Anita Shete Pooja Shinde Pragya Yadav Mallika Lavania |
| author_facet | Sanjaykumar Tikute Pratik Deshmukh Nutan Chavan Anita Shete Pooja Shinde Pragya Yadav Mallika Lavania |
| author_sort | Sanjaykumar Tikute |
| collection | DOAJ |
| description | Coxsackievirus-A6 (CV-A6) is responsible for more severe dermatological manifestations compared to other enteroviruses such as CV-A10, CV-A16, and EV-A71, causing HFMD in children and adults. Between 2005 and 2007, the recombinant subclade D3/RF-A started to expand globally, and a CV-A6 pandemic started. The study aimed to conduct whole-genome sequencing (WGS) of an isolated CV-A6 strain from currently circulating HFMD cases from India in 2022. Gene-specific RT-PCR and sequencing were used to perform molecular characterization of the isolated virus. Confirmation of these isolates was also performed by transmission electron microscopy and WGS. Among eleven positive clinical enterovirus specimens, eight CV-A6 strains were successfully isolated in the RD cell line. Isolates confirmed the presence of the CV-A6 strain based on VP1 and VP2 gene-specific RT-PCR. Sequences of isolates were clustered and identified as the novel CV-A6 strain of the D3/Y sub-genotype in India. The studies revealed that the D3/Y sub-genotype is being introduced into Indian circulation. The predicted putative functional loops found in VP1 of CV-A6 showed that the nucleotide sequences of the amino acid were a remarkably conserved loop prediction compatible with neutralizing linear epitopes. Therefore, this strain represents a potential candidate for vaccine development and antiviral studies. |
| first_indexed | 2024-04-24T18:00:45Z |
| format | Article |
| id | doaj.art-b53f27a6bda34359b9c05338bba7e732 |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-04-24T18:00:45Z |
| publishDate | 2024-02-01 |
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| series | Microorganisms |
| spelling | doaj.art-b53f27a6bda34359b9c05338bba7e7322024-03-27T13:55:37ZengMDPI AGMicroorganisms2076-26072024-02-0112349010.3390/microorganisms12030490Emergence of Recombinant Subclade D3/Y in Coxsackievirus A6 Strains in Hand-Foot-and-Mouth Disease (HFMD) Outbreak in India, 2022Sanjaykumar Tikute0Pratik Deshmukh1Nutan Chavan2Anita Shete3Pooja Shinde4Pragya Yadav5Mallika Lavania6Enteric Viruses Group, ICMR-National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune 411001, Maharashtra, IndiaEnteric Viruses Group, ICMR-National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune 411001, Maharashtra, IndiaEnteric Viruses Group, ICMR-National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune 411001, Maharashtra, IndiaMaximum Containment Laboratory, ICMR-National Institute of Virology, 130, MCC, 1, Pashan—Sus Rd, Pashan, Pune 411021, Maharashtra, IndiaEnteric Viruses Group, ICMR-National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune 411001, Maharashtra, IndiaMaximum Containment Laboratory, ICMR-National Institute of Virology, 130, MCC, 1, Pashan—Sus Rd, Pashan, Pune 411021, Maharashtra, IndiaEnteric Viruses Group, ICMR-National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune 411001, Maharashtra, IndiaCoxsackievirus-A6 (CV-A6) is responsible for more severe dermatological manifestations compared to other enteroviruses such as CV-A10, CV-A16, and EV-A71, causing HFMD in children and adults. Between 2005 and 2007, the recombinant subclade D3/RF-A started to expand globally, and a CV-A6 pandemic started. The study aimed to conduct whole-genome sequencing (WGS) of an isolated CV-A6 strain from currently circulating HFMD cases from India in 2022. Gene-specific RT-PCR and sequencing were used to perform molecular characterization of the isolated virus. Confirmation of these isolates was also performed by transmission electron microscopy and WGS. Among eleven positive clinical enterovirus specimens, eight CV-A6 strains were successfully isolated in the RD cell line. Isolates confirmed the presence of the CV-A6 strain based on VP1 and VP2 gene-specific RT-PCR. Sequences of isolates were clustered and identified as the novel CV-A6 strain of the D3/Y sub-genotype in India. The studies revealed that the D3/Y sub-genotype is being introduced into Indian circulation. The predicted putative functional loops found in VP1 of CV-A6 showed that the nucleotide sequences of the amino acid were a remarkably conserved loop prediction compatible with neutralizing linear epitopes. Therefore, this strain represents a potential candidate for vaccine development and antiviral studies.https://www.mdpi.com/2076-2607/12/3/490HFMDenterovirusesCV-A6RD cell lineTEMnonsynonymous mutation |
| spellingShingle | Sanjaykumar Tikute Pratik Deshmukh Nutan Chavan Anita Shete Pooja Shinde Pragya Yadav Mallika Lavania Emergence of Recombinant Subclade D3/Y in Coxsackievirus A6 Strains in Hand-Foot-and-Mouth Disease (HFMD) Outbreak in India, 2022 Microorganisms HFMD enteroviruses CV-A6 RD cell line TEM nonsynonymous mutation |
| title | Emergence of Recombinant Subclade D3/Y in Coxsackievirus A6 Strains in Hand-Foot-and-Mouth Disease (HFMD) Outbreak in India, 2022 |
| title_full | Emergence of Recombinant Subclade D3/Y in Coxsackievirus A6 Strains in Hand-Foot-and-Mouth Disease (HFMD) Outbreak in India, 2022 |
| title_fullStr | Emergence of Recombinant Subclade D3/Y in Coxsackievirus A6 Strains in Hand-Foot-and-Mouth Disease (HFMD) Outbreak in India, 2022 |
| title_full_unstemmed | Emergence of Recombinant Subclade D3/Y in Coxsackievirus A6 Strains in Hand-Foot-and-Mouth Disease (HFMD) Outbreak in India, 2022 |
| title_short | Emergence of Recombinant Subclade D3/Y in Coxsackievirus A6 Strains in Hand-Foot-and-Mouth Disease (HFMD) Outbreak in India, 2022 |
| title_sort | emergence of recombinant subclade d3 y in coxsackievirus a6 strains in hand foot and mouth disease hfmd outbreak in india 2022 |
| topic | HFMD enteroviruses CV-A6 RD cell line TEM nonsynonymous mutation |
| url | https://www.mdpi.com/2076-2607/12/3/490 |
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