Whole genome analysis of rotavirus strains circulating in Benin before vaccine introduction, 2016–2018
Species A rotaviruses (RVA) still play a major role in causing acute diarrhea in children under five years old worldwide. Currently, an 11-gene classification system is used to designate the full genotypic constellations of circulating strains. Viral proteins and non-structural proteins in the order...
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Elsevier
2022-05-01
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| Series: | Virus Research |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S0168170222000430 |
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| author | Jijoho Michel Agbla Mathew D. Esona Jose Jaimes Rashi Gautam Alidéhou Jerrold Agbankpé Eric Katz Tamegnon Victorien Dougnon Annick Capo-Chichi Nafissatou Ouedraogo Osseni Razack Honoré Sourou Bankolé Michael D. Bowen |
| author_facet | Jijoho Michel Agbla Mathew D. Esona Jose Jaimes Rashi Gautam Alidéhou Jerrold Agbankpé Eric Katz Tamegnon Victorien Dougnon Annick Capo-Chichi Nafissatou Ouedraogo Osseni Razack Honoré Sourou Bankolé Michael D. Bowen |
| author_sort | Jijoho Michel Agbla |
| collection | DOAJ |
| description | Species A rotaviruses (RVA) still play a major role in causing acute diarrhea in children under five years old worldwide. Currently, an 11-gene classification system is used to designate the full genotypic constellations of circulating strains. Viral proteins and non-structural proteins in the order VP7-VP4-VP6-VP1-VP2-VP3-NSP1-NSP2-NSP3-NSP4-NSP5/6 are represented by the genotypes Gx-P[x]-Ix-Rx-Cx-Mx-Ax-Nx-Tx-Ex-Hx, respectively. In Benin, ROTAVAC® vaccine was introduced into the Expanded Programme on Immunization in December 2019. To monitor circulating RVA strains for changes that may affect vaccine performance, in-depth analysis of strains prior to vaccine introduction are needed. Here we report, the whole-gene characterization (11 ORFs) for 72 randomly selected RVA strains of common and unusual genotypes collected in Benin from the 2016 to 2018 seasons. The sequenced strains were 15 G1P[8], 20 G2P[4], 5 G9P[8], 14 G12P[8], 9 G3P[6], 2 G1P[6], 3 G2P[6], 2 G9P[4], 1 G12P[6], and 1 G1G9P[8]/P[4]. The study strains exhibited two genetic constellations designed as Wa-like G1/G9/G12-P[6]/P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1 and DS-1-like G2/G3/G12-P[4]/P[6]-I2-R2-C2-M2-A2-N2-T2-E2-H2. Genotype G9P[4] strains possessed a DS-1-like genetic constellation with an E6 NSP4 gene, G9-P[4]-I2-R2-C2-M2-A2-N2-T2-E6-H2. The mixed genotype showed both Wa-like and DS-1-like profiles with a T6 NSP3 gene G1/G9P[8]/[4]-I1/I2-R1/R2-C1/C2-M1/M2-A1/A2-N1/N2-T1/T6-E1/E6-H1/H2. At the allelic level, the analysis of the Benin strains, reference strains (with known alleles), vaccine strains (with known alleles) identified 2–13 and 1–17 alleles for DS-1-like and Wa-like strains, respectively. Most of the study strains clustered into previously defined alleles, but we defined 3 new alleles for the VP7 (G3 = 1 new allele and G12 = 2 new alleles) and VP4 (P[4] = 1 new allele and P[6] = 2 new alleles) genes which formed the basis of the VP7 and VP4 gene clusters, respectively. For the remaining 9 genes, 0-6 new alleles were identified for both Wa-like and DS-1-like strains. This analysis of whole genome sequences of RVA strains circulating in Benin described genetic point mutations and reassortment events as well as novel alleles. Further detailed studies on these new alleles are needed and these data can also provide a baseline for studies on RVA in the post-vaccination period. |
| first_indexed | 2024-03-08T17:07:32Z |
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| id | doaj.art-1805c0b603a549e08802d473c48ae111 |
| institution | Directory Open Access Journal |
| issn | 1872-7492 |
| language | English |
| last_indexed | 2024-03-08T17:07:32Z |
| publishDate | 2022-05-01 |
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| series | Virus Research |
| spelling | doaj.art-1805c0b603a549e08802d473c48ae1112024-01-04T04:35:57ZengElsevierVirus Research1872-74922022-05-01313198715Whole genome analysis of rotavirus strains circulating in Benin before vaccine introduction, 2016–2018Jijoho Michel Agbla0Mathew D. Esona1Jose Jaimes2Rashi Gautam3Alidéhou Jerrold Agbankpé4Eric Katz5Tamegnon Victorien Dougnon6Annick Capo-Chichi7Nafissatou Ouedraogo8Osseni Razack9Honoré Sourou Bankolé10Michael D. Bowen11National Health Laboratory, Ministry of Public Health, 01 P.O. Box 418, Cotonou, Benin; Research Unit in Applied Microbiology and Pharmacology of Natural Substances, Research Laboratory in Applied Biology, Polytechnic School of Abomey-Calavi, University of Abomey-Calavi, 01 P.O. Box 2009, Cotonou, BeninViral Gastroenteritis Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, NCIRD, 1600 Clifton Rd NE, Atlanta, GA 30329, USA; Corresponding author.Viral Gastroenteritis Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, NCIRD, 1600 Clifton Rd NE, Atlanta, GA 30329, USAViral Gastroenteritis Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, NCIRD, 1600 Clifton Rd NE, Atlanta, GA 30329, USAResearch Unit in Applied Microbiology and Pharmacology of Natural Substances, Research Laboratory in Applied Biology, Polytechnic School of Abomey-Calavi, University of Abomey-Calavi, 01 P.O. Box 2009, Cotonou, BeninViral Gastroenteritis Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, NCIRD, 1600 Clifton Rd NE, Atlanta, GA 30329, USAResearch Unit in Applied Microbiology and Pharmacology of Natural Substances, Research Laboratory in Applied Biology, Polytechnic School of Abomey-Calavi, University of Abomey-Calavi, 01 P.O. Box 2009, Cotonou, BeninEpidemiological Surveillance Service, Ministry of Public Health, 01 P.O. Box 418, Cotonou, BeninTraining and Research Unit/Applied Sciences and Technologies, University of Dedougou, Burkina FasoCentral Clinic of Abomey Calavi, 01 P.O. Box 418, Cotonou, BeninNational Health Laboratory, Ministry of Public Health, 01 P.O. Box 418, Cotonou, Benin; Research Unit in Applied Microbiology and Pharmacology of Natural Substances, Research Laboratory in Applied Biology, Polytechnic School of Abomey-Calavi, University of Abomey-Calavi, 01 P.O. Box 2009, Cotonou, BeninViral Gastroenteritis Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, NCIRD, 1600 Clifton Rd NE, Atlanta, GA 30329, USASpecies A rotaviruses (RVA) still play a major role in causing acute diarrhea in children under five years old worldwide. Currently, an 11-gene classification system is used to designate the full genotypic constellations of circulating strains. Viral proteins and non-structural proteins in the order VP7-VP4-VP6-VP1-VP2-VP3-NSP1-NSP2-NSP3-NSP4-NSP5/6 are represented by the genotypes Gx-P[x]-Ix-Rx-Cx-Mx-Ax-Nx-Tx-Ex-Hx, respectively. In Benin, ROTAVAC® vaccine was introduced into the Expanded Programme on Immunization in December 2019. To monitor circulating RVA strains for changes that may affect vaccine performance, in-depth analysis of strains prior to vaccine introduction are needed. Here we report, the whole-gene characterization (11 ORFs) for 72 randomly selected RVA strains of common and unusual genotypes collected in Benin from the 2016 to 2018 seasons. The sequenced strains were 15 G1P[8], 20 G2P[4], 5 G9P[8], 14 G12P[8], 9 G3P[6], 2 G1P[6], 3 G2P[6], 2 G9P[4], 1 G12P[6], and 1 G1G9P[8]/P[4]. The study strains exhibited two genetic constellations designed as Wa-like G1/G9/G12-P[6]/P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1 and DS-1-like G2/G3/G12-P[4]/P[6]-I2-R2-C2-M2-A2-N2-T2-E2-H2. Genotype G9P[4] strains possessed a DS-1-like genetic constellation with an E6 NSP4 gene, G9-P[4]-I2-R2-C2-M2-A2-N2-T2-E6-H2. The mixed genotype showed both Wa-like and DS-1-like profiles with a T6 NSP3 gene G1/G9P[8]/[4]-I1/I2-R1/R2-C1/C2-M1/M2-A1/A2-N1/N2-T1/T6-E1/E6-H1/H2. At the allelic level, the analysis of the Benin strains, reference strains (with known alleles), vaccine strains (with known alleles) identified 2–13 and 1–17 alleles for DS-1-like and Wa-like strains, respectively. Most of the study strains clustered into previously defined alleles, but we defined 3 new alleles for the VP7 (G3 = 1 new allele and G12 = 2 new alleles) and VP4 (P[4] = 1 new allele and P[6] = 2 new alleles) genes which formed the basis of the VP7 and VP4 gene clusters, respectively. For the remaining 9 genes, 0-6 new alleles were identified for both Wa-like and DS-1-like strains. This analysis of whole genome sequences of RVA strains circulating in Benin described genetic point mutations and reassortment events as well as novel alleles. Further detailed studies on these new alleles are needed and these data can also provide a baseline for studies on RVA in the post-vaccination period.http://www.sciencedirect.com/science/article/pii/S0168170222000430RotavirusWhole genomeAllelesBeninPre-vaccine era strains |
| spellingShingle | Jijoho Michel Agbla Mathew D. Esona Jose Jaimes Rashi Gautam Alidéhou Jerrold Agbankpé Eric Katz Tamegnon Victorien Dougnon Annick Capo-Chichi Nafissatou Ouedraogo Osseni Razack Honoré Sourou Bankolé Michael D. Bowen Whole genome analysis of rotavirus strains circulating in Benin before vaccine introduction, 2016–2018 Virus Research Rotavirus Whole genome Alleles Benin Pre-vaccine era strains |
| title | Whole genome analysis of rotavirus strains circulating in Benin before vaccine introduction, 2016–2018 |
| title_full | Whole genome analysis of rotavirus strains circulating in Benin before vaccine introduction, 2016–2018 |
| title_fullStr | Whole genome analysis of rotavirus strains circulating in Benin before vaccine introduction, 2016–2018 |
| title_full_unstemmed | Whole genome analysis of rotavirus strains circulating in Benin before vaccine introduction, 2016–2018 |
| title_short | Whole genome analysis of rotavirus strains circulating in Benin before vaccine introduction, 2016–2018 |
| title_sort | whole genome analysis of rotavirus strains circulating in benin before vaccine introduction 2016 2018 |
| topic | Rotavirus Whole genome Alleles Benin Pre-vaccine era strains |
| url | http://www.sciencedirect.com/science/article/pii/S0168170222000430 |
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