Interspecies recombination in NSP3 gene in the first porcine rotavirus H in Russia identified using nanopore-based metagenomic sequencing
During the last decade, porcine rotavirus H was detected in the USA, Asian regions, South Africa, Brazil, and a couple of European countries. In the presented study, the virus was identified in piglets on a farrow-to-finish farm in Russia during metagenomic surveillance. Currently, it is the first i...
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2023-12-01
|
| Series: | Frontiers in Veterinary Science |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fvets.2023.1302531/full |
| _version_ | 1827595626355884032 |
|---|---|
| author | Nikita Krasnikov Anton Yuzhakov |
| author_facet | Nikita Krasnikov Anton Yuzhakov |
| author_sort | Nikita Krasnikov |
| collection | DOAJ |
| description | During the last decade, porcine rotavirus H was detected in the USA, Asian regions, South Africa, Brazil, and a couple of European countries. In the presented study, the virus was identified in piglets on a farrow-to-finish farm in Russia during metagenomic surveillance. Currently, it is the first identification of this species in the country. As a diagnostic method, nanopore-based metagenomic sequencing was applied. The obtained nanopore reads allowed for the assembly of 10 genome segments out of 11. The phylogenetic analysis revealed the virus belonged to the porcine cluster and had GX-P3-I3-R3-C3-M8-A7-N1-T5-E3-H3 genome constellation. Moreover, three potential new genotype groups for VP3, NSP1, and NSP3 genes were determined. Additionally, a recombination between RVH and RVC in the NSP3 gene was detected. The study provides significant information about a novel RVH strain. |
| first_indexed | 2024-03-09T02:57:09Z |
| format | Article |
| id | doaj.art-8ba6a9f851f340c68fa56ad2b365b826 |
| institution | Directory Open Access Journal |
| issn | 2297-1769 |
| language | English |
| last_indexed | 2024-03-09T02:57:09Z |
| publishDate | 2023-12-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Veterinary Science |
| spelling | doaj.art-8ba6a9f851f340c68fa56ad2b365b8262023-12-05T04:23:55ZengFrontiers Media S.A.Frontiers in Veterinary Science2297-17692023-12-011010.3389/fvets.2023.13025311302531Interspecies recombination in NSP3 gene in the first porcine rotavirus H in Russia identified using nanopore-based metagenomic sequencingNikita KrasnikovAnton YuzhakovDuring the last decade, porcine rotavirus H was detected in the USA, Asian regions, South Africa, Brazil, and a couple of European countries. In the presented study, the virus was identified in piglets on a farrow-to-finish farm in Russia during metagenomic surveillance. Currently, it is the first identification of this species in the country. As a diagnostic method, nanopore-based metagenomic sequencing was applied. The obtained nanopore reads allowed for the assembly of 10 genome segments out of 11. The phylogenetic analysis revealed the virus belonged to the porcine cluster and had GX-P3-I3-R3-C3-M8-A7-N1-T5-E3-H3 genome constellation. Moreover, three potential new genotype groups for VP3, NSP1, and NSP3 genes were determined. Additionally, a recombination between RVH and RVC in the NSP3 gene was detected. The study provides significant information about a novel RVH strain.https://www.frontiersin.org/articles/10.3389/fvets.2023.1302531/fullrotavirus Hswine diseasesnanopore sequencingphylogeneticsmetagenomicsviral recombination |
| spellingShingle | Nikita Krasnikov Anton Yuzhakov Interspecies recombination in NSP3 gene in the first porcine rotavirus H in Russia identified using nanopore-based metagenomic sequencing Frontiers in Veterinary Science rotavirus H swine diseases nanopore sequencing phylogenetics metagenomics viral recombination |
| title | Interspecies recombination in NSP3 gene in the first porcine rotavirus H in Russia identified using nanopore-based metagenomic sequencing |
| title_full | Interspecies recombination in NSP3 gene in the first porcine rotavirus H in Russia identified using nanopore-based metagenomic sequencing |
| title_fullStr | Interspecies recombination in NSP3 gene in the first porcine rotavirus H in Russia identified using nanopore-based metagenomic sequencing |
| title_full_unstemmed | Interspecies recombination in NSP3 gene in the first porcine rotavirus H in Russia identified using nanopore-based metagenomic sequencing |
| title_short | Interspecies recombination in NSP3 gene in the first porcine rotavirus H in Russia identified using nanopore-based metagenomic sequencing |
| title_sort | interspecies recombination in nsp3 gene in the first porcine rotavirus h in russia identified using nanopore based metagenomic sequencing |
| topic | rotavirus H swine diseases nanopore sequencing phylogenetics metagenomics viral recombination |
| url | https://www.frontiersin.org/articles/10.3389/fvets.2023.1302531/full |
| work_keys_str_mv | AT nikitakrasnikov interspeciesrecombinationinnsp3geneinthefirstporcinerotavirushinrussiaidentifiedusingnanoporebasedmetagenomicsequencing AT antonyuzhakov interspeciesrecombinationinnsp3geneinthefirstporcinerotavirushinrussiaidentifiedusingnanoporebasedmetagenomicsequencing |