Enteric viruses other than rotavirus and norovirus in children under 5 years of age with gastroenteritis in Argentina, 2010-2021. A descriptive study. / Virus entéricos distintos de rotavirus y norovirus en menores de 5 años con gastroenteritis en Argentina, 2010-2021. Estudio descriptivo.

Introduction. Data on the frequency of enteric adenoviruses, sapoviruses, and astroviruses in cases of sporadic acute gastroenteritis in Argentina are scarce. Methods. Descriptive design of a selection of fecal samples of children with diarrhea younger than 5 years referred between 2010 and 2021, with a previous negative result for rotavirus and norovirus. The presence of enteric adenovirus, sapovirus, and astrovirus was tested by molecular methods, with subsequent genotyping of positive samples. Results. At least 1 of the tested viruses was detected in 226 (39.4%) of the 574 selected samples. Specifically, adenovirus, sapovirus, and astrovirus were detected in 30.7%, 5.6%, and 3.1% of the samples, respectively. The most frequent viruses detected were adenovirus 41, sapoviruses GI.1 and GI.2, and astrovirus 1. Non-classic astroviruses were detected in 2 samples. Conclusions. Despite being less frequent, these enteropathogens are responsible for a large number of sporadic diarrhea events. Therefore, their study and surveillance contribute significantly to reduce the gap of undiagnosed cases.

Introducción. Los datos de frecuencia de los adenovirus entéricos, sapovirus y astrovirus en casos de gastroenteritis aguda esporádica en Argentina son escasos. Métodos. Diseño descriptivo sobre una selección de muestras de heces de menores de 5 años con diarrea remitidas durante el período 2010-2021, con resultado previo negativo para rotavirus y norovirus. Se estudió la presencia de adenovirus entéricos, sapovirus y astrovirus por métodos moleculares, con posterior genotipificación de las muestras positivas. Resultados. De 574 muestras seleccionadas, en 226 (39,4 %) se identificó al menos uno de los virus estudiados. En particular, se detectaron adenovirus, sapovirus y astrovirus en el 30,7 %, el 5,6 % y el 3,1 %, respectivamente. El adenovirus 41, los sapovirus GI.1 y GI.2, y el astrovirus 1 fueron los más frecuentemente detectados. Se identificaron dos muestras con astrovirus no clásicos. Conclusiones. A pesar de ser menos frecuentes, estos enteropatógenos son responsables de un número considerable de episodios de diarrea esporádica. Por lo tanto, su estudio y vigilancia contribuye significativamente a reducir la brecha de casos no diagnosticados.

Genome-wide analyses of human noroviruses provide insights on evolutionary dynamics and evidence of coexisting viral populations evolving under recombination constraints.

Norovirus is a major cause of acute gastroenteritis worldwide. Over 30 different genotypes, mostly from genogroup I (GI) and II (GII), have been shown to infect humans. Despite three decades of genome sequencing, our understanding of the role of genomic diversification across continents and time is incomplete. To close the spatiotemporal gap of genomic information of human noroviruses, we conducted a large-scale genome-wide analyses that included the nearly full-length sequencing of 281 archival viruses circulating since the 1970s in over 10 countries from four continents, with a major emphasis on norovirus genotypes that are currently underrepresented in public genome databases. We provided new genome information for 24 distinct genotypes, including the oldest genome information from 12 norovirus genotypes. Analyses of this new genomic information, together with those publicly available, showed that (i) noroviruses evolve at similar rates across genomic regions and genotypes; (ii) emerging viruses evolved from transiently-circulating intermediate viruses; (iii) diversifying selection on the VP1 protein was recorded in genotypes with multiple variants; (iv) non-structural proteins showed a similar branching on their phylogenetic trees; and (v) contrary to the current understanding, there are restrictions on the ability to recombine different genomic regions, which results in co-circulating populations of viruses evolving independently in human communities. This study provides a comprehensive genetic analysis of diverse norovirus genotypes and the role of non-structural proteins on viral diversification, shedding new light on the mechanisms of norovirus evolution and transmission.

Norovirus passive surveillance as an alternative strategy for genetic diversity assessment in developing countries.

In developing countries, the acute gastroenteritis outbreaks submitted for viral testing are limited due to deficient surveillance programs. The aim of this study was to analyze a passive surveillance strategy for monitoring the molecular epidemiology of norovirus (NV) and counterbalance the genetic diversity data gap. Laboratory-confirmed rotavirus negative sporadic stool samples (N = 523) collected between 2010 and 2017 from children were selected from our archival collection and were tested for NV and sequencing was performed on the positive samples. Passive surveillance information was compared with the genetic diversity data that was available from local norovirus-confirmed gastroenteritis outbreaks. Each year, norovirus detection in the sporadic samples ranged from 12 to 29%. GI and GII norovirus were detected in 7 (1.3%) and 101 (19.3%) of the specimens, respectively. Four GI and six GII capsid genotypes were identified. Six out of 9 strains detected in the NV outbreaks panel were also identified in the set of sporadic samples either coincidently in the same year, the previous or the later year. Also, this set of samples depicted even better the circulating epidemic strain. Thus, implementing norovirus testing and genotyping in stool samples collected with other purposes represent a suitable strategy for providing genetic diversity information.

Persistent infection with a rotavirus vaccine strain in a child suffering from Severe Combined Immunodeficiency in Argentina.

Due to the high burden of disease associated with rotavirus, the massive vaccination in children before six months of age has been encouraged. Currently licensed oral live vaccines have shown low risk of associated adverse events in the general population. Noteworthy, postmarketing reports of severe gastroenteritis with persistent vaccine viral shedding in children with severe combined immunodeficiency (SCID) have led companies to include this inborn error of immunity as an additional contraindication. SCID is not usually screened in newborns from developing countries. Therefore, the administration of live attenuated vaccines represents the first contact of these patients with life-threatening pathogens. We describe a clinical case of an infant with SCID who suffered from persistent rotavirus symptomatic diarrhea after receiving the rotavirus oral vaccine and was found to be infected with the vaccine strain. This case attempts to contribute to the discussion of those diseases that need to be incorporated into a screening program since an early diagnosis permits clinicians to withhold live attenuated immunization.

Molecular epidemiology of norovirus outbreaks in Argentina, 2013-2018.

Noroviruses are a leading cause of endemic and epidemic acute gastroenteritis in all age groups. However, in Latin America, there are limited and updated data regarding circulating genotypes. The aim of this study was to assess the prevalence and genetic diversity of norovirus outbreaks in Argentina from 2013 to 2018. Stool samples from 29 acute gastroenteritis (AGE) outbreaks were available for viral testing. Norovirus was detected in samples from 18 (62.1%) outbreaks (2 GI and 16 GII). Both GI outbreaks were typed as GI.6[P11] whereas 10 different GII genotypes were detected, in which GII.4 viruses were the most frequently detected (29.4%, associated with GII.P31 and GII.P16) followed by GII.1[P33] and GII.6[P7] (17.6% each). Like GII.4 viruses, GII.2 viruses were also detected in association with different polymerases (GII.P2 and GII.P16). Our findings underscore the importance of dual RNA-dependent RNA polymerase-VP1 typing since recombinant strains with new polymerase sequences emerge frequently suggesting a possible role in improved fitness of these viruses. This study represents the most recent multi-year assessment of the molecular epidemiology of norovirus strains associated with AGE outbreaks in Argentina. Molecular surveillance of norovirus has to be considered to monitor possible changes in dominant genotypes which may assist to inform the formulation of future vaccines.

Recombinant Nontypeable Genotype II Human Noroviruses in the Americas.

We report multiple nontypeable genotype II noroviruses circulating in South America; nucleotides differed by >25% from those of other genotypes. These viruses have been circulating in the Americas for ≈20 years and show recombination with other genotypes. Clues to norovirus natural history can guide development of treatment and prevention plans.

Detection of novel GII.17 norovirus in Argentina, 2015.

During the winter of 2014-2015 a novel GII.17 norovirus strain emerged as a cause of large gastroenteritis outbreaks in Asia; displacing the long-term predominant strain, GII.4. Although sporadically detected, the emerging GII.17 virus was described in North America and Europe. In this study, we describe the presence of this novel strain in Argentina (South America), and provide new information on the genetic diversity of GII.17 noroviruses. Ten stool samples from individuals (1-88years old; median: 5years old) experiencing gastroenteritis symptoms from San Martín de los Andes, Argentina were tested for Norovirus using RT-PCR. Subsequently, Norovirus positive samples were analyzed by sequencing. Norovirus was found in four out of 10 samples received. Partial sequencing of the ORF2 was available for 3/4 samples: two samples belonged to genotype GII.4 and one to genotype GII.17 (Arg13099). Sequence analyses of the VP1 encoding region revealed that the GII.17 Argentinean strain presented characteristics from both, the new (cluster C), and older (cluster A and B) GII.17 strains. Phylogenetic and sequence analyses of the RdRp region showed that this strain was closely related to strains from genotypes GII.P3, GII.P13 and GII.P17; however, did not cluster within any of them. This study represents the first report of this emergent strain in South America, and presents further evidence of the genetic plasticity of the GII.17.

Increased frequency of rotavirus G3P[8] and G12P[8] in Argentina during 2008-2009: whole-genome characterization of emerging G12P[8] strains.

BACKGROUND: Group A rotaviruses are the leading cause of non-bacterial severe diarrhea disease in infants and young children. In humans, the most common genotypes are G1-G4 and G9. Recently, G12 strains have been sporadically reported in several countries, including Argentina, Brazil and Paraguay. OBJECTIVES: To analyze rotavirus strain diversity in Argentina during 2008-2009 and to describe the whole genome-based classification of emerging G12P[8] strains detected in our country. STUDY DESIGN: Rotavirus positive-samples (n=544) were collected from Argentinean children during 2008-2009, as a part of the National Surveillance Network for Viral Diarrheas. Specimens were genotyped by reverse transcription-polymerase chain reaction (RT-PCR) followed by nested-multiplex PCR. Sequencing of 11 genome segments was performed in 3 randomly selected G12P[8] strains. RESULTS: G9P[8] was the most frequent strain in 2008, but in 2009 G3P[8] and G12P[8] were the most frequent strains in different geographical regions of the country. The novel emerging G12P[8] strains presented the following combination of genes: G12-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1 (i.e. genotype1, Wa-like strains). The phylogenetic analysis of the VP7 gene of the G12P[8] strains grouped them within lineage III. Previously reported Argentinean G12P[9] strains presented genes from genotype 3 (AU-1-like strains) with a VP7 gene from lineage II. CONCLUSIONS: The emergence of G12P[8] rotaviruses was due to the introduction of a new strain, rather than to a reassortment of the G12P[9] strains previously circulating in our country. This study assesses the temporal and geographical changes in genotypes prevalence as well as the periodic emergence of unusual G genotypes.

Burden and typing of rotavirus group A in Latin America and the Caribbean: systematic review and meta-analysis.

The efficacy of licensed rotavirus vaccines has only been shown against certain rotavirus group A (RV-A) types. It is critical to understand the burden of rotavirus gastroenteritis (RVGE) and its prevalent types to assess the potential impact of these vaccines in Latin America and the Caribbean (LA&C). We performed a systematic review and meta-analyses of all the available evidence reported from 1990 to 2009 on the burden of rotavirus disease and strains circulating in LA&C. Eligible studies--185 country-level reports, 174 951 faecal samples--were selected from MEDLINE, Cochrane Library, EMBASE, LILACS, regional Ministries of Health, PAHO, regional proceedings, doctoral theses, reference lists of included studies and consulting experts. Arc-sine transformations and DerSimonian-Laird random-effects model were used for meta-analyses. The proportion of gastroenteritis cases due to rotavirus was 24.3% (95%CI 22.3-26.4) and the incidence of RVGE was 170 per 1000 children-years (95%CI 130-210). We estimated a global annual mortality for 22 countries of 88.2 (95%CI 79.3-97.1) deaths per 100 000 under 5 years (47 000 deaths).The most common G type detected was G1 (34.2%), followed by G9 (14.6%), and G2 (14.4%). The most common P types detected were P[8] (56.2%), P[4] (22.1%) and P[1] 5.4%, and the most prevalent P-G type associations were P[8]G1 17.9%, P[4]G2 9.1% and P[8]G9 8.8%. In the last 10 years, G9 circulation increased remarkably and G5 almost disappeared. More recently, G12 appeared and P[4]G2 re-emerged. To our knowledge, this is the first meta-analysis of rotavirus infection and burden of disease in LA&C.

National Rotavirus Surveillance in Argentina: high incidence of G9P[8] strains and detection of G4P[6] strains with porcine characteristics.

Group A rotaviruses are the most frequently detected viral agents associated with diarrhea in infants and children worldwide. It has been estimated that every year almost 120,000 cases of diarrhea associated with rotavirus occur in children under 5 years old in Argentina. In this work, we present the rotavirus strain diversity detected during the first 2 years of the National Surveillance Network for Diarrheas implemented by the Ministry of Health in Argentina. During 2006 and 2007 a total of 464 rotavirus positive samples were G and P genotyped. The predominant genotype combination was G9P[8] (54.1%), followed by G2P[4] (26.5%) and G4P[8] (4.3%). Of note is that four samples were found possessing the G3 genotype, and two the genotype combination G4P[6]. The phylogenetic analysis of the VP7 gene grouped the Argentinean G9 and G3 strains within the lineages currently circulating in humans worldwide, i.e. lineages III and Ia respectively; however, the sequence and phylogenetic analyses of the VP7, NSP4 and the VP8* fragment from the Argentinean G4P[6] strains suggest a porcine origin. In agreement with this, the phylogenetic tree of the VP7 gene from G4 strains suggests the presence of at least two porcine lineages currently circulating in the Americas. In addition, the inclusion of new sequences available in public databases and the sequences reported in this work allowed us to describe new lineages and sublineages within the G4 and P[6] genotypes.

Molecular characterization of calicivirus strains detected in outbreaks of gastroenteritis in Argentina.

Eight outbreaks of acute gastroenteritis occurred in Argentina in 2004 were tested for the presence of Calicivirus, Rotavirus and Astrovirus as possible causative agents. Caliciviruses were found in 39 out of the 100 tested samples, followed by six Astrovirus-positive samples and two Rotavirus-positive samples. Thirty-seven out of the 39 Calicivirus-positive samples were typed as Norovirus while the remaining two were typed as Sapovirus. Sequence and phylogenetic analyses of 13 Norovirus-positive samples revealed the presence of strains from the genogroups GI, GII, and GIV. Six Norovirus strains were grouped with the GIV-1 strains, three with the GIIb strains, two with the Farmington Hill-cluster (GII-4) strains, and the remaining two with the GI strains. To our knowledge, this study constitutes the first report of molecular epidemiology of human Caliciviruses associated to gastroenteritis outbreaks in Argentina and the circulation of GIIb and GIV-1 strains in South-America.

Detection of human rotavirus G9P[8] strains circulating in Argentina: phylogenetic analysis of VP7 and NSP4 genes.

During the surveillance of rotavirus strains that were circulating in Argentinean children from 2000 to 2004, seven rotaviruses were detected bearing the genotype combination G9P[8]. The molecular characterization of the VP7 and NSP4 genes and the RNA migration patterns support the hypothesis that rotaviruses G9 could have been reintroduced into Argentina as a novel G9P[8] strain, rather than represent VP7 gene reassortants from G9P[6] strains that had been circulating previously in this country.