Citation: Miño, S.O.; Badaracco, A.; Uriarte, E.L.; Ciarlet, M.; Parreño, V. Evolution of Animal South American RVA Told by the NSP4 Gene E12 Genotype. Viruses 2022, 14, 2506. https://doi.org/10.3390/v14112506 Academic Editor: Alice Fusaro Received: 17 October 2022 Accepted: 10 November 2022 Published: 12 November 2022 Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- iations. Copyright: © 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). viruses Brief Report Evolution of Animal South American RVA Told by the NSP4 Gene E12 Genotype Samuel Orlando Miño 1, * , Alejandra Badaracco 2 , Enrique Louge Uriarte 3 , Max Ciarlet 4 and Viviana Parreño 5,6, * 1 Instituto Nacional de Tecnología Agropecuaria INTA, EEA Cerro Azul, Ruta Nacional 14, km 836 (CP3313), Cerro Azul 3313, Argentina 2 Instituto Nacional de Tecnología Agropecuaria INTA, EEA Montecarlo,Av. El Libertador N ◦ 2472 (CP3384), Montecarlo 3384, Argentina 3 Instituto Nacional de Tecnología Agropecuaria INTA, EEA Balcarce, Ruta 226 km 73.5 (CP7620), Balcarce 7620, Argentina 4 Clinical Development, Icosavax, Seattle, WA 98101, USA 5 Instituto Nacional de Tecnología Agropecuaria INTA, CICVyA, INTA Castelar, De las Cabañas y De los Reseros s/n (CP1686), Hurlingham 1686, Argentina 6 Instituto de Virología e Innovaciones Tecnológicas (IVIT), CICVyA, INTA Castelar, De las Cabañas y De los Reseros s/n (CP1686), Hurlingham 1686, Argentina * Correspondence: mino.samuel@inta.gob.ar (S.O.M.); parreno.viviana@inta.gob.ar(V.P.); Tel.: +54-3764-494740 (S.O.M.); Tel.: +54-11-3754-8464(V.P.) Abstract: Rotavirus A (RVA) possesses a genome of 11 double-stranded (ds) RNA segments, and each segment encodes one protein, with the exception of segment 11. NSP4 is a non-structural multifunctional protein encoded by segment 10 that defines the E-genotype. From the 31 E-genotypes described, genotype E12 has been described in Argentina, Uruguay, Paraguay, and Brazil in RVA strains infecting different animal species and humans. In this work, we studied the evolutionary relationships of RVA strains carrying the E12 genotype in South America using phylogenetic and phylodynamic approaches. We found that the E12 genotype has a South American origin, with a guanaco (Lama guanicoe) strain as natural host. Interestingly, all the other reported RVA strains carrying the E12 genotype in equine, bovine, caprine, and human strains are related to RVA strains of camelid origin. The evolutionary path and genetic footprint of the E12 genotype were reconstructed starting with the introduction of non-native livestock species into the American continent with the Spanish conquest in the 16th century. The imported animal species were in close contact with South American camelids, and the offspring were exposed to the native RVA strains brought from Europe and the new RVA circulating in guanacos, resulting in the emergence of new RVA strains in the current lineages’ strongly species-specific adaption. In conclusion, we proposed the NSP4 E12 genotype as a genetic geographic marker in the RVA strains circulating in different animal species in South America. Keywords: genome reassortment; phylogeny; evolution in segmented viruses; phylodynamic 1. Introduction Rotavirus A (RVA) belongs to the Reoviridae family (genus Rotavirus, Rotavirus species A). The rotavirus particle is composed of three concentric capsid layers, with a genome of 11 double-stranded (ds) RNA segments, and each segment encodes one protein only with the exception of segment 11. The segments 1–6 encode the virion proteins (VP), while the remaining segments encode the non-structural proteins (NSPs) [1]. The rotavirus NSPs then coordinate various stages of genome replication and viral assembly by adapting and modifying the cellular machinery, which leads to productive release of mature particles through cell lysis [2]. RVA strains have been classified since 2008 based on the complete genomic constella- tion describing the genotype of all eleven segments [3]. With the advent of sequencing, all Viruses 2022, 14, 2506. https://doi.org/10.3390/v14112506 https://www.mdpi.com/journal/viruses