Journal articles: 'Rotavirus DS-1 strain'

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Monnier, Nilah, Kyoko Higo-Moriguchi, Zhen-Yu J. Sun, B. V. Venkataram Prasad, Koki Taniguchi, and Philip R. Dormitzer. "High-Resolution Molecular and Antigen Structure of the VP8* Core of a Sialic Acid-Independent Human Rotavirus Strain." Journal of Virology 80, no. 3 (February 1, 2006): 1513–23. http://dx.doi.org/10.1128/jvi.80.3.1513-1523.2006.

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ABSTRACT The most intensively studied rotavirus strains initially attach to cells when the “heads” of their protruding spikes bind cell surface sialic acid. Rotavirus strains that cause disease in humans do not bind this ligand. The structure of the sialic acid binding head (the VP8* core) from the simian rotavirus strain RRV has been reported, and neutralization epitopes have been mapped onto its surface. We report here a 1.6-Å resolution crystal structure of the equivalent domain from the sialic acid-independent rotavirus strain DS-1, which causes gastroenteritis in humans. Although the RRV and DS-1 VP8* cores differ functionally, they share the same galectin-like fold. Differences between the RRV and DS-1 VP8* cores in the region that corresponds to the RRV sialic acid binding site make it unlikely that DS-1 VP8* binds an alternative carbohydrate ligand in this location. In the crystals, a surface cleft on each DS-1 VP8* core binds N-terminal residues from a neighboring molecule. This cleft may function as a ligand binding site during rotavirus replication. We also report an escape mutant analysis, which allows the mapping of heterotypic neutralizing epitopes recognized by human monoclonal antibodies onto the surface of the VP8* core. The distribution of escape mutations on the DS-1 VP8* core indicates that neutralizing antibodies that recognize VP8* of human rotavirus strains may bind a conformation of the spike that differs from those observed to date.

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Nakagomi, Toyoko, Yen Hai Doan, Winifred Dove, Bagrey Ngwira, Miren Iturriza-Gómara, Osamu Nakagomi, and Nigel A. Cunliffe. "G8 rotaviruses with conserved genotype constellations detected in Malawi over 10 years (1997–2007) display frequent gene reassortment among strains co-circulating in humans." Journal of General Virology 94, no. 6 (June 1, 2013): 1273–95. http://dx.doi.org/10.1099/vir.0.050625-0.

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Rotavirus A, the most common cause of severe diarrhoea in children worldwide, occurs in five major VP7 (G) and VP4 (P) genotype combinations, comprising G1P[8], G2P[4], G3P[8], G4P[8] and G9P[8]. However, G8, a common bovine rotavirus genotype, has been reported frequently among children in African countries. Surveillance of rotavirus gastroenteritis conducted in a sentinel hospital in Blantyre, Malawi between 1997 and 2007 provided a rare opportunity to examine the whole genotype constellation of G8 strains and their evolution over time. A sample of 27 (9.0 %) of 299 G8 strains was selected to represent each surveillance year and a range of P genotypes, which shifted in predominance from P[6] to P[4] and P[8] during the study period. Following cell culture adaptation, whole genome sequencing demonstrated that the genetic background of 26 strains possessed the DS-1 genotype constellation. A single G8P[6] strain was a reassortant in which both NSP2 and NSP5 genes from strains with the Wa genotype constellation had been inserted into a strain with the DS-1 genotype background. Phylogenetic analysis suggested frequent reassortment among co-circulating strains with the DS-1 genotype constellation. Little evidence was identified to suggest the introduction of contemporary bovine rotavirus genes into any of the 27 G8 strains examined. In conclusion, Malawian G8 strains are closely related to other human strains with the DS-1 genotype constellation. They have evolved over the last decade through genetic reassortment with other human rotaviruses, changing their VP4 genotypes while maintaining a conserved genotype constellation for the remaining structural and non-structural proteins.

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Ghosh, Souvik, Noriaki Adachi, Zipporah Gatheru, James Nyangao, Dai Yamamoto, Masaho Ishino, Noriko Urushibara, and Nobumichi Kobayashi. "Whole-genome analysis reveals the complex evolutionary dynamics of Kenyan G2P[4] human rotavirus strains." Journal of General Virology 92, no. 9 (September 1, 2011): 2201–8. http://dx.doi.org/10.1099/vir.0.033001-0.

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Although G2P[4] rotaviruses are common causes of acute childhood diarrhoea in Africa, to date there are no reports on whole genomic analysis of African G2P[4] strains. In this study, the nearly complete genome sequences of two Kenyan G2P[4] strains, AK26 and D205, detected in 1982 and 1989, respectively, were analysed. Strain D205 exhibited a DS-1-like genotype constellation, whilst strain AK26 appeared to be an intergenogroup reassortant with a Wa-like NSP2 genotype on the DS-1-like genotype constellation. The VP2-4, VP6-7, NSP1, NSP3 and NSP5 genes of strain AK26 and the VP2, VP4, VP7 and NSP1–5 genes of strain D205 were closely related to those of the prototype or other human G2P[4] strains. In contrast, their remaining genes were distantly related, and, except for NSP2 of AK26, appeared to originate from or share a common origin with rotavirus genes of artiodactyl (ruminant and camelid) origin. These observations highlight the complex evolutionary dynamics of African G2P[4] rotaviruses.

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Matthijnssens, Jelle, Mustafizur Rahman, and Marc Van Ranst. "Two out of the 11 genes of an unusual human G6P[6] rotavirus isolate are of bovine origin." Journal of General Virology 89, no. 10 (October 1, 2008): 2630–35. http://dx.doi.org/10.1099/vir.0.2008/003780-0.

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In 2003, we described the first human G6P[6] rotavirus strain (B1711). To investigate further the molecular origin of this strain and to determine the possible reassortments leading to this new gene constellation, the complete genome of strain B1711 was sequenced. SimPlot analyses were conducted to compare strain B1711 with other known rotavirus gene segments, and phylogenetic dendrograms were constructed to analyse the origin of the eleven genome segments of strain B1711. Our analysis indicated that strain B1711 acquired its VP1-, VP2-, VP4-, VP6- and NSP1–5-encoding gene segments from human DS-1-like P[6] rotavirus strains, and its VP3 and VP7 gene segments from a bovine rotavirus strain through reassortment. The introduction of animal–human reassortant strains, which might arise in either of the hosts, into the human rotavirus population is an important mechanism for the generation of rotavirus diversity, and might be a challenge for the current rotavirus vaccines and vaccines under development.

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Mwangi, Peter N., Milton T. Mogotsi, Sebotsana P. Rasebotsa, Mapaseka L. Seheri, M. Jeffrey Mphahlele, Valantine N. Ndze, Francis E. Dennis, Khuzwayo C. Jere, and Martin M. Nyaga. "Uncovering the First Atypical DS-1-like G1P[8] Rotavirus Strains That Circulated during Pre-Rotavirus Vaccine Introduction Era in South Africa." Pathogens 9, no. 5 (May 20, 2020): 391. http://dx.doi.org/10.3390/pathogens9050391.

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Emergence of DS-1-like G1P[8] group A rotavirus (RVA) strains during post-rotavirus vaccination period has recently been reported in several countries. This study demonstrates, for the first time, rare atypical DS-1-like G1P[8] RVA strains that circulated in 2008 during pre-vaccine era in South Africa. Rotavirus positive samples were subjected to whole-genome sequencing. Two G1P[8] strains (RVA/Human-wt/ZAF/UFS-NGS-MRC-DPRU1971/2008/G1P[8] and RVA/Human-wt/ZAF/UFS-NGS-MRC-DPRU1973/2008/G1P[8]) possessed a DS-1-like genome constellation background (I2-R2-C2-M2-A2-N2-T2-E2-H2). The outer VP4 and VP7 capsid genes of the two South African G1P[8] strains had the highest nucleotide (amino acid) nt (aa) identities of 99.6–99.9% (99.1–100%) with the VP4 and the VP7 genes of a locally circulating South African strain, RVA/Human-wt/ZAF/MRC-DPRU1039/2008/G1P[8]. All the internal backbone genes (VP1–VP3, VP6, and NSP1-NSP5) had the highest nt (aa) identities with cognate internal genes of another locally circulating South African strain, RVA/Human-wt/ZAF/MRC-DPRU2344/2008/G2P[6]. The two study strains emerged through reassortment mechanism involving locally circulating South African strains, as they were distinctly unrelated to other reported atypical G1P[8] strains. The identification of these G1P[8] double-gene reassortants during the pre-vaccination period strongly supports natural RVA evolutionary mechanisms of the RVA genome. There is a need to maintain long-term whole-genome surveillance to monitor such atypical strains.

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Ghosh, Souvik, Shyamal Kumar Paul, Mohammad Akram Hossain, Mohammed Mahbub Alam, Muzahed Uddin Ahmed, and Nobumichi Kobayashi. "Full genomic analyses of two human G2P[4] rotavirus strains detected in 2005: identification of a caprine-like VP3 gene." Journal of General Virology 92, no. 5 (May 1, 2011): 1222–27. http://dx.doi.org/10.1099/vir.0.029868-0.

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Although G2P[4] rotaviruses are common causes of infantile diarrhoea, to date only the full genomes of the prototype (strain DS-1) and another old strain, TB-Chen, have been analysed. We report here the full genomic analyses of two Bangladeshi G2P[4] strains, MMC6 and MMC88, detected in 2005. Both the strains exhibited a DS-1-like genotype constellation. Excluding the VP4 and VP7 genes, and except for VP3 of MMC88, the MMC strains were genetically more closely related to the contemporary G2P[4] and several non-G2P[4] human strains than the prototype G2P[4] strain. However, by phylogenetic analyses, the VP2, VP3 (except MMC88), NSP1 and NSP3–5 genes of these strains appeared to share a common origin with those of the prototype strain, whilst their VP1, VP6 and NSP2 genes clustered near a caprine strain. The VP3 gene of MMC88 exhibited maximum relatedness to a local caprine strain, representing the first reported human G2P[4] strain with a gene of animal origin.

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Moutelíková, Sauer, Dvořáková Heroldová, Holá, and Prodělalová. "Emergence of Rare Bovine–Human Reassortant DS-1-Like Rotavirus A Strains with G8P[8] Genotype in Human Patients in the Czech Republic." Viruses 11, no. 11 (November 1, 2019): 1015. http://dx.doi.org/10.3390/v11111015.

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Group A Rotaviruses (RVA) are the leading cause of acute gastroenteritis in children and a major cause of childhood mortality in low-income countries. RVAs are mostly host-specific, but interspecies transmission and reassortment between human and animal RVAs significantly contribute to their genetic diversity. We investigated the VP7 and VP4 genotypes of RVA isolated from 225 stool specimens collected from Czech patients with gastroenteritis during 2016–2019. The most abundant genotypes were G1P[8] (42.7%), G3P[8] (11.1%), G9P[8] (9.8%), G2P[4] (4.4%), G4P[8] (1.3%), G12P[8] (1.3%), and, surprisingly, G8P[8] (9.3%). Sequence analysis of G8P[8] strains revealed the highest nucleotide similarity of all Czech G8 sequences to the G8P[8] rotavirus strains that were isolated in Vietnam in 2014/2015. The whole-genome backbone of the Czech G8 strains was determined with the use of next-generation sequencing as DS-1-like. Phylogenetic analysis of all segments clustered the Czech isolates with RVA strains that were formerly described in Southeast Asia, which had emerged following genetic reassortment between bovine and human RVAs. This is the first time that bovine–human DS1-like G8P[8] strains were detected at a high rate in human patients in Central Europe. Whether the emergence of this unusual genotype reflects the establishment of a new RVA strain in the population requires the continuous monitoring of rotavirus epidemiology.

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Zhou, Xuan, Yuan-Hong Wang, Bei-Bei Pang, Nan Chen, and Nobumichi Kobayashi. "Surveillance of Human Rotavirus in Wuhan, China (2011–2019): Predominance of G9P[8] and Emergence of G12." Pathogens 9, no. 10 (October 2, 2020): 810. http://dx.doi.org/10.3390/pathogens9100810.

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Rotaviruses are a major etiologic agent of gastroenteritis in infants and young children worldwide. To learn the shift of genotypes and genetic characteristics of Rotavirus A (RVA) causing diarrhea in children and adults, a hospital-based surveillance of rotavirus was conducted in Wuhan, China from June 2011 through May 2019, and representative virus strains were phylogenetically analyzed. Among a total of 6733 stool specimens collected from both children and adults with acute gastroenteritis, RVA was detected in 25.5% (1125/4409) and 12.3% (285/2324) of specimens, respectively. G9P[8] was the most common genotype (74.5%), followed by G1P[8] (8.7%), G2P[4] (8.4%), and G3P[8] (7.3%), with G9P[8] increasing rapidly during the study period. The predominant genotype shifted from G1P[8] to G9P[8] in 2012–2013 epidemic season. G12P[6] strain RVA/Human-wt/CHN/Z2761/2019/G12P[6] was detected in April 2019 and assigned to G12-P[6]-I1-R1-C1-M1-A1-N1-T2-E1-H1 genotypes. Phylogenetic analysis revealed that VP7, VP4, VP6, VP3, NSP1, NSP2, and NSP5 genes of Z2761 clustered closely with those of Korean G12P[6] strain CAU_214, showing high nucleotide identities (98.0–98.8%). The NSP3 gene of Z2761 was closely related to those of G2P[4] and G12P[6] rotaviruses in Asia. All the eleven gene segments of Z2761 kept distance from those of cocirculating G9P[8], G1P[8], and G3P[8] strains detected in Wuhan during this study period. This is the first identification of G12 rotavirus in China. It is deduced that Z2761 is a reassortant having DS-1-like NSP3 gene in the background of G12P[6] rotavirus genetically close to CAU_214.

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Lee, Chun-Nan, Yu-Lan Wang, Chuan-Liang Kao, Chih-Ling Zao, Chin-Yun Lee, and Hsiao-Neng Chen. "NSP4 Gene Analysis of Rotaviruses Recovered from Infected Children with and without Diarrhea." Journal of Clinical Microbiology 38, no. 12 (2000): 4471–77. http://dx.doi.org/10.1128/jcm.38.12.4471-4477.2000.

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The transmembrane glycoprotein NSP4 functions as a viral enterotoxin capable of inducing diarrhea in young mice. It has been suggested that NSP4 may be a key determinant of rotavirus pathogenicity and a target for vaccine development. Twenty two G1P[6] rotaviruses from babies with and without diarrhea were comparatively analyzed along with reference strains and another 22 Taiwanese human rotaviruses of G and P combination types different from the G1P[6] type. The sequence variations in the NSP4 genes were studied by direct sequencing analysis of the amplicons of reverse transcription-PCR. Two genetic groups could be identified in this analysis. While the majority of these strains were closely related to the Wa strain, the G2 viruses were closely related to the S2 strain. Furthermore, phylogenetic analysis of the NSP4 gene among the G2 rotaviruses revealed three distinct lineages associated with DS-1, S2, and E210, respectively, as has been reported previously for the VP7 gene. However, we found no apparent correlation in the deduced amino acid sequences corresponding to the proposed enterotoxic peptide region between the rotaviruses recovered from individuals with and without diarrhea. The NSP4 gene product being a pathogenic determinant may not be a generalized phenomenon.

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Ciarlet, Max, Mary K. Estes, Christopher Barone, Robert F. Ramig, and Margaret E. Conner. "Analysis of Host Range Restriction Determinants in the Rabbit Model: Comparison of Homologous and Heterologous Rotavirus Infections." Journal of Virology 72, no. 3 (March 1, 1998): 2341–51. http://dx.doi.org/10.1128/jvi.72.3.2341-2351.1998.

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ABSTRACT The main limitation of both the rabbit and mouse models of rotavirus infection is that human rotavirus (HRV) strains do not replicate efficiently in either animal. The identification of individual genes necessary for conferring replication competence in a heterologous host is important to an understanding of the host range restriction of rotavirus infections. We recently reported the identification of the P type of the spike protein VP4 of four lapine rotavirus strains as being P[14]. To determine whether VP4 is involved in host range restriction in rabbits, we evaluated infection in rotavirus antibody-free rabbits inoculated orally with two P[14] HRVs, PA169 (G6) and HAL1166 (G8), and with several other HRV strains and animal rotavirus strains of different P and G types. We also evaluated whether the parental rhesus rotavirus (RRV) (P5B[3], G3) and the derived RRV-HRV reassortant candidate vaccine strains RRV × D (G1), RRV × DS-1 (G2), and RRV × ST3 (G4) would productively infect rabbits. Based on virus shedding, limited replication was observed with the P[14] HRV strains and with the SA11 Cl3 (P[2], G3) and SA11 4F (P6[1], G3) animal rotavirus strains, compared to the homologous ALA strain (P[14], G3). However, even limited infection provided complete protection from rotavirus infection when rabbits were challenged orally 28 days postinoculation (DPI) with 103 50% infective doses of ALA rabbit rotavirus. Other HRVs did not productively infect rabbits and provided no significant protection from challenge, in spite of occasional seroconversion. Simian RRV replicated as efficiently as lapine ALA rotavirus in rabbits and provided complete protection from ALA challenge. Live attenuated RRV reassortant vaccine strains resulted in no, limited, or productive infection of rabbits, but all rabbits were completely protected from heterotypic ALA challenge. The altered replication efficiency of the reassortants in rabbits suggests a role for VP7 in host range restriction. Also, our results suggest that VP4 may be involved in, but is not exclusively responsible for, host range restriction in the rabbit model. The replication efficiency of rotavirus in rabbits also is not controlled by the product of gene 5 (NSP1) alone, since a reassortant rotavirus with ALA gene 5 and all other genes from SA11 was more severely replication restricted than either parental rotavirus strain.

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Komoto, Satoshi, Masanori Kugita, Jun Sasaki, and Koki Taniguchi. "Generation of Recombinant Rotavirus with an Antigenic Mosaic of Cross-Reactive Neutralization Epitopes on VP4." Journal of Virology 82, no. 13 (April 23, 2008): 6753–57. http://dx.doi.org/10.1128/jvi.00601-08.

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ABSTRACT Recombinant rotavirus (RV) with cDNA-derived chimeric VP4 was generated using recently developed reverse genetics for RV. The rescued virus, KU//rVP4(SA11)-II(DS-1), contains SA11 (simian RV strain, G3P[2])-based VP4, in which a cross-reactive neutralization epitope (amino acids 381 to 401) on VP5* is replaced by the corresponding sequence of a different P-type DS-1 (human RV strain, G2P[4]). Serological analyses with a panel of anti-VP4- and -VP7-neutralizing monoclonal antibodies revealed that the rescued virus carries a novel antigenic mosaic of cross-reactive neutralization epitopes on its VP4 surface. This is the first report of the generation of a recombinant RV with artificial amino acid substitutions.

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Yamamoto, Seiji P., Atsushi Kaida, Hideyuki Kubo, and Nobuhiro Iritani. "Gastroenteritis Outbreaks Caused by a DS-1–like G1P[8] Rotavirus Strain, Japan, 2012–2013." Emerging Infectious Diseases 20, no. 6 (June 2014): 1030–33. http://dx.doi.org/10.3201/eid2006.131326.

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Kamiya, Hajime, Ratana Tacharoenmuang, Tomihiko Ide, Manami Negoro, Takaaki Tanaka, Kazutoyo Asada, Haruna Nakamura, et al. "Characterization of an Unusual DS-1-Like G8P[8] Rotavirus Strain from Japan in 2017: Evolution of Emerging DS-1-Like G8P[8] Strains through Reassortment." Japanese Journal of Infectious Diseases 72, no. 4 (2019): 256–60. http://dx.doi.org/10.7883/yoken.jjid.2018.484.

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Wang, Yuhuan, Theresa Resch, Mathew D. Esona, Sung-Sil Moon, and Baoming Jiang. "A DS-1 like G9P[6] human strain CDC-6 as a new rotavirus vaccine candidate." Vaccine 36, no. 45 (October 2018): 6844–49. http://dx.doi.org/10.1016/j.vaccine.2018.08.055.

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McDonald, Sarah M., and John T. Patton. "Molecular Characterization of a Subgroup Specificity Associated with the Rotavirus Inner Capsid Protein VP2." Journal of Virology 82, no. 6 (January 23, 2008): 2752–64. http://dx.doi.org/10.1128/jvi.02492-07.

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ABSTRACT Group A rotaviruses are classified into serotypes, based on the reactivity pattern of neutralizing antibodies to VP4 and VP7, as well as into subgroups (SGs), based on non-neutralizing antibodies directed against VP6. The inner capsid protein (VP2) has also been described as a SG antigen; however, little is known regarding the molecular determinants of VP2 SG specificity. In this study, we characterize VP2 SGs by correlating genetic markers with the immunoreactivity of the SG-specific monoclonal antibody (YO-60). Our results show that VP2 proteins similar in sequence to that of the prototypic human strain Wa are recognized by YO-60, classifying them as VP2 SG-II. In contrast, proteins not bound by YO-60 are similar to those of human strains DS-1 or AU-1 and represent VP2 SG-I. Using a mutagenesis approach, we identified residues that determine recognition by either YO-60 or the group A-specific VP2 monoclonal antibody (6E8). We found that YO-60 binds to a conformationally dependent epitope that includes Wa VP2 residue M328. The epitope for 6E8 is also contingent upon VP2 conformation and resides within a single region of the protein (Wa VP2 residues A440 to T530). Using a high-resolution structure of bovine rotavirus double-layered particles, we predicted these epitopes to be spatially distinct from each other and located on opposite surfaces of VP2. This study reveals the extent of genetic variation among group A rotavirus VP2 proteins and illuminates the molecular basis for a previously described SG specificity associated with the rotavirus inner capsid protein.

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Luchs, A., A. Cilli, S. Morillo, L. Boen, R. D. C. Carmona, and M. D. C. S. T. Timenetsky. "Spread of the emerging equine-like G3P[8] DS-1-like genetic backbone rotavirus strain in Brazil." International Journal of Infectious Diseases 73 (August 2018): 190. http://dx.doi.org/10.1016/j.ijid.2018.04.3845.

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Martinez-Gutierrez, Marlen, Estiven Hernandez-Mira, Santiago Rendon-Marin, and Julian Ruiz-Saenz. "Wa-1 Equine-Like G3P[8] Rotavirus from a Child with Diarrhea in Colombia." Viruses 13, no. 6 (June 4, 2021): 1075. http://dx.doi.org/10.3390/v13061075.

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Rotavirus A (RVA) has been considered the main cause of diarrheal disease in children under five years in emergency services in both developed and developing countries. RVA belongs to the Reoviridae family, which comprises 11 segments of double-stranded RNA (dsRNA) as a genomic constellation that encodes for six structural and five to six nonstructural proteins. RVA has been classified in a binary system with Gx[Px] based on the spike protein (VP4) and the major outer capsid glycoprotein (VP7), respectively. The emerging equine-like G3P[8] DS-1-like strains reported worldwide in humans have arisen an important concern. Here, we carry out the complete genome characterization of a previously reported G3P[8] strain in order to recognize the genetic diversity of RVA circulating among infants in Colombia. A near-full genome phylogenetic analysis was done, confirming the presence of the novel equine-like G3P[8] with a Wa-like backbone for the first time in Colombia. This study demonstrated the importance of surveillance of emerging viruses in the Colombian population; furthermore, additional studies must focus on the understanding of the spread and transmission dynamic of this important RVA strain in different areas of the country.

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Sircar, Shubhankar, Prashant Kumar, Mohd Ikram Ansari, Sudipta Bhat, Jobin Jose Kattoor, O. R. Vinodhkumar, Ranjit Sah, Kuldeep Dhama, and Yashpal Singh Malik. "Non-structural Enterotoxin (NSP4) Gene based Molecular Characterization of Caprine and Ovine Rotavirus A, India." Journal of Pure and Applied Microbiology 14, no. 4 (November 26, 2020): 2303–11. http://dx.doi.org/10.22207/jpam.14.4.09.

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Rotavirus A (RVA) causes viral gastroenteritis in humans and animals, including calves, piglets, and foals. The current study reports the genetic characterization of the full-length enterotoxin gene, NSP4, from caprine and ovine species. Upon characterizing eight full-length NSP4 genes by sequencing, it was found that the four caprine and three ovine RVAs NSP4 genes are of E2 genotype and the sole ovine RVA isolate was found to be of E1 genotype. In the sequence and phyloanalysis of the NSP4 gene the seven E2 genotypes clustered with bovine, human, and caprine isolates from India and Bangladesh, respectively. The E1 genotype of ovine RVA was closer to human RVA isolate from India. The nucleotide per cent identity analysis revealed that all E2 genotype strains of caprine and ovine species ranged from 88.4% to 90.4% and it was found common to both the reference human RVA isolates DS-1 and AU-1. Whereas, the E1 genotype ovine strain clustered with human RVA isolates with 93.1% nucleotide per cent identity. The RVA strains circulating in caprine and ovine populations may share a common origin which is usually found in artiodactyl species because humans share a common dwelling with animals. Future studies are needed to confirm these findings of their relationship with humans and large animals.

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Saikruang, Wilaiporn, Pattara Khamrin, Rungnapa Malasao, Kattareeya Kumthip, Hiroshi Ushijima, and Niwat Maneekarn. "Complete genome analysis of a rare G12P[6] rotavirus isolated in Thailand in 2012 reveals a prototype strain of DS-1-like constellation." Virus Research 224 (September 2016): 38–45. http://dx.doi.org/10.1016/j.virusres.2016.08.002.

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Luchs, Adriana, Antonio Charlys da Costa, Audrey Cilli, Shirley Cavalcante Vasconcelos Komninakis, Rita de Cássia Compagnoli Carmona, Lais Boen, Simone Guadagnucci Morillo, Ester Cerdeira Sabino, and Maria do Carmo Sampaio Tavares Timenetsky. "Spread of the emerging equine-like G3P[8] DS-1-like genetic backbone rotavirus strain in Brazil and identification of potential genetic variants." Journal of General Virology 100, no. 1 (January 1, 2019): 7–25. http://dx.doi.org/10.1099/jgv.0.001171.

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Matthijnssens, Jelle, Max Ciarlet, Erica Heiman, Ingrid Arijs, Thomas Delbeke, Sarah M. McDonald, Enzo A. Palombo, et al. "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." Journal of Virology 82, no. 7 (January 23, 2008): 3204–19. http://dx.doi.org/10.1128/jvi.02257-07.

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ABSTRACT Group A rotavirus classification is currently based on the molecular properties of the two outer layer proteins, VP7 and VP4, and the middle layer protein, VP6. As reassortment of all the 11 rotavirus gene segments plays a key role in generating rotavirus diversity in nature, a classification system that is based on all the rotavirus gene segments is desirable for determining which genes influence rotavirus host range restriction, replication, and virulence, as well as for studying rotavirus epidemiology and evolution. Toward establishing such a classification system, gene sequences encoding VP1 to VP3, VP6, and NSP1 to NSP5 were determined for human and animal rotavirus strains belonging to different G and P genotypes in addition to those available in databases, and they were used to define phylogenetic relationships among all rotavirus genes. Based on these phylogenetic analyses, appropriate identity cutoff values were determined for each gene. For the VP4 gene, a nucleotide identity cutoff value of 80% completely correlated with the 27 established P genotypes. For the VP7 gene, a nucleotide identity cutoff value of 80% largely coincided with the established G genotypes but identified four additional distinct genotypes comprised of murine or avian rotavirus strains. Phylogenetic analyses of the VP1 to VP3, VP6, and NSP1 to NSP5 genes showed the existence of 4, 5, 6, 11, 14, 5, 7, 11, and 6 genotypes, respectively, based on nucleotide identity cutoff values of 83%, 84%, 81%, 85%, 79%, 85%, 85%, 85%, and 91%, respectively. In accordance with these data, a revised nomenclature of rotavirus strains is proposed. The novel classification system allows the identification of (i) distinct genotypes, which probably followed separate evolutionary paths; (ii) interspecies transmissions and a plethora of reassortment events; and (iii) certain gene constellations that revealed (a) a common origin between human Wa-like rotavirus strains and porcine rotavirus strains and (b) a common origin between human DS-1-like rotavirus strains and bovine rotaviruses. These close evolutionary links between human and animal rotaviruses emphasize the need for close simultaneous monitoring of rotaviruses in animals and humans.

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Sashina, T. A., O. V. Morozova, N. V. Epifanova, A. U. Kashnikov, A. V. Leonov, and N. A. Novikova. "Molecular monitoring of the rotavirus (Reoviridae: Sedoreovirinae: Rotavirus: Rotavirus A) strains circulating in Nizhny Novgorod (2012–2020): detection of the strains with the new genetic features." Problems of Virology 66, no. 2 (May 15, 2021): 140–51. http://dx.doi.org/10.36233/0507-4088-46.

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Introduction. The pentavalent rotavirus vaccine has been registered in Russia, however, the vaccination coverage remains low, and an annual increase in the incidence of rotavirus infection is unavoidable. In this regard, molecular monitoring of rotaviruses in order to search for new variants possessing epidemic potential is an urgent task. Material and methods. PCR genotyping and VP4 and VP7 genes sequencing were used to characterize rotaviruses circulating in Nizhny Novgorod in 2012–2020. The phylogenetic analysis of the strains was carried out using the BEAST software package.Results. The spectrum included 17 genotypes with predominance of G9P[8] (37,4%). Detected in this study genotypes G1P[4], G1P[9], G2P[8], G4P[4], G4P[6], G8P[8], and G9P[4] were not previously identified in Nizhny Novgorod. The circulation of DS-1-like strains possessing genotypes G1P[8], G3P[8], G8P[8], or G9P[8] and a short RNA pattern had been shown. Rotaviruses of the common genotypes were genetically heterogeneous and belonged to different phylogenetic lineages and/or sublineages (P[4]-IV-a; P[4]-IV-b; P[8]-3.1; P[8]-3.3; P[8]-3.4 and P[8]-3.6; G1-I; G1-II; G2-IVa-1; G2-IVa-3; G3-1; G3-3; G4-I-c; G9-III; G9-VI).Discussion. These results extend the available data on the genotypic structure of rotavirus populations in Russia and show the genetic diversity of viral strains. G3P[8] DS-1-like viruses were representatives of the G3-1 lineage, new for the territory of Russia, and had the largest number of amino acid substitutions in the VP7 antigenic epitopes.Conclusion. The emergence and spread of strains with new genetic features may allow rotavirus to overcome the immunological pressure formed by natural and vaccine-induced immunity, and maintain or increase the incidence of rotavirus infection.

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Yuzhakov, Anton, Ksenia Yuzhakova, Nadezhda Kulikova, Lidia Kisteneva, Stanislav Cherepushkin, Svetlana Smetanina, Marina Bazarova, Anton Syroeshkin, and Tatiana Grebennikova. "Prevalence and Genetic Diversity of Group A Rotavirus Genotypes in Moscow (2019–2020)." Pathogens 10, no. 6 (May 30, 2021): 674. http://dx.doi.org/10.3390/pathogens10060674.

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Group A rotavirus (RVA) infection is the leading cause of hospitalization of children under 5 years old, presenting with symptoms of acute gastroenteritis. The aim of our study was to explore the genetic diversity of RVA among patients admitted to Moscow Infectious Disease Clinical Hospital No. 1 with symptoms of acute gastroenteritis. A total of 653 samples were collected from May 2019 through March 2020. Out of them, 135 (20.67%) fecal samples were found to be positive for rotavirus antigen by ELISA. RT-PCR detected rotavirus RNA in 80 samples. Seven G-genotypes (G1, G2, G3, G4, G8, G9, and G12) and three P-genotypes (P[8], P[4], and P[6]) formed 9 different combinations. The most common combination was G9P[8]. However, for the first time in Moscow, the combination G3P[8] took second place. Moreover, all detected viruses of this combination belonged to Equine-like G3P[8] viruses that had never been detected in Russia before. The genotype G8P[8] and G9P[4] rotaviruses were also detected in Moscow for the first time. Among the studied rotaviruses, there were equal proportions of Wa and DS-1-like strains; previous studies showed that Wa-like strains accounted for the largest proportion of rotaviruses in Russia.

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Nakagomi, Toyoko. "Vaccine Effectiveness against DS-1–Like Rotavirus Strains." Emerging Infectious Diseases 26, no. 1 (January 2020): 184. http://dx.doi.org/10.3201/eid2601.191377.

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Giammanco, Giovanni M., Floriana Bonura, Mark Zeller, Elisabeth Heylen, Marc Van Ranst, Vito Martella, Kristián Bányai, Jelle Matthijnssens, and Simona De Grazia. "Evolution of DS-1-like human G2P[4] rotaviruses assessed by complete genome analyses." Journal of General Virology 95, no. 1 (January 1, 2014): 91–109. http://dx.doi.org/10.1099/vir.0.056788-0.

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Group A rotaviruses (RVAs) are a leading cause of viral gastroenteritis in children, with G2P[4] RVA being one of the most common human strains worldwide. The complete genome sequences of nine G2P[4] RVA strains, selected from a 26-year archival collection (1985–2011) established in Palermo, Italy, were determined. A strain associated with a peak of G2P[4] RVA activity in 1996 resembled a reassortant strain identified in Kenya in 1982 and differed completely in genomic make up from more recent strains that circulated during 2004–2011. Conversely, the 2004–2011 G2P[4] RVAs were genetically more similar to contemporary RVA strains circulating globally. Recent G2P[4] strains possessed either single or multiple genome segments (VP1, VP3 and/or NSP4) likely derived from ruminant viruses through intra-genotype reassortment. Amino acid substitutions were selected and maintained over time in the VP7 and VP8* antigenic proteins, allowing the circulation of two contemporary G2P[4] variants to be distinguished. Altogether, these findings suggest that major changes in the genomic composition of recent G2P[4] RVAs occurred in the early 2000s, leading to the appearance of a novel variant of the DS-1-like genotype constellation. Whether the modifications observed in the neutralizing antigens and in the genome composition of modern G2P[4] RVAs may affect the long-term effectiveness of the vaccination programmes remains to be explored.

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Morozova, O. V., T. A. Sashina, and N. A. Novikova. "Detection and molecular characterization of reassortant DS-1-like G1P [8] strains of rotavirus A." Problems of Virology, Russian journal 62, no. 2 (April 20, 2017): 91–96. http://dx.doi.org/10.18821/0507-4088-2017-62-2-91-96.

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Group A rotaviruses (RVA) are the main cause of viral gastroenteritis in children worldwide. In this study we provide the molecular characteristics of reassortant DS-1-like G1P[8] RVA strains detected in Russia for the first time. Previously, such reassortant strains were detected in Japan and Thailand. The G1P[8] RVAs with DS-1-like short electropherotype RNA-PAGE were isolated from children hospitalised with an acute gastroenteritis during the 2013-2014 period. The DS-1-like G1P[8] strains accounted for 2.6% of all RVA strains detected continuously throughout the season. A phylogenetic analysis was made on the basis of the established nucleotide sequences of genes VP7, VP8* (VP4), VP6 and NSP4. The Nizhny Novgorod strains belong to G1-I and G1-II alleles of VP7 gene and to P[8]-3 allele of VP4. According to their VP6 sequences, two Russian samples clustered with the reassortant strains isolated in Japan, Thailand and Australia and two other strains were phylogenetically close to the typical G2P[4] DS-1-like RVA. Nucleotide sequences of G1P[8] strains that belong to NSP4 gene form a separate cluster from G3P[8] DS-1-like rotaviruses detected in Thailand and Australia. The RVA alleles included in Rotarix and RotaTeq vaccine strains were clustered separately from the studied reassortant RVAs. On the grounds of phylogenetic analysis we assume a polyphyletic origin of reassortants between Wa- and DS-1-like strains. Mutation rates evaluated by Bayesian inference in clusters with reassortant RVA strains were 1.004Е-3 (VP7), 1.227E-3 (VP4), 3.909E-4 (VP6), and 4.014Е-4 (NSP4). Analysis of tMRCA showed relatively contemporary origin of alleles DS-1-like G1P[8] rotaviruses: VP7 - 1998 (G1-I) and 1981 (G1-II), VP4 - 1998, VP6 - 1994, NSP4 - 1979.

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Komoto, Satoshi, Ratana Tacharoenmuang, Ratigorn Guntapong, Tomihiko Ide, Takao Tsuji, Tetsushi Yoshikawa, Piyanit Tharmaphornpilas, Somchai Sangkitporn, and Koki Taniguchi. "Reassortment of Human and Animal Rotavirus Gene Segments in Emerging DS-1-Like G1P[8] Rotavirus Strains." PLOS ONE 11, no. 2 (February 4, 2016): e0148416. http://dx.doi.org/10.1371/journal.pone.0148416.

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Heiman, Erica M., Sarah M. McDonald, Mario Barro, Zenobia F. Taraporewala, Tamara Bar-Magen, and John T. Patton. "Group A Human Rotavirus Genomics: Evidence that Gene Constellations Are Influenced by Viral Protein Interactions." Journal of Virology 82, no. 22 (September 10, 2008): 11106–16. http://dx.doi.org/10.1128/jvi.01402-08.

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ABSTRACT Group A human rotaviruses (HRVs) are the major cause of severe viral gastroenteritis in infants and young children. To gain insight into the level of genetic variation among HRVs, we determined the genome sequences for 10 strains belonging to different VP7 serotypes (G types). The HRVs chosen for this study, D, DS-1, P, ST3, IAL28, Se584, 69M, WI61, A64, and L26, were isolated from infected persons and adapted to cell culture to use as serotype references. Our sequencing results revealed that most of the individual proteins from each HRV belong to one of three genotypes (1, 2, or 3) based on their similarities to proteins of genogroup strains (Wa, DS-1, or AU-1, respectively). Strains D, P, ST3, IAL28, and WI61 encode genotype 1 (Wa-like) proteins, whereas strains DS-1 and 69M encode genotype 2 (DS-1-like) proteins. Of the 10 HRVs sequenced, 3 of them (Se584, A64, and L26) encode proteins belonging to more than one genotype, indicating that they are intergenogroup reassortants. We used amino acid sequence alignments to identify residues that distinguish proteins belonging to HRV genotype 1, 2, or 3. These genotype-specific changes cluster in definitive regions within each viral protein, many of which are sites of known protein-protein interactions. For the intermediate viral capsid protein (VP6), the changes map onto the atomic structure at the VP2-VP6, VP4-VP6, and VP7-VP6 interfaces. The results of this study provide evidence that group A HRV gene constellations exist and may be influenced by interactions among viral proteins during replication.

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Tacharoenmuang, Ratana, Satoshi Komoto, Ratigorn Guntapong, Tomihiko Ide, Phakapun Sinchai, Sompong Upachai, Tetsushi Yoshikawa, Piyanit Tharmaphornpilas, Somchai Sangkitporn, and Koki Taniguchi. "Full Genome Characterization of Novel DS-1-Like G8P[8] Rotavirus Strains that Have Emerged in Thailand: Reassortment of Bovine and Human Rotavirus Gene Segments in Emerging DS-1-Like Intergenogroup Reassortant Strains." PLOS ONE 11, no. 11 (November 1, 2016): e0165826. http://dx.doi.org/10.1371/journal.pone.0165826.

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Agbemabiese, Chantal Ama, Toyoko Nakagomi, Minh Quang Nguyen, Punita Gauchan, and Osamu Nakagomi. "Reassortant DS-1-like G1P[4] Rotavirus A strains generated from co-circulating strains in Vietnam, 2012/2013." Microbiology and Immunology 61, no. 8 (August 2017): 328–36. http://dx.doi.org/10.1111/1348-0421.12501.

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Jere, Khuzwayo C., Naor Bar-Zeev, Adams Chande, Aisleen Bennett, Louisa Pollock, Pedro F. Sanchez-Lopez, Osamu Nakagomi, et al. "Vaccine Effectiveness against DS-1–Like Rotavirus Strains in Infants with Acute Gastroenteritis, Malawi, 2013–2015." Emerging Infectious Diseases 25, no. 9 (September 2019): 1734–37. http://dx.doi.org/10.3201/eid2509.190258.

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Komoto, Satoshi, Tomihiko Ide, Manami Negoro, Takaaki Tanaka, Kazutoyo Asada, Masakazu Umemoto, Haruo Kuroki, et al. "Characterization of unusual DS‐1‐like G3P[8] rotavirus strains in children with diarrhea in Japan." Journal of Medical Virology 90, no. 5 (February 5, 2018): 890–98. http://dx.doi.org/10.1002/jmv.25016.

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Fukuda, Saori, Ratana Tacharoenmuang, Ratigorn Guntapong, Sompong Upachai, Phakapun Singchai, Tomihiko Ide, Riona Hatazawa, et al. "Full genome characterization of novel DS-1-like G9P[8] rotavirus strains that have emerged in Thailand." PLOS ONE 15, no. 4 (April 22, 2020): e0231099. http://dx.doi.org/10.1371/journal.pone.0231099.

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Matthijnssens, J., M. Rahman, X. Yang, T. Delbeke, I. Arijs, J. P. Kabue, J. J. T. Muyembe, and M. Van Ranst. "G8 Rotavirus Strains Isolated in the Democratic Republic of Congo Belong to the DS-1-Like Genogroup." Journal of Clinical Microbiology 44, no. 5 (May 1, 2006): 1801–9. http://dx.doi.org/10.1128/jcm.44.5.1801-1809.2006.

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Silva Serra, Ana C., Edivaldo CS Júnior, Jonas F. Cruz, Patrícia S. Lobo, Edvaldo TP Júnior, Renato S. Bandeira, Delana AM Bezerra, Joana DP Mascarenhas, Sylvia F. Santos Guerra, and Luana S. Soares. "Molecular analysis of G3P[6] rotavirus in the Amazon region of Brazil: evidence of reassortment with equine-like strains." Future Microbiology 16, no. 12 (August 2021): 847–62. http://dx.doi.org/10.2217/fmb-2020-0002.

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Aim: To perform a molecular analysis of rotavirus A (RVA) G3P[6] strains detected in 2012 and 2017 in the Amazon region of Brazil. Materials & methods: Eighteen RVA G3P[6] strains were collected from children aged under 10 years hospitalized with acute gastroenteritis, and partial sequencing of each segment genome was performed using Sanger sequencing. Results: Phylogenetic analysis showed that all G3P[6] strains had a DS-1-like genotype constellation. Two strains had the highest nucleotide identities with equine-like G3P[6]/G3P[8] genotypes. Several amino acid alterations in VP4 and VP7 neutralizing epitopes of equine-like RVA G3P[6] strains were observed in comparison with vaccine strains. Conclusion: These findings suggest that equine-like RVA G3P[6] strains have been circulating in the Amazon region of Brazil as a result of direct importation, and support natural RVA evolutionary mechanisms.

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Yamamoto, D., A. Tandoc, E. Mercado, F. Quicho, S. Lupisan, M. Obata-Saito, M. Okamoto, et al. "First detection of DS-1-like G1P[8] human rotavirus strains from children with diarrhoea in the Philippines." New Microbes and New Infections 18 (July 2017): 54–57. http://dx.doi.org/10.1016/j.nmni.2017.04.001.

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Komoto, Satoshi, Ratana Tacharoenmuang, Ratigorn Guntapong, Tomihiko Ide, Kei Haga, Kazuhiko Katayama, Takema Kato, et al. "Emergence and Characterization of Unusual DS-1-Like G1P[8] Rotavirus Strains in Children with Diarrhea in Thailand." PLOS ONE 10, no. 11 (November 5, 2015): e0141739. http://dx.doi.org/10.1371/journal.pone.0141739.

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Hoa-Tran, T. N., T. Nakagomi, H. M. Vu, L. P. Do, P. Gauchan, C. A. Agbemabiese, T. T. T. Nguyen, O. Nakagomi, and N. T. H. Thanh. "Abrupt emergence and predominance in Vietnam of rotavirus A strains possessing a bovine-like G8 on a DS-1-like background." Archives of Virology 161, no. 2 (November 19, 2015): 479–82. http://dx.doi.org/10.1007/s00705-015-2682-x.

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Nyaga, Martin M., Karla M. Stucker, Mathew D. Esona, Khuzwayo C. Jere, Bakari Mwinyi, Annie Shonhai, Enyonam Tsolenyanu, et al. "Whole-genome analyses of DS-1-like human G2P[4] and G8P[4] rotavirus strains from Eastern, Western and Southern Africa." Virus Genes 49, no. 2 (June 22, 2014): 196–207. http://dx.doi.org/10.1007/s11262-014-1091-7.

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Fujii, Yoshiki, Toyoko Nakagomi, Naoko Nishimura, Atsuko Noguchi, Sinobu Miura, Hisato Ito, Yen Hai Doan, et al. "Spread and predominance in Japan of novel G1P[8] double-reassortant rotavirus strains possessing a DS-1-like genotype constellation typical of G2P[4] strains." Infection, Genetics and Evolution 28 (December 2014): 426–33. http://dx.doi.org/10.1016/j.meegid.2014.08.001.

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Nakagomi, Toyoko, Minh Quang Nguyen, Punita Gauchan, Chantal Ama Agbemabiese, Miho Kaneko, Loan Phuong Do, Thiem Dinh Vu, and Osamu Nakagomi. "Evolution of DS-1-like G1P[8] double-gene reassortant rotavirus A strains causing gastroenteritis in children in Vietnam in 2012/2013." Archives of Virology 162, no. 3 (November 23, 2016): 739–48. http://dx.doi.org/10.1007/s00705-016-3155-6.

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Donato, Celeste, Nevada Pingault, Elena Demosthenous, Susie Roczo-Farkas, and Julie Bines. "Characterisation of a G2P[4] Rotavirus Outbreak in Western Australia, Predominantly Impacting Aboriginal Children." Pathogens 10, no. 3 (March 16, 2021): 350. http://dx.doi.org/10.3390/pathogens10030350.

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In May, 2017, an outbreak of rotavirus gastroenteritis was reported that predominantly impacted Aboriginal children ≤4 years of age in the Kimberley region of Western Australia. G2P[4] was identified as the dominant genotype circulating during this period and polyacrylamide gel electrophoresis revealed the majority of samples exhibited a conserved electropherotype. Full genome sequencing was performed on representative samples that exhibited the archetypal DS-1-like genome constellation: G2-P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2 and phylogenetic analysis revealed all genes of the outbreak samples were closely related to contemporary Japanese G2P[4] samples. The outbreak samples consistently fell within conserved sub-clades comprised of Hungarian and Australian G2P[4] samples from 2010. The 2017 outbreak variant was not closely related to G2P[4] variants associated with prior outbreaks in Aboriginal communities in the Northern Territory. When compared to the G2 component of the RotaTeq vaccine, the outbreak variant exhibited mutations in known antigenic regions; however, these mutations are frequently observed in contemporary G2P[4] strains. Despite the level of vaccine coverage achieved in Australia, outbreaks continue to occur in vaccinated populations, which pose challenges to regional areas and remote communities. Continued surveillance and characterisation of emerging variants are imperative to ensure the ongoing success of the rotavirus vaccination program in Australia.

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Strydom, Amy, Eva Dora João, Lithabiso Motanyane, Martin M. Nyaga, A. Christiaan Potgieter, Assa Cuamba, Inacio Mandomando, Marta Cassocera, Nilsa de Deus, and Hester G. O'Neill. "Whole genome analyses of DS-1-like Rotavirus A strains detected in children with acute diarrhoea in southern Mozambique suggest several reassortment events." Infection, Genetics and Evolution 69 (April 2019): 68–75. http://dx.doi.org/10.1016/j.meegid.2019.01.011.

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Hoa-Tran, Thi Nguyen, Toyoko Nakagomi, Hung Manh Vu, Chikako Kataoka, Trang Thi Thu Nguyen, Anh Thi Hai Dao, Anh The Nguyen, et al. "Whole genome characterization of feline-like G3P[8] reassortant rotavirus A strains bearing the DS-1-like backbone genes detected in Vietnam, 2016." Infection, Genetics and Evolution 73 (September 2019): 1–6. http://dx.doi.org/10.1016/j.meegid.2019.04.007.

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Hoa-Tran, Thi Nguyen, Toyoko Nakagomi, Hung Manh Vu, Trang Thu Thi Nguyen, Taichiro Takemura, Futoshi Hasebe, Anh Thi Hai Dao, et al. "Detection of three independently-generated DS-1-like G9P[8] reassortant rotavirus A strains during the G9P[8] dominance in Vietnam, 2016–2018." Infection, Genetics and Evolution 80 (June 2020): 104194. http://dx.doi.org/10.1016/j.meegid.2020.104194.

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Akane, Yusuke, Takeshi Tsugawa, Yoshiki Fujii, Saho Honjo, Kenji Kondo, Shuji Nakata, Shinsuke Fujibayashi, et al. "Molecular and clinical characterization of the equine-like G3 rotavirus that caused the first outbreak in Japan, 2016." Journal of General Virology 102, no. 3 (March 1, 2021). http://dx.doi.org/10.1099/jgv.0.001548.

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Since 2013, equine-like G3 rotavirus (eG3) strains have been detected throughout the world, including in Japan, and the strains were found to be dominant in some countries. In 2016, the first eG3 outbreak in Japan occurred in Tomakomai, Hokkaido prefecture, and the strains became dominant in other Hokkaido areas the following year. There were no significant differences in the clinical characteristics of eG3 and non-eG3 rotavirus infections. The eG3 strains detected in Hokkaido across 2 years from 2016 to 2017 had DS-1-like constellations (i.e. G3-P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2), and the genes were highly conserved (97.5–100 %). One strain, designated as To16-12 was selected as the representative strain for these strains, and all 11 genes of this strain (To16-12) exhibited the closest identity to one foreign eG3 strain (STM050) seen in Indonesia in 2015 and two eG3 strains (IS1090 and MI1125) in another Japanese prefecture in 2016, suggesting that this strain might be introduced into Japan from Indonesia. Sequence analyses of VP7 genes from animal and human G3 strains found worldwide did not identify any with close identity (>92 %) to eG3 strains, including equine RV Erv105. Analysis of another ten genes indicated that the eG3 strain had low similarity to G2P[4] strains, which are considered traditional DS-1-like strains, but high similarity to DS-1-like G1P[8] strains, which first appeared in Asia in 2012. These data suggest that eG3 strains were recently generated in Asia as mono-reassortant strain between DS-1-like G1P[8] strains and unspecified animal G3 strains. Our results indicate that rotavirus surveillance in the postvaccine era requires whole-genome analyses.

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Sircar, Shubhankar, Yashpal Singh Malik, Prashant Kumar, Mohd Ikram Ansari, Sudipta Bhat, S. Shanmuganathan, Jobin Jose Kattoor, et al. "Genomic Analysis of an Indian G8P[1] Caprine Rotavirus-A Strain Revealing Artiodactyl and DS-1-Like Human Multispecies Reassortment." Frontiers in Veterinary Science 7 (January 27, 2021). http://dx.doi.org/10.3389/fvets.2020.606661.

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The surveillance studies for the presence of caprine rotavirus A (RVA) are limited in India, and the data for the whole-genome analysis of the caprine RVA is not available. This study describes the whole-genome-based analysis of a caprine rotavirus A strain, RVA/Goat-wt/IND/K-98/2015, from a goat kid in India. The genomic analysis revealed that the caprine RVA strain K-98, possess artiodactyl-like and DS-1 human-like genome constellation G8P[1]-I2-R2-C2-M2-A3-N2-T6-E2-H3. The three structural genes (VP2, VP4, and VP7) were close to caprine host having nucleotide-based identity range between 97.5 and 98.9%. Apart from them, other gene segments showed similarity with either bovine or human like genes, ultimately pointing toward a common evolutionary origin having an artiodactyl-type backbone of strain K-98. Phylogenetically, the various genes of the current study isolate also clustered inside clades comprising Human-Bovine-Caprine isolates from worldwide. The current findings add to the knowledge on caprine rotaviruses and might play a substantial role in designing future vaccines or different alternative strategies combating such infections having public health significance. To the best of our knowledge, this is the first report on the whole-genome characterization of a caprine RVA G8P[1] strain from India. Concerning the complex nature of the K-98 genome, whole-genome analyses of more numbers of RVA strains from different parts of the country are needed to comprehend the genomic nature and genetic diversity among caprine RVA.

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Banga-Mingo, Virginie, Mathew D. Esona, Naga S. Betrapally, Rashi Gautam, Jose Jaimes, Eric Katz, Diane Waku-Kouomou, Michael D. Bowen, and Ionela Gouandjika-Vasilache. "Whole gene analysis of a genotype G29P[6] human rotavirus strain identified in Central African Republic." BMC Research Notes 14, no. 1 (May 31, 2021). http://dx.doi.org/10.1186/s13104-021-05634-4.

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Abstract Objective Rotavirus A (RVA) remains the main causative agent of gastroenteritis in young children and the young of many mammalian and avian species. In this study we describe a RVA strain detected from a 6-month-old child from Central African Republic (CAR). Results We report the 11 open reading frame sequences of a G29-P[6]-I2-R2-C2-M2-A2-N2-T2-E2-H2 rotavirus strain, RVA/Human-wt/CAR/CAR91/2014/G29P[6]. Nine genes (VP1–VP3, VP6, NSP1–NSP5) shared 90–100% sequence similarities with genogroup 2 rotaviruses. Phylogenetically, backbone genes, except for VP3 and NSP4 genes, were linked with cognate gene sequences of human DS-1-like genogroup 2, hence their genetic origin. The VP3 and NSP4 genes, clustered genetically with both human and animal strains, an indication genetic reassortment human and animal RVA strains has taken place. The VP7 gene shared nucleotide (93–94%) and amino acid (95.5–96.7%) identities with Kenyan and Belgian human G29 strains, as well as to buffalo G29 strain from South Africa, while the VP4 gene most closely resembled P[6]-lineage I strains from Africa and Bangladesh (97%).

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Katz, Eric M., Mathew D. Esona, Rashi Gautam, and Michael D. Bowen. "Development of a real-time reverse transcription-PCR assay to detect and quantify group A rotavirus equine-like G3 strains." Journal of Clinical Microbiology, August 25, 2021. http://dx.doi.org/10.1128/jcm.02602-20.

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Since 2013, group A rotavirus strains characterized as novel DS-1-like inter-genogroup reassortant ‘equine-like G3’ strains have emerged and spread across five continents among human populations in at least 14 countries. Here we report a novel one-step TaqMan quantitative real-time reverse transcription-PCR assay developed to genotype and quantify the viral load for samples containing rotavirus equine-like G3 strains. Using a universal G forward primer and a newly designed reverse primer and TaqMan probe, we developed and validated an assay with a linear dynamic range of 2.3 × 10 9 – 227 copies per reaction and a limit of detection of 227 copies. The percent positive agreement, percent negative agreement, and precision of our assay were 100.00%, 99.63%, and 100.00%, respectively. This assay can simultaneously detect and quantify the viral load for samples containing DS-1-like inter-genogroup reassortant equine-like G3 strains with high sensitivity and specificity, faster turnaround time, and decreased cost and will be valuable for high-throughput screening of stool samples collected to monitor equine-like G3 strain prevalence and circulation among human populations throughout the world.

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Esona, Mathew D., Rashi Gautam, Eric Katz, Jose Jaime, M. Leanne Ward, Mary E. Wikswo, Naga S. Betrapally, et al. "Comparative genomic analysis of genogroup 1 and genogroup 2 rotaviruses circulating in seven US cities, 2014–2016." Virus Evolution 7, no. 1 (January 2021). http://dx.doi.org/10.1093/ve/veab023.

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Abstract For over a decade, the New Vaccine Surveillance Network (NVSN) has conducted active rotavirus (RVA) strain surveillance in the USA. The evolution of RVA in the post-vaccine introduction era and the possible effects of vaccine pressure on contemporary circulating strains in the USA are still under investigation. Here, we report the whole-gene characterization (eleven ORFs) for 157 RVA strains collected at seven NVSN sites during the 2014 through 2016 seasons. The sequenced strains included 52 G1P[8], 47 G12P[8], 18 G9P[8], 24 G2P[4], 5 G3P[6], as well as 7 vaccine strains, a single mixed strain (G9G12P[8]), and 3 less common strains. The majority of the single and mixed strains possessed a Wa-like backbone with consensus genotype constellation of G1/G3/G9/G12-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1, while the G2P[4], G3P[6], and G2P[8] strains displayed a DS-1-like genetic backbone with consensus constellation of G2/G3-P[4]/P[6]/P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2. Two intergenogroup reassortant G1P[8] strains were detected that appear to be progenies of reassortment events between Wa-like G1P[8] and DS-1-like G2P[4] strains. Two Rotarix® vaccine (RV1) and two RV5 derived (vd) reassortant strains were detected. Phylogenetic and similarity matrices analysis revealed 2–11 sub-genotypic allelic clusters among the genes of Wa- and DS-1-like strains. Most study strains clustered into previously defined alleles. Amino acid (AA) substitutions occurring in the neutralization epitopes of the VP7 and VP4 proteins characterized in this study were mostly neutral in nature, suggesting that these RVA proteins were possibly under strong negative or purifying selection in order to maintain competent and actual functionality, but fourteen radical (AA changes that occur between groups) AA substitutions were noted that may allow RVA strains to gain a selective advantage through immune escape. The tracking of RVA strains at the sub-genotypic allele constellation level will enhance our understanding of RVA evolution under vaccine pressure, help identify possible mechanisms of immune escape, and provide valuable information for formulation of future RVA vaccines.

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Journal articles on the topic 'Rotavirus DS-1 strain'

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