Abstract
One of the challenges associated with introducing a vaccine is monitoring its impact through clinical and molecular surveillance. The aims of this study were to analyze the genetic diversity of rotavirus A in Argentina between 2019 and 2022 and to assess the phylogenetic and phylodynamic features of the unusual G6 strains detected. A significant decline in the Wa-like genogroup strains was observed, and G6 strains were detected for the first time in Argentina, in association with P[8] and P[9]. Spatiotemporal analysis showed that the G6-lineage I strains detected recently in Argentina and Brazil might have emerged from European strains. This study provides recent evidence of the genetic diversity of rotaviruses in isolated cases. It is considered important to support continuous surveillance of rotavirus in the post-vaccine scenario, mainly to evaluate potential changes that may occur after the COVID-19 pandemic.
Data availability
The datasets generated and/or analysed in the current study are available from the corresponding author on reasonable request.
References
Tate JE, Burton AH, Boschi-Pinto C et al (2016) Global, regional, and national estimates of rotavirus mortality in children <5 Years of Age, 2000–2013. Clin Infect Dis 62(Suppl 2):S96–S105. https://doi.org/10.1093/cid/civ1013
GBD 2016 Diarrhoeal Disease Collaborators (2018) Estimates of the global, regional, and national morbidity, mortality, and aetiologies of diarrhoea in 195 countries: a systematic analysis for the Global Burden of Disease Study 2016. Lancet Infect Dis 18:1211–1228. https://doi.org/10.1016/S1473-3099(18)30362-1
Hungerford D, Vivancos R, EuroRotaNet network members et al (2016) In-season and out-of-season variation of rotavirus genotype distribution and age of infection across 12 European countries before the introduction of routine vaccination, 2007/08 to 2012/13. Euro Surveill. https://doi.org/10.2807/1560-7917.ES.2016.21.2.30106
Desselberger U (2014) Rotaviruses. Virus Res 190:75–96. https://doi.org/10.1016/j.virusres.2014.06.016
Matthijnssens J, Ciarlet M, Rahman M et al (2008) Recommendations for the classification of group A rotaviruses using all 11 genomic RNA segments. Arch Virol 153:1621–1629. https://doi.org/10.1007/s00705-008-0155-1
Matthijnssens J, Ciarlet M, Heiman E et al (2008) Full genome-based classification of rotaviruses reveals a common origin between human Wa-Like and porcine rotavirus strains and human DS-1-like and bovine rotavirus strains. J Virol 82:3204–3219. https://doi.org/10.1128/JVI.02257-07
Luchs A, da Costa AC, Cilli A et al (2019) Spread of the emerging equine-like G3P[8] DS-1-like genetic backbone rotavirus strain in Brazil and identification of potential genetic variants. J Gen Virol 100:7–25. https://doi.org/10.1099/jgv.0.001171
Mwangi PN, Mogotsi MT, Rasebotsa SP et al (2020) Uncovering the first atypical DS-1-like G1P[8] rotavirus strains that circulated during pre-rotavirus vaccine introduction era in South Africa. Pathogens 9:391. https://doi.org/10.3390/pathogens9050391
Castells M, Caffarena RD, Casaux ML et al (2020) Phylogenetic analyses of rotavirus A from cattle in Uruguay reveal the circulation of common and uncommon genotypes and suggest interspecies transmission. Pathogens 9:570. https://doi.org/10.3390/pathogens9070570
Badaracco A, Garaicoechea L, Rodríguez D et al (2012) Bovine rotavirus strains circulating in beef and dairy herds in Argentina from 2004 to 2010. Vet Microbiol 158:394–399. https://doi.org/10.1016/j.vetmic.2011.12.011
Gerna G, Sarasini A, Parea M et al (1992) Isolation and characterization of two distinct human rotavirus strains with G6 specificity. J Clin Microbiol 30:9–16. https://doi.org/10.1128/jcm.30.1.9-16.1992
Yamamoto D, Kawaguchiya M, Ghosh S et al (2011) Detection and full genomic analysis of G6P[9] human rotavirus in Japan. Virus Genes 43:215–223. https://doi.org/10.1007/s11262-011-0624-6
Afrad MH, Matthijnssens J, Moni S et al (2013) Genetic characterization of a rare bovine-like human VP4 mono-reassortant G6P[8] rotavirus strain detected from an infant in Bangladesh. Infect Genet Evol 19:120–126. https://doi.org/10.1016/j.meegid.2013.06.030
De Grazia S, Martella V, Rotolo V et al (2011) Molecular characterization of genotype G6 human rotavirus strains detected in Italy from 1986 to 2009. Infect Genet Evol 11:1449–1455. https://doi.org/10.1016/j.meegid.2011.05.015
Pietsch C, Liebert UG (2018) Evidence for presumable feline origin of sporadic G6P[9] rotaviruses in humans. Infect Genet Evol 63:180–194. https://doi.org/10.1016/j.meegid.2018.05.030
Cooney MA, Gorrell RJ, Palombo EA (2001) Characterisation and phylogenetic analysis of the VP7 proteins of serotype G6 and G8 human rotaviruses. J Med Microbiol 50:462–467. https://doi.org/10.1099/0022-1317-50-5-462
Gutierrez MB, de Assis RMS, Arantes I, Fumian TM (2022) Full genotype constellations analysis of unusual DS-1-like G12P[6] and G6P[8] rotavirus strains detected in Brazil, 2019. Virology 577:74–83. https://doi.org/10.1016/j.virol.2022.10.010
Gouvea V, Glass RI, Woods P et al (1990) Polymerase chain reaction amplification and ty** of rotavirus nucleic acid from stool specimens. J Clin Microbiol 28:276–282. https://doi.org/10.1128/jcm.28.2.276-282.1990
Das BK, Gentsch JR, Cicirello HG et al (1994) Characterization of rotavirus strains from newborns in New Delhi, India. J Clin Microbiol 32:1820–1822. https://doi.org/10.1128/jcm.32.7.1820-1822.1994
Trifinopoulos J, Nguyen L-T, von Haeseler A, Minh BQ (2016) W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Res 44:W232-235. https://doi.org/10.1093/nar/gkw256
Hoang DT, Chernomor O, von Haeseler A et al (2018) UFBoot2: improving the ultrafast bootstrap approximation. Mol Biol Evol 35:518–522. https://doi.org/10.1093/molbev/msx281
Degiuseppe JI, Stupka JA, Argentinean Rotavirus Surveillance Network (2021) Emergence of unusual rotavirus G9P[4] and G8P[8] strains during post vaccination surveillance in Argentina, 2017–2018. Infect Genet Evol 93:104940. https://doi.org/10.1016/j.meegid.2021.104940
Gentile Á, Juárez MDV, Lución MF, Degiuseppe JI (2023) 2do Informe Especial del Observatorio de la Infancia y Adolescencia SAP-UNICEF: “El desafío de recuperar las coberturas de vacunación en Argentina.” Observatorio de la Infancia y la Adolescencia, Buenos Aires, Argentina
McKell AO, Nichols JC, McDonald SM (2013) PCR-based approach to distinguish group A human rotavirus genotype 1 vs. genotype 2 genes. J Virol Methods 194:197–205. https://doi.org/10.1016/j.jviromet.2013.08.025
Heiman EM, McDonald SM, Barro M et al (2008) Group A human rotavirus genomics: evidence that gene constellations are influenced by viral protein interactions. J Virol 82:11106–11116. https://doi.org/10.1128/JVI.01402-08
McDonald SM, Nelson MI, Turner PE, Patton JT (2016) Reassortment in segmented RNA viruses: mechanisms and outcomes. Nat Rev Microbiol 14:448–460. https://doi.org/10.1038/nrmicro.2016.46
Medeiros RS, França Y, Viana E et al (2023) Genomic constellation of human rotavirus G8 strains in Brazil over a 13-year period: detection of the Novel Bovine-like G8P[8] Strains with the DS-1-like backbone. Viruses 15:664. https://doi.org/10.3390/v15030664
Degiuseppe JI, Torres C, Mbayed VA, Stupka JA (2022) Phylogeography of rotavirus G8P[8] detected in Argentina: evidence of transpacific dissemination. Viruses 14:2223. https://doi.org/10.3390/v14102223
Acknowledgements
Here, the members of Argentinean Rotavirus Surveillance Network are listed who contributed to this study: M. L. Benvenutti (Htal. Penna, Buenos Aires), L. Cabral (Htal Barreyro, Misiones), C. Cano (Htal de la Madre y el Niño, La Rioja), P. Cortes (Htal. del Niño Jesús, Córdoba), V. Eibar (Htal. Notti, Mendoza), R. Farfán (Htal Papa Francisco, Salta), S. Flores (Htal. Eva Perón, Tucumán), L. López (Htal. Durand, CABA), E. Lozano (Htal Quintana, Jujuy), N. Lucero (Htal. Schestakow, Mendoza), M. Maresca (Htal Materno Infantil, Salta), J. Palau (Htal. Sor María Ludovica, Buenos Aires), M. Roncallo (Htal. Cipolletti, Río Negro), G. Ruiz de Huidobro (Laboratorio de Salud Pública, Tucumán), I. Silveyra (Htal. Centeno, La Pampa), G. Sucin (Htal. Castelán, Chaco), A. Zurschmitten (Htal. Junín de los Andes, Neuquén).
Funding
The authors declare that no funds, grants, or other support were received during the preparation of this article.
Author information
Authors and Affiliations
Consortia
Contributions
JID and JAS contributed to the study conception and design. Material preparation, data collection, and analysis were performed by JID, AM, and CBM. The first draft of the manuscript was written by JID, and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.
Corresponding author
Ethics declarations
Conflict of interest
The authors have no relevant financial or non-financial interests to disclose.
Additional information
Handing Editor -Hester G O'Neill.
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Supplementary Fig. S1
Maximum-clade-credibility tree rendered in .kml format (SpreaD3 software) (KML 245 KB)
Supplementary Fig. S2
Bayes factor rendered in .kml format (SpreaD3 software) (KML 2115 KB)
Supplementary Fig. S3
Maximum-clade-credibility tree of G6-lineage I strains. Branches are color-coded according to their country of origin (ARG, Argentina; BEL, Belgium; BFA, Burkina Faso; BGR, Bulgaria; BRA, Brazil; CMR, Cameroon; COG, Democratic Republic of Congo; GER, Germany; GHA, Ghana; HUN, Hungary; ITA, Italy; JPN, Japan; RUS, Russia; TUN, Tunisia; USA, United States). The timescale is indicated below the tree. Clade posterior probability values are shown at each branch (EPS 482 KB)
Rights and permissions
About this article
Cite this article
Degiuseppe, J.I., Martelli, A., Barrios Mathieur, C. et al. Genetic diversity of rotavirus A in Argentina during 2019-2022: detection of G6 strains and insights regarding its dissemination. Arch Virol 168, 251 (2023). https://doi.org/10.1007/s00705-023-05874-8
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s00705-023-05874-8