RESUMO
BACKGROUND: Viral gastrointestinal infections remain a major public health concern in developing countries. In Burkina Faso, there are very limited updated data on the circulating viruses and their genetic diversity. OBJECTIVES: This study investigates the detection rates and characteristics of rotavirus A (RVA), norovirus (NoV), sapovirus (SaV) and human astrovirus (HAstV) in patients of all ages with acute gastrointestinal infection in urban and rural areas. STUDY DESIGN & METHODS: From 2018 to 2021, stool samples from 1,295 patients with acute gastroenteritis were collected and screened for RVA, NoV, SaV and HAstV. Genotyping and phylogenetic analyses were performed on a subset of samples. RESULTS: At least one virus was detected in 34.1% of samples. NoV and SaV were predominant with detection rates of respectively 10.5 and 8.8%. We identified rare genotypes of NoV GII, RVA and HAstV, recombinant HAstV strains and a potential zoonotic RVA transmission event. CONCLUSIONS: We give an up-to-date epidemiological picture of enteric viruses in Burkina Faso, showing a decrease in prevalence but a high diversity of circulating strains. However, viral gastroenteritis remains a public health burden, particularly in pediatric settings. Our data advocate for the implementation of routine viral surveillance and updated management algorithms for diarrheal disease.
Assuntos
Gastroenterite , Variação Genética , Genótipo , Norovirus , Filogenia , Rotavirus , População Rural , Humanos , Burkina Faso/epidemiologia , Gastroenterite/virologia , Gastroenterite/epidemiologia , Pré-Escolar , Lactente , Criança , Masculino , Feminino , Rotavirus/genética , Rotavirus/classificação , Rotavirus/isolamento & purificação , Adolescente , Adulto , Norovirus/genética , Norovirus/classificação , Norovirus/isolamento & purificação , Adulto Jovem , Fezes/virologia , Sapovirus/genética , Sapovirus/isolamento & purificação , Sapovirus/classificação , Pessoa de Meia-Idade , População Urbana , Recém-Nascido , Infecções por Caliciviridae/epidemiologia , Infecções por Caliciviridae/virologia , Mamastrovirus/genética , Mamastrovirus/classificação , Mamastrovirus/isolamento & purificação , Idoso , PrevalênciaRESUMO
The gut of healthy neonates is devoid of viruses at birth, but rapidly becomes colonised by normal viral commensals that aid in important physiological functions like metabolism but can, in some instances, result in gastrointestinal illnesses. However, little is known about how this colonisation begins, its variability and factors shaping the gut virome composition. Thus, understanding the development, assembly, and progression of enteric viral communities over time is key. To explore early-life virome development, metagenomic sequencing was employed in faecal samples collected longitudinally from a cohort of 17 infants during their first six months of life. The gut virome analysis revealed a diverse and dynamic viral community, formed by a richness of different viruses infecting humans, non-human mammals, bacteria, and plants. Eukaryotic viruses were detected as early as one week of life, increasing in abundance and diversity over time. Most of the viruses detected are commonly associated with gastroenteritis and include members of the Caliciviridae, Picornaviridae, Astroviridae, Adenoviridae, and Sedoreoviridae families. The most common co-occurrences involved asymptomatic norovirus-parechovirus, norovirus-sapovirus, sapovirus-parechovirus, observed in at least 40 % of the samples. Majority of the plant-derived viruses detected in the infants' gut were from the Virgaviridae family. This study demonstrates the first longitudinal characterisation of the gastrointestinal virome in infants, from birth up to 6 months of age, in sub-Saharan Africa. Overall, the findings from this study delineate the composition and variability of the healthy infants' gut virome over time, which is a significant step towards understanding the dynamics and biogeography of viral communities in the infant gut.
Assuntos
Fezes , Viroma , Humanos , África do Sul , Lactente , Estudos Longitudinais , Fezes/virologia , Recém-Nascido , Microbioma Gastrointestinal , Masculino , Feminino , Vírus/classificação , Vírus/isolamento & purificação , Vírus/genética , Metagenômica , Trato Gastrointestinal/virologia , Gastroenterite/virologia , Sapovirus/genética , Sapovirus/isolamento & purificação , Sapovirus/classificação , Norovirus/genética , Norovirus/isolamento & purificação , Norovirus/classificação , Picornaviridae/genética , Picornaviridae/classificação , Picornaviridae/isolamento & purificação , Caliciviridae/genética , Caliciviridae/isolamento & purificação , Caliciviridae/classificação , MetagenomaRESUMO
Sapovirus (SaV) is one of the pathogens related to acute gastroenteritis (AGE) in adults and children worldwide. This study reported the diversity of SaV genotypes in children with AGE in Japan from July 2014 to June 2017. Of a total of 2259 stool samples tested by using reverse transcription-PCR method and further analyzed by nucleotide sequencing, 114 (5.0%) were positive for SaV and GI.1 (83.3%) was the most predominant genotype, followed by GII.1, GIV.1, GI.2, GI.3, and GII.3 genotypes. Monthly distribution analysis demonstrated two epidemic peaks from July to December 2015 and February to May 2017. However, no detection peak was observed in 2014 and 2016. Phylogenetic analysis of the complete VP1 nucleotide sequences of these GI.1 strains revealed two major clusters of GI.1 and each of which contained GI.1 strains of both 2015 and 2017. This study suggests that the continuous surveillance of SaV is needed to monitor high genetic diversity in Japanese children with AGE.
Assuntos
Infecções por Caliciviridae/virologia , Gastroenterite/virologia , Sapovirus/genética , Doença Aguda , Infecções por Caliciviridae/epidemiologia , Proteínas do Capsídeo/genética , Criança , Pré-Escolar , Coinfecção/epidemiologia , Coinfecção/virologia , Fezes/virologia , Gastroenterite/epidemiologia , Variação Genética , Genótipo , Humanos , Japão/epidemiologia , Filogenia , Prevalência , Reinfecção/epidemiologia , Reinfecção/virologia , Sapovirus/classificação , Estações do AnoRESUMO
Human sapovirus (SaV) is an important causative agent of nonbacterial gastroenteritis in humans. However, little is known about its circulation in China. To study the prevalence and diversity of human SaV genotypes circulating in eastern China, a 3-year environmental surveillance combined with next generation sequencing (NGS) technology was conducted. A total of 36 raw sewage samples were collected from January 2017 to December 2019 in Jinan and processed. Thirty-five (97.22%) samples were positive for human SaV genome in quantitative RT-PCR assay; 33 (91.67%) samples were positive in nested RT-PCR assay on partial capsid VP1 sequence and all amplicons were further analyzed separately by NGS. Among those, ten genotypes belonging to the genogroups of GI, GII, GIV, and GV were identified by NGS, including 4 major genotypes (GI.2, GI.1, GV.1 and GI.3) and 6 uncommon genotypes (GII.5, GII.1, GII.NA1, GII.3, GI.6 and GIV.1). A temporal switch of predominant genotype was observed from GI.2 to GI.1 around June 2019. Local and foreign sequences clustered together in some branches according to phylogenetic analysis, indicating frequent transmission of various lineages in different regions of the world. Environmental surveillance provides a comprehensive picture of human SaV in China. NGS-based environmental surveillance improves our knowledge on human SaV circulating in communities greatly and should be encouraged as a sensitive surveillance tool.
Assuntos
Infecções por Caliciviridae/virologia , Sapovirus/isolamento & purificação , Esgotos/virologia , Biodiversidade , China , Monitoramento Ambiental , Genótipo , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Filogenia , Reação em Cadeia da Polimerase , Sapovirus/classificação , Sapovirus/genéticaRESUMO
Sapovirus is a common cause of acute gastroenteritis in all age groups. Sapovirus infections are seldom investigated in Spain, and its epidemiology in the country is not well known. The use of molecular diagnostic procedures has allowed a more frequent detection of sapoviruses in patients with diarrhea. A total of 2545 stool samples from patients with acute gastroenteritis attended from June 2018 to February 2020 at the Clinic University Hospital in Valencia, Spain, were analyzed by reverse transcription (RT) and real-time multiplex PCR (RT-PCR) to investigate the etiology of enteric infections. Sapovirus was the second enteric virus detected with a positive rate of 8%, behind norovirus (12.2%) and ahead of rotavirus (7.1%), astrovirus (4.9%) and enteric adenoviruses (2.9%). Most sapovirus infections occurred in infants and young children under 3 years of age (74%) with the highest prevalence in autumn and early winter. Coinfections were found in 25% of the patients with sapovirus diarrhea, mainly with other enteric viruses. Genotyping demonstrated the circulation of seven different genotypes during the study period, with a predominance of genotypes GI.1, GI.2, and GII.1. Phylogenetic analysis showed that genogroup GII strains form a cluster separated from genogroup GI and GV, being genotype GV.1 strains related to genotype GI.1 and GI.2 strains.
Assuntos
Infecções por Caliciviridae/epidemiologia , Infecções por Caliciviridae/virologia , Gastroenterite/epidemiologia , Gastroenterite/virologia , Sapovirus/genética , Fatores Etários , Infecções por Caliciviridae/diagnóstico , Coinfecção/epidemiologia , Coinfecção/microbiologia , Coinfecção/virologia , Diarreia/diagnóstico , Diarreia/epidemiologia , Diarreia/virologia , Feminino , Gastroenterite/diagnóstico , Variação Genética , Genótipo , Humanos , Masculino , Epidemiologia Molecular , Reação em Cadeia da Polimerase Multiplex , Filogenia , Prevalência , RNA Viral/genética , Sapovirus/classificação , Sapovirus/isolamento & purificação , Estações do Ano , Espanha/epidemiologiaRESUMO
On October 4, 2018, an outbreak of gastroenteritis associated with sapovirus occurred among elementary school students in Gyeonggi-do, Korea. Epidemiologic studies were conducted in a retrospective cohort approach. Using self-administered questionnaires, we collected information on symptoms and food items consumed. Of the 999 subjects, 17 developed patients that met the case definition. The main symptom was vomiting (100%), and the symptomatic age was 6-12 years. Positive samples were identified by conventional reverse transcription polymerase chain reaction for sequencing. They were classified into genotype GI.3 by phylogenetic analysis. This is the first report of an outbreak associated with sapovirus GI.3 in Korea.
Assuntos
Infecções por Caliciviridae/diagnóstico , Gastroenterite/diagnóstico , Sapovirus/isolamento & purificação , Infecções por Caliciviridae/epidemiologia , Infecções por Caliciviridae/virologia , Criança , Surtos de Doenças , Feminino , Gastroenterite/epidemiologia , Gastroenterite/virologia , Genótipo , Humanos , Masculino , Filogenia , RNA Viral/análise , República da Coreia/epidemiologia , Estudos Retrospectivos , Sapovirus/classificação , Sapovirus/genética , Instituições AcadêmicasRESUMO
PURPOSE OF REVIEW: Sapovirus, a genus in the Caliciviridae family alongside norovirus, is increasingly recognized as an important cause of childhood diarrhea. Some challenges exist in our ability to better understand sapovirus infections, including the inability to grow sapovirus in cell culture, which has hindered diagnosis and studies of immunity. Another challenge is that individuals with sapovirus infection are commonly coinfected with other enteric pathogens, complicating our ability to attribute the diarrhea episode to a single pathogen. RECENT FINDINGS: Development of molecular methods for sapovirus detection has increased our ability to measure disease prevalence. The prevalence of sapovirus varies between 1 and 17% of diarrhea episodes worldwide, with the highest burden in young children and older adults. Further, epidemiological studies have used novel approaches to account for the presence of coinfections with other enteric pathogens; one multisite cohort study of children under two years of age found that sapovirus had the second-highest attributable incidence among all diarrheal pathogens studied. SUMMARY: Especially in settings where rotavirus vaccines have been introduced, efforts to reduce the overall burden of childhood diarrhea should focus on the reduction of sapovirus transmission and disease burden.
Assuntos
Infecções por Caliciviridae/epidemiologia , Diarreia/epidemiologia , Diarreia/virologia , Gastroenterite/virologia , Sapovirus/isolamento & purificação , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Infecções por Caliciviridae/diagnóstico , Infecções por Caliciviridae/transmissão , Infecções por Caliciviridae/virologia , Criança , Pré-Escolar , Estudos de Coortes , Coinfecção/virologia , Fezes/virologia , Gastroenterite/epidemiologia , Variação Genética , Genótipo , Humanos , Incidência , Lactente , Recém-Nascido , Pessoa de Meia-Idade , Fatores de Risco , Vacinas contra Rotavirus , Sapovirus/classificação , Sapovirus/genética , Adulto JovemRESUMO
Sapoviruses are increasingly being recognized as pathogens associated with gastroenteritis in humans. Human sapoviruses are currently assigned to 18 genotypes (GI.1-7, GII.1-8, GIV.1, and GV.1-2) based on the sequence of the region encoding the major structural protein. In this study, we evaluated 11 polymerase chain reaction (PCR) assays using published and newly designed/modified primers and showed that four PCR assays with different primer combinations amplified all of the tested human sapovirus genotypes using either synthetic DNA or cDNA prepared from human sapovirus-positive fecal specimens. These assays can be used as improved broadly reactive screening tests or as tools for molecular characterization of human sapoviruses.
Assuntos
Infecções por Caliciviridae/virologia , Primers do DNA/química , Gastroenterite/virologia , Reação em Cadeia da Polimerase Via Transcriptase Reversa/métodos , Sapovirus/genética , Proteínas Estruturais Virais/genética , Sequência de Bases , Infecções por Caliciviridae/diagnóstico , Primers do DNA/genética , Fezes/virologia , Gastroenterite/diagnóstico , Expressão Gênica , Genótipo , Humanos , Tipagem Molecular/métodos , Filogenia , Sapovirus/classificação , Sapovirus/isolamento & purificação , Alinhamento de SequênciaRESUMO
Human sapovirus is a causative agent of acute gastroenteritis in all age groups. The use of full-length viral genomes has proven beneficial to investigate evolutionary dynamics and transmission chains. In this study, we developed a full-length genome sequencing platform for human sapovirus and sequenced the oldest available strains (collected in the 1970s) to analyse diversification of sapoviruses. Sequence analyses from five major genotypes (GI.1, GI.2, GII.1, GII.3, and GIV.1) showed limited intra-genotypic diversification for over 20-40 years. The accumulation of amino acid mutations in VP1 was detected for GI.2 and GIV.1 viruses, while having a similar rate of nucleotide evolution to the other genotypes. Differences in the phylogenetic clustering were detected between RdRp and VP1 sequences of our archival strains as well as other reported putative recombinants. However, the lack of the parental strains and differences in diversification among genomic regions suggest that discrepancies in the phylogenetic clustering of sapoviruses could be explained, not only by recombination, but also by disparate nucleotide substitution patterns between RdRp and VP1 sequences. Together, this study shows that, contrary to noroviruses, sapoviruses present limited diversification by means of intra-genotype variation and recombination.
Assuntos
Infecções por Caliciviridae/virologia , Evolução Molecular , Genoma Viral , Sapovirus/genética , Sequência de Bases , Fezes/virologia , Gastroenterite/virologia , Variação Genética , Genômica , Genótipo , Humanos , Filogenia , Sapovirus/classificação , Sapovirus/isolamento & purificaçãoRESUMO
In this review, we describe the distribution and genetic diversity of sapoviruses detected among humans, animals and the environment in African countries. Databases were searched for studies conducted in African countries and published between Jan 2005 and Mar 2019. Only studies where RT- PCR was used for initial detection were included in the systematic review. We identified 27 studies from 14 African countries with 18 focused on human sapoviruses, two on animal sapoviruses and seven on sapoviruses observed in the environment. Samples. The overall estimated pooled prevalence of human sapovirus infections among symptomatic and asymptomatic individuals was similar at 5.0% (95% Confidence Interval (CI): 3.0-7.0) and 2.0% (95% CI: 1.0-3.0), respectively. In environmental samples sapovirus detection rates ranged from 0% to 90% while in animal studies it was 1.7% to 34.8%. Multiple causes of gastroenteritis, sensitivity of detection method used, diversity of sapovirus strains and rotavirus vaccine coverage rate are some of the factors that could have contributed to the wide range of sapovirus detection rates that were reported. The studies reported human genogroups GI, GII, and GIV, with genogroup GI being the most prevalent. Some potential novel strains were detected from animal samples. Most studies genotyped a small portion of either the capsid and/or polymerase region. However, this is a limitation as it does not allow for detection of recombinants that occur frequently in sapoviruses. More studies with harmonized genotyping protocols that cover longer ranges of the sapovirus genome are needed to provide more information on the genomic characterization of sapoviruses circulating in African countries. Further investigations on animal to human transmission for sapoviruses are needed as inter-species transmissions have been documented for other viruses.
Assuntos
Infecções por Caliciviridae/veterinária , Infecções por Caliciviridae/virologia , Variação Genética , Sapovirus/genética , África/epidemiologia , Animais , Infecções por Caliciviridae/epidemiologia , Gastroenterite/epidemiologia , Gastroenterite/virologia , Genótipo , Humanos , Filogenia , Sapovirus/classificação , Sapovirus/isolamento & purificaçãoRESUMO
The first porcine Sapovirus (SaV) Cowden strain was discovered in 1980. To date, eight genogroups (GIII, V-IX) and three genogroups (GIII, GV, and GVI) of porcine SaVs have been detected from domestic pigs worldwide and wild boars in Japan, respectively based on the capsid sequences. Although GIII Cowden strain replicated in the villous epithelial cells and caused intestinal lesions in the proximal small intestines (mainly in duodenal and less in jejunum), leading to mild to severe diarrhea, in the orally inoculated neonatal gnotobiotic pigs, the significance of porcine SaVs in different ages of pigs with diarrhea in the field is still undetermined. This is due to two reasons: 1) similar prevalence of porcine SaVs was detected in diarrheic and non-diarrheic pigs; and 2) co-infection of porcine SaVs with other enteric pathogens is common in pigs. Diagnosis of porcine SaV infection is mainly based on the detection of viral nucleic acids using reverse transcription (RT)-PCR and sequencing. Much is unknown about these genetically diverse viruses to understand their role in pig health and to evaluate whether vaccines are needed to prevent SaV infection.
Assuntos
Infecções por Caliciviridae/epidemiologia , Infecções por Caliciviridae/veterinária , Variação Genética , Sapovirus/genética , Sapovirus/patogenicidade , Doenças dos Suínos/diagnóstico , Animais , Infecções por Caliciviridae/diagnóstico , Diarreia/veterinária , Diarreia/virologia , Fezes/virologia , Genoma Viral , Filogenia , RNA Viral/genética , Sapovirus/classificação , Suínos , Doenças dos Suínos/virologiaRESUMO
Sapoviruses (SAVs), including several genogroups (GI to GV), are one of the causes of acute gastroenteritis (AGE). In this study, viral metagenomics revealed the presence of sapoviruses of different genogroups in stool from children with AGE. Eight different complete SAV genomes were determined, of which five belonged to GI and the other three belonged to GII, GIV and GV, respectively. Although they were highly similar to published sequences, the GIV and GV were the first complete genome sequences of these SAVs found in China. In a prevalence investigation, 19% of subjects with AGE were positive for SAVs, while none of the control group was positive.
Assuntos
Infecções por Caliciviridae/virologia , Fezes/virologia , Gastroenterite/virologia , Sapovirus/isolamento & purificação , Pré-Escolar , China , Feminino , Genoma Viral , Humanos , Lactente , Masculino , Metagenômica , Filogenia , Sapovirus/classificação , Sapovirus/genéticaRESUMO
Sapovirus (SaV) and astrovirus (AstV) increasingly are recognized as cause of acute viral gastroenteritis (AGE). We evaluated the real-time RT-PCR assays RIDA®GENE SaV and viral stool panel II (RGN RT-PCR) for detection of SaV, AstV, adenovirus (AdV) F40/41 and rotavirus (RoV) in clinical stool samples (nâ¯=â¯69). Results were compared with reference singleplex RT-PCRs. The sensitivity for SaV, AstV and RoV are 100%, the specificity ranges from 98.1% to 100%. In 10 out of 11 AdV (all types) samples, the RGN RT-PCR for AdV F40/41 displayed negative results. Retrospectively, 196 stool specimens from adult patients previously tested negative for norovirus (NoV) were analyzed. In about 10% of NoV-negative stool samples, AdV (nâ¯=â¯9), RoV (nâ¯=â¯6), AstV (nâ¯=â¯3) or SaV (nâ¯=â¯3) were found. The RGN RT-PCR assays are useful for detection of enteric viruses other than NoV. This study emphasizes the need for further testing of NoV-negative stool samples in patients with AGE.
Assuntos
Adenoviridae/genética , Fezes/virologia , Gastroenterite/diagnóstico , Gastroenterite/virologia , Mamastrovirus/genética , Reação em Cadeia da Polimerase em Tempo Real/métodos , Rotavirus/genética , Sapovirus/genética , Adenoviridae/classificação , Adenoviridae/isolamento & purificação , Adulto , Feminino , Humanos , Masculino , Mamastrovirus/classificação , Mamastrovirus/isolamento & purificação , Reação em Cadeia da Polimerase em Tempo Real/normas , Reprodutibilidade dos Testes , Rotavirus/classificação , Rotavirus/isolamento & purificação , Sapovirus/classificação , Sapovirus/isolamento & purificação , Sensibilidade e Especificidade , SuíçaRESUMO
Sapoviruses (SaVs) are enteric viruses that have been detected in human and animals previously; however, SaVs have not been identified in wild boar yet. Using a metagenomics approach, we identified SaVs in fecal samples of free-living wild boars in Japan for the first time. Six of the 48 specimens identified belonged to one genogroup (G)III, one GV and four GVI SaV sequence reads. We successfully determined complete genome of GV and GVI SaV strains using the long reverse transcription PCR strategy and the 5' rapid amplification of cDNA end method. Phylogenetic tree analysis and pairwise distance calculation revealed that GV SaV detected from wild boar was related to recently assigned GV.5 strains from pig, while GVI SaV was assigned to a new genotype within GVI. Moreover, wild boar may act as a reservoir for transmission of SaVs to the pig population (and vice versa) because GIII, GV, and GVI SaVs were all detected in pigs previously.
Assuntos
Genoma Viral , Genótipo , Sapovirus/classificação , Exantema Vesicular de Suínos/virologia , Animais , Genômica/métodos , Japão , Filogenia , SuínosRESUMO
Sapovirus enteric disease affects people of all ages across the globe, in both sporadic cases and outbreak settings. Sapovirus is seldom assessed in Germany and its epidemiology in the country is essentially unknown. Thus, sapovirus occurrence and genetic diversity were studied by real-time reverse transcription polymerase chain reaction (RT-PCR) and partial sequencing of major viral structural protein (VP1) gene in two different sets of stool samples: 1) a selection of 342 diarrheal stools collected from inpatient children during 2008-2009, and 2) 5555 stool samples collected during 2010-2018 from inpatients of all age groups with gastrointestinal complaints. Results showed year-round circulation of sapoviruses, with peaks during cooler months. In total, 30 samples (8.8%) of the first and 112 samples of the second set of samples (2.0%) were sapovirus positive. Capsid gene sequencing was successful in 134/142 samples (94.4%) and showed circulation of all known human pathogenic genogroups. Genotype GI.1 predominated (31.8%), followed by GII.1 (16.7%), GII.3 (14.5%), GI.2 (13.8%) and GV.1 (12.3%). Additionally, minor circulation of GI.3, GI.6, GII.2, GII.4, GII.6 and GIV.1 was shown. Consequently, sapovirus diagnostics need broadly reactive RT-PCR protocols and should particularly be considered in infants and young children. Further studies from other sampling sites are essential to extend our knowledge on sapovirus epidemiology in Germany.
Assuntos
Infecções por Caliciviridae/epidemiologia , Infecções por Caliciviridae/virologia , Gastroenterite/epidemiologia , Gastroenterite/virologia , Variação Genética , Pacientes Internados , Sapovirus/classificação , Sapovirus/genética , Infecções por Caliciviridae/história , Criança , Pré-Escolar , Infecção Hospitalar/epidemiologia , Infecção Hospitalar/história , Infecção Hospitalar/virologia , Gastroenterite/história , Genótipo , Alemanha/epidemiologia , História do Século XXI , Humanos , Epidemiologia Molecular , Filogenia , Vigilância em Saúde Pública , Proteínas Estruturais Virais/genéticaRESUMO
Sapoviruses (SaVs) are enteric viruses belonging to the family Caliciviridae that infect humans and animals, including pigs. To date, SaVs have been classified into 19 genogroups (G) based on complete VP1 sequences; however, complete genome sequences of some SaV Gs are not yet available. In this study, we determined the full genome sequences of four SaVs (two GX and two GXI SaVs) and analyzed them together with those of other SaVs. The complete genome sequences of GX and GXI SaVs, excluding the poly(A) tails, were 7124, 7142, 7170, and 7179 nucleotides, which were shorter than those of other SaVs, except for porcine GVI and GVII viruses. Genetic characterization revealed that GX SaVs and GXI SaVs shared common features with GVI and GVII viruses, such as the first 10 amino acid residues in the ORF1 coding region, a shorter ORF1 than that of the other genogroups, and the predicted secondary structure of the 5' end of the genome and the starting region of non-structural protein/structural protein junction. Phylogenetic analyses showed that GX and GXI SaVs branched with porcine GVI, GVII, and GIX SaVs and formed a clade consisting of only porcine SaVs. These findings suggest that porcine GX and GXI SaVs together with porcine GVI, GVII, and possibly GIX SaVs, evolved from a common ancestor in the porcine population.
Assuntos
Sapovirus/genética , Suínos/virologia , Animais , Sequência de Bases , Fezes/virologia , Genoma Viral , Genótipo , Conformação de Ácido Nucleico , Filogenia , RNA Viral/genética , Sapovirus/classificaçãoRESUMO
Human sapovirus (SaV) is an important viral agent for acute diarrhea worldwide, but timely prevalence data of human SaV in South China are still lacking. In this study, a 4-year surveillance was conducted to characterize the prevalence and genetic characteristics of the circulating SaV associated with sporadic diarrhea in South China. From November 2013 to October 2017, 569 fecal samples from patients with acute diarrhea were collected. SaV was detected in 11 samples with a positive rate of 1.93%. Three human genogroups of GI, GII, and GIV were identified, including five GI.1 strains, three GI.2 strains, one GI.3 strain, one GII.8 strain, and one GIV strain. Furthermore, multiple alignments of complete capsid protein VP1 genes of five local GI.1 strains and other available GI.1 strains in GenBank were performed. Average pairwise identities were calculated at 95.33% and 99.36% at nucleotide and amino acid levels, and only six variable amino acid sites were found during its 36-years' evolution process. GI.1 strains could be further phylogenetically divided into four clusters with an approximate temporal evolution pattern, and local strains belonged to Cluster-d with other four strains from China and Japan. In summary, SaV was identified as an etiological agent responsible for sporadic gastroenteritis in Guangzhou with a low prevalence rate as in other Chinese cities, but its high genetic diversity suggested the necessity of continuous SaV surveillance in the future.
Assuntos
Infecções por Caliciviridae/epidemiologia , Infecções por Caliciviridae/virologia , Gastroenterite/epidemiologia , Gastroenterite/virologia , Sapovirus/classificação , Sapovirus/isolamento & purificação , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Criança , China/epidemiologia , Fezes/virologia , Feminino , Genótipo , Humanos , Masculino , Pessoa de Meia-Idade , Filogenia , Prevalência , Estudos Retrospectivos , Sapovirus/genética , Adulto JovemRESUMO
The efficiency of rotating biodisks and natural oxidizing lagoon procedures is investigated at a Tunisian semi-industrial pilot plant, El Menzeh I, where the wastewater is mainly provided by three different neighbouring hospital clinics. Throughout 2011, 102 wastewater samples were collected from the two mentioned wastewater treatment procedures. Results showed that the Sapovirus (SaV) frequency was approximately 29.4% using the real-time reverse transcription polymerase chain reaction (RT-PCR) technique, and about 16.6% using the conventional RT-PCR. Also, the SaV genogroups and genotypes were identified and genotyping revealed that all of the four Tunisian SaV strains obtained belonged to the two genogroups GIV.1 and GGI.3. In addition, two new genotypes, D and C, were detected. A moderate decrease in the SaV frequencies was observed at the exit of the two treatment processes and the SaV removal rate was around 90% in the natural oxidizing lagoons and 94% in the rotating biodisks procedure showing the temperate sensitivity of these viruses to the implemented biological wastewater. Therefore, an urgent disinfection process should be implemented downstream of the two biological treatment procedures for safe release of treated effluent in the different natural environments. Abbreviations: NoV: Noroviruses; SaV: Sapoviruses; EC: Electrical Conductivity; COD: Chemical Oxygen Demand; BOD5: Biological Oxygen Demand; SS: Suspended Solids; NH4-N: Ammonium Nitrogen; P-PO4: Ortho-Phosphate; AlCl3: aluminum chloride.
Assuntos
Sapovirus/isolamento & purificação , Águas Residuárias/virologia , Variação Genética , Genótipo , Eliminação de Resíduos de Serviços de Saúde/estatística & dados numéricos , Filogenia , Sapovirus/classificação , Sapovirus/genética , Estações do Ano , Tunísia , Águas Residuárias/químicaRESUMO
Norovirus (NoV) and sapovirus (SaV) are recognized as the causative agents of acute gastroenteritis, and NoV is one of the leading pathogens reported worldwide. This study reports on the distribution of NoV and SaV genotypes in children hospitalized with acute gastroenteritis in Chiang Mai, Thailand, from January 2015 to February 2017. From a total of 843 stool samples, 170 (20.2%) and 16 (1.9%) were identified as having NoV and SaV infections, respectively. Two samples (0.2%) were positive for both NoV and SaV. Of these, NoV GII.4 (57.2%) was the dominant genotype, followed by GII.2, GII.3, GII.17, GII.6, GII.7, GII.13, GII.14, GII.15, GII.21, GI.6, and GI.5. Among the NoV GII.4 variants, Sydney 2012 was the dominant variant during the period 2015-2016, while the other variants detected in this study were Asia 2003 and New Orleans 2009. Interestingly, an increase of NoV GII.2 was observed in 2016 and 2017. Characterization of partial RNA-dependent RNA polymerase and VP1 nucleotide sequences of GII.2 strains revealed that more than half of the GII.2 strains circulating in 2016 and 2017 were recombinant strains of GII.P16/GII.2. For SaV, the majority of strains belonged to GI.1 (55.6%) and GI.2 (33.3%), while GII.5 accounted for 11.1%. In conclusion, this study demonstrates the diversity of NoV and SaV, and the emergence of NoV GII.P16/GII.2 recombinant strains in 2016 and 2017 in Chiang Mai, Thailand.
Assuntos
Infecções por Caliciviridae/virologia , Doenças Transmissíveis Emergentes/virologia , Genótipo , Norovirus/genética , Recombinação Genética , Sapovirus/genética , Adolescente , Infecções por Caliciviridae/epidemiologia , Criança , Pré-Escolar , Doenças Transmissíveis Emergentes/epidemiologia , Fezes/virologia , Feminino , Hospitalização , Humanos , Lactente , Masculino , Epidemiologia Molecular , Norovirus/classificação , Norovirus/isolamento & purificação , Estudos Prospectivos , Sapovirus/classificação , Sapovirus/isolamento & purificação , Tailândia/epidemiologiaRESUMO
Sapoviruses are associated with acute gastroenteritis. Human sapoviruses are classified into four distinct genogroups (GI, GII, GIV, and GV) based on their capsid gene sequences. A TaqMan probe-based real-time reverse transcription-polymerase chain reaction (RT-PCR) assay that detects the representative strains of these four genogroups is widely used for screening fecal specimens, shellfish, and environmental water samples. However, since the development of this test, more genetically diverse sapovirus strains have been reported, which are not detectable by the previously established assays. In this study, we report the development of a broader-range sapovirus real-time RT-PCR assay. The assay can detect 2.5 × 107 and 2.5 × 10 1 copies of sapovirus and therefore is as sensitive as the previous test. Analysis using clinical stool specimens or synthetic DNA revealed that the new system detected strains representative of all the 18 human sapovirus genotypes: GI.1-7, GII.1-8, GIV.1, and GV.1, 2. No cross-reactivity was observed against other representative common enteric viruses (norovirus, rotavirus, astrovirus, and adenovirus). This new assay will be useful as an improved, broadly reactive, and specific screening tool for human sapoviruses.