scholarly journals Multiple novel astrovirus species in human stool

2009 ◽  
Vol 90 (12) ◽  
pp. 2965-2972 ◽  
Author(s):  
A. Kapoor ◽  
L. Li ◽  
J. Victoria ◽  
B. Oderinde ◽  
C. Mason ◽  
...  

Diarrhoea remains a significant cause of morbidity and mortality in developing countries where numerous cases remain without identified aetiology. Astroviruses are a recently identified cause of animal gastroenteritis which currently includes two species suspected of causing human diarrhoea. Using pan-astrovirus RT-PCR, we analysed human stool samples from different continents for astrovirus-related RNA sequences. We identified variants of the two known human astrovirus species plus, based on genetic distance criteria, three novel astrovirus species all distantly related to mink and ovine astroviruses, which we provisionally named HMOAstV species A–C. The complete genome of species A displayed all the conserved characteristics of mammalian astroviruses. Each of the now three groups of astroviruses found in human stool (HAstV, AstV-MLB and HMOAstV) were more closely related to animal astroviruses than to each other, indicating that human astroviruses may periodically emerge from zoonotic transmissions. Based on the pathogenic impact of their closest phylogenetic relatives in animals, further investigations of the role of HMOAstV, so far detected in Nigeria, Nepal and Pakistan, in human gastroenteritis are warranted.

2021 ◽  
Vol 10 (15) ◽  
Author(s):  
Arnold W. Lambisia ◽  
My V. T. Phan ◽  
Zaydah R. de Laurent ◽  
Matthew Cotten ◽  
D. James Nokes ◽  
...  

ABSTRACT Here, using a sequence-independent sequencing approach (M. V. Phan, P. Hong Anh, N. Van Cuong, B. Oude Munnink, et al., Virus Evol 2:vew027, 2016, https://doi.org/10.1093/ve/vew027), we determined human astrovirus (HAstV) genome sequences from eight diarrheal stool samples collected in coastal Kenya in 2019. Phylogenetic analysis identified the following 4 genotypes: HAstV-1 (n = 4), HAstV-2 (n = 1), HAstV-3 (n = 1), and HAstV-5 (n = 2).


2021 ◽  
Vol 11 ◽  
Author(s):  
Sanjaya Kumar Shrestha ◽  
Jasmin Shrestha ◽  
Ashild K. Andreassen ◽  
Tor A. Strand ◽  
Susanne Dudman ◽  
...  

Objective: This study describes the types of Human astroviruses detected in stool samples collected from a birth cohort of children in Nepal.Methods: Using a commercial kit (ProSpecT), a total of 5,224 diarrheal and non-diarrheal stool samples were screened for Human astrovirus by ELISA. RT-PCR was performed on ELISA positive samples (2.8%) for further confirmation. The primary RT-PCR assay used targets the ORF2 region and detects human astrovirus type 1–8. Samples that were negative in this assay were further analyzed using primers that target the ORF1b region of human astrovirus which detect both classical type (HAstV 1–8) and novel types (MLB1–5, VA 1–5). PCR positive samples were analyzed by Sanger sequencing to determine the genotype.Results: A total of 148 available ELISA positive stool samples were analyzed by RT-PCR and further genotyped. RT-PCR analysis of these samples using the ORF2 and ORF1b assay revealed that 124 (84%) were positive for classical human types (HAstV 1–8). Seven different classical HAstV genotypes based on ORF2 and ORF1a were identified (HAstV 1- HAstV 8) with the greatest prevalence of HAstV 5 genotype (42.2%), followed by HAstV 1 (34.7%), HAstV 2 and HAstV 8 (7.4%), HAstV 4 (4.1%), HAstV 3 (3.3%), and HAstV 6 (0.8%). Non-classical types were not detected in our study.Conclusion: A high diversity of circulating Astrovirus strains were detected in young children, both with and without symptoms of gastroenteritis. HAstV 5 and HAstV 1 were the most common genotypes in young children in Nepal.


mSphere ◽  
2019 ◽  
Vol 4 (6) ◽  
Author(s):  
Francisco J. Pérez-Rodriguez ◽  
Gael Vieille ◽  
Lara Turin ◽  
Soner Yildiz ◽  
Caroline Tapparel ◽  
...  

ABSTRACT Human astroviruses (HAstV) are among the most common causative agents of viral gastroenteritis, especially in children, and extraintestinal manifestations have also been described. These viruses are transmitted by the fecal-oral route, implying that stool composition and the gut microbiota may impact their ability to remain infectious. For some enteric viruses, individual bacterial envelope components and other polysaccharide-containing molecules, which are abundant in stools, have been shown to enhance capsid stability. However, the role of the complex stool environment and, most importantly, the role of interindividual differences have been poorly studied. We used HAstV as a model to investigate how the stool environment in itself, its interindividual variability, and some specific stool components could affect HAstV stability and infectivity. Using two different HAstV genotypes, we found that stools as a whole modulate astrovirus infectivity not only in an individual-dependent manner but also in a manner that depends on the viral genotype. A virus-protective effect was observed after incubation with various Gram-positive and Gram-negative bacteria as well as with bacterial components, such as lipopolysaccharide and peptidoglycan. These results were further confirmed in human intestinal tissues, a more physiologically relevant system. Astrovirus infectivity was also preserved by mucin, a major component of intestinal mucus. We further confirmed that these components stabilize the viral capsid. These results show that although HAstV benefits from the stabilizing effect of fecal components, the complexity and variability of the stool composition and the multiple potential interactions may explain the interindividual differences in viral transmission observed in real life. IMPORTANCE To ensure transmission, enteric viruses must maintain their infectivity during the various environmental challenges that they face in transit within and between hosts. Increased knowledge of the factors affecting enteric virus survival may help to control their transmission. This study reveals that specific fecal bacterial components preserve classic human astrovirus infectivity by stabilizing viral particles. However, the outcomes of stool-virus interactions are very variable, ranging from protection to a reduction of viral infectivity, depending on the viral genotype and the individual from whom the stool has been collected. We show that the transmissibility of enteric viruses is dependent on the intestinal contents of the infected individual and highlight the complex multiple interactions that could explain the stochastic nature of enteric virus transmission in humans.


2019 ◽  
Vol 55 (1) ◽  
pp. 48
Author(s):  
Reza Gunadi Ranuh ◽  
Alpha Fardah Athiyyah ◽  
Deanty Ayu PA ◽  
Andy Darma ◽  
Dadik Rahardjo ◽  
...  

In developing countries, Norovirus is the second-leading cause of acute diarrhea, after rotavirus. The approved gold standard method for diagnosis of norovirus infection is RT-PCR. The rapid immunochromatographic test is a novel and expedient method for diagnosing norovirus that is relatively affordable. However, the use of the rapid immunochromatographic test remains controversial because of its accuracy. This study aimed to explore whether the rapid immunochromatographic test could be used for diagnosing norovirus-related diarrhea in children. Rapid immunochromatographic test (QuickNaviTM-Norovirus2) and RT-PCR on stool samples was used to diagnose norovirus. Stool samples were obtained from pediatric patients aged between 1 and 60 months who had diarrhea and were admitted to the pediatric ward at Dr. Soetomo General Hospital Surabaya, between April 2013 and March 2014. Ninety-four subjects provided stool samples that were tested using QuickNaviTM-Noro2 and RT-PCR. Using the test, 64 samples tested positive for norovirus and 30 tested negatives. The sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of the rapid immunochromatographic test were consecutively 90.3%, 42.9%, 43.8%, 90%, and 58.5%. RT-PCR was used to test all samples to assess the accuracy, which showed that one from 31 samples contained the GI strain (1.1%), while 30 samples (32%) contained the GII strain. This study definitively establishes that the rapid immunochromatography test is not sufficiently accurate for use as a screening or diagnostic tool in norovirus-related diarrhea cases in children.


2012 ◽  
Vol 141 (3) ◽  
pp. 524-528 ◽  
Author(s):  
S. DE GRAZIA ◽  
V. MARTELLA ◽  
M. CHIRONNA ◽  
F. BONURA ◽  
F. TUMMOLO ◽  
...  

SUMMARYThe study investigated the genetic diversity of human astroviruses (HAstVs) detected in children hospitalized with gastroenteritis in Italy in 2008–2009. A total of 1321 faecal samples were collected in Parma (northern Italy), Bari (southern Italy), and Palermo (Sicily) and screened for the presence of HAstVs. RT–PCR amplification of a portion at the 5′-end of ORF2 allowed the detection of HAstVs in 3·95% of the patients. Four different genotypes (HAstV-1, HAstV-2, HAstV-4, HAstV-5) were found to be circulating during the study period, with HAstV-1 being the predominant type. Interestingly, a novel lineage, proposed as HAstV-2d, was found to have emerged in Parma in 2009. Investigating the genetic variability of HAstVs will be important for understanding the epidemiological trends and evolution of these viruses.


2011 ◽  
Vol 152 (2) ◽  
pp. 45-50 ◽  
Author(s):  
Péter Pankovics ◽  
Ákos Boros ◽  
Melinda Rovács ◽  
Erika Nagy ◽  
Erika Krisztián ◽  
...  

Human astroviruses are one of the known pathogens of gastroenteritis in infants, children and rarely in elderly. It causes 4.2-7.3% of the sporadic gastroenteritis cases with diarrhea and vomiting in children. The etiological role of astrovirus has not been confirmed yet in outbreaks of gastroenteritis in Hungary. Aims: The first description of the detection and molecular epidemiology of astrovirus in outbreaks of gastroenteritis in Hungary. Materials and methods: Stool samples originated from Komárom-Esztergom County, from a day-care center (nursery) where a gastroenteritis outbreak occurred in June, 2010. Astrovirus was detected by RT-PCR methods. The nucleotide sequence of the nearly complete genome was sequenced. Clinical and epidemiological data were collected by epidemiological investigation. Results: Out of the 29 exposed persons (24 children and 5 adults) 7 (24.1%) children had gastroenteritis with diarrhea, and vomiting in one case, in the period of June 4-15, 2010. Bacterial pathogens, rotavirus, adenovirus and norovirus were not detected, but genotype 1 astrovirus could be identified in 3 (42.8%) stool samples (HQ398856). The nucleotide sequence of the astrovirus ORF1a/ORF1b/ORF2/3’UTR regions was determined. The source of the outbreak was presumably the firstly recognized ill child and the virus was spread by fecal-oral route with direct contact in the children community. Conclusions: Epidemiologic and clinical characteristics of the astrovirus outbreak in the nursery are described in details to prove that the possible etiological role of astroviruses in viral gastroenteritis which should not forget in order after rotaviruses, caliciviruses (norovirus and sapovirus) and enteric adenoviruses. Orv. Hetil., 2011, 152, 45–50.


1997 ◽  
Vol 35 (11-12) ◽  
pp. 243-247 ◽  
Author(s):  
A. Bosch ◽  
R. M. Pintó ◽  
C. Villena ◽  
F. X. Abad

Large gastroenteritis outbreaks associated with astroviruses are being reported with increasing frequency suggesting that astrovirus may be an important agent of epidemic acute non-bacterial gastroenteritis in children and adults. In this study, a procedure, based on infection of CaCo-2 cell monolayers followed by reverse-transcription polymerase chain reaction, was developed to ascertain the persistence of infectious human astroviruses in tap and marine water at 4±1°C and 20±1°C. The adequacy of this methodology for monitoring the decay of infectious fastidious viruses was assessed by determining the survival of a cytocidal virus (poliovirus 1) concomitantly by MPNCU and cell infection plus RT-PCR. After 60d in dechlorinated tap water, the decay of astrovirus infectivity was lower than 2 logs at 4±1°C and around 3.6 logs at 20±1°C, while after 90d the titre reduction was around 3.3 and 4.3 logs at 4±1°C and 20±1°C respectively. In natural non-autoclaved seawater at 20°C, astrovirus showed a lower level of persistence. The possibility to acquire data on the survival of fastidious viruses in the environment opens new perspectives on the epidemiology of some health significant infections transmitted by the faecal-oral route.


2002 ◽  
Vol 83 (9) ◽  
pp. 2215-2223 ◽  
Author(s):  
A. C. Potgieter ◽  
A. D. Steele ◽  
A. A. van Dijk

Cloning full-length large (>3 kb) dsRNA genome segments from small amounts of dsRNA has thus far remained problematic. Here, a single-primer amplification sequence-independent dsRNA cloning procedure was perfected for large genes and tailored for routine use to clone complete genome sets or individual genes. Nine complete viral genome sets were amplified by PCR, namely those of two human rotaviruses, two African horsesickness viruses (AHSV), two equine encephalosis viruses (EEV), one bluetongue virus (BTV), one reovirus and bacteriophage Φ12. Of these amplified genomes, six complete genome sets were cloned for viruses with genes ranging in size from 0·8 to 6·8 kb. Rotavirus dsRNA was extracted directly from stool samples. Co-expressed EEV VP3 and VP7 assembled into core-like particles that have typical orbivirus capsomeres. This work presents the first EEV sequence data and establishes that EEV genes have the same conserved termini (5′ GUU and UAC 3′) and coding assignment as AHSV and BTV. To clone complete genome sets, one-tube reactions were developed for oligo-ligation, cDNA synthesis and PCR amplification. The method is simple and efficient compared to other methods. Complete genomes can be cloned from as little as 1 ng dsRNA and a considerably reduced number of PCR cycles (22–30 cycles compared to 30–35 of other methods). This progress with cloning large dsRNA genes is important for recombinant vaccine development and determination of the role of terminal sequences for replication and gene expression.


Viruses ◽  
2019 ◽  
Vol 11 (7) ◽  
pp. 585 ◽  
Author(s):  
Diem-Lan Vu ◽  
Aurora Sabrià ◽  
Nuria Aregall ◽  
Kristina Michl ◽  
Virginia Rodriguez Garrido ◽  
...  

A remarkable percentage of acute gastroenteritis cases remain etiologically undiagnosed. The aim of the study was to determine the prevalence of common and emerging enteric viruses, such as novel human astroviruses, among undiagnosed samples from children with acute gastroenteritis. Epidemiological studies for novel human astroviruses are still scarce. Stool samples collected over two consecutive winter seasons (2016–2017) from children with gastroenteritis in Spain, which were negative for bacteria, rotavirus, and adenovirus by routine diagnostics were screened by real-time RT-PCR assays for the presence of classical and novel astrovirus, rotavirus, norovirus GI and GII, sapovirus, and adenovirus. Overall, 220/384 stool samples (57.3%) were positive for at least one virus. Co-infections were identified in 21% of cases. Among a total of 315 viruses identified, adenovirus was the most prevalent (n = 103), followed by rotavirus (n = 51), sapovirus (n = 50), classical astrovirus (n = 43), novel astroviruses (n = 42), and norovirus (n = 26). Novel astroviruses were present in 13.3% of virus-positive cases. Most novel astroviruses were found in children <2-year-old (30/39 children, 77%, p = 0.01) and were found in co-infection (66%). Only classical astroviruses demonstrated significant differences in the Cq values during mono-infections compared to co-infections. In conclusion, common enteric viruses may be frequently found in children with undiagnosed gastroenteritis, indicating the need to implement more sensitive diagnostic methods. Novel astroviruses circulate in the community and could be the cause of gastroenteritis among young children.


2021 ◽  
Vol 55 (1) ◽  
pp. 48
Author(s):  
Reza Gunadi Ranuh ◽  
Alpha Fardah Athiyyah ◽  
Deanty Ayu PA ◽  
Andy Darma ◽  
Dadik Raharjo ◽  
...  

In developing countries, Norovirus is the second-leading cause of acute diarrhea, after rotavirus. The approved gold standard method for diagnosis of norovirus infection is RT-PCR. The rapid immunochromatographic test is a novel and expedient method for diagnosing norovirus that is relatively affordable. However, the use of the rapid immunochromatographic test remains controversial because of its accuracy. This study aimed to explore whether the rapid immunochromatographic test could be used for diagnosing norovirus-related diarrhea in children. Rapid immunochromatographic test (QuickNaviTM-Norovirus2) and RT-PCR on stool samples was used to diagnose norovirus. Stool samples were obtained from pediatric patients aged between 1 and 60 months who had diarrhea and were admitted to the pediatric ward at Dr. Soetomo General Hospital Surabaya, between April 2013 and March 2014. Ninety-four subjects provided stool samples that were tested using QuickNaviTM-Noro2 and RT-PCR. Using the test, 64 samples tested positive for norovirus and 30 tested negatives. The sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of the rapid immunochromatographic test were consecutively 90.3%, 42.9%, 43.8%, 90%, and 58.5%. RT-PCR was used to test all samples to assess the accuracy, which showed that one from 31 samples contained the GI strain (1.1%), while 30 samples (32%) contained the GII strain. This study definitively establishes that the rapid immunochromatography test is not sufficiently accurate for use as a screening or diagnostic tool in norovirus-related diarrhea cases in children.


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