The first evidence of shaking mink syndrome-astrovirus associated encephalitis in farmed minks, China.

A novel neurological disorder, shaking mink syndrome (SMS), emerged in Denmark and Sweden in 2000. SMS has seldom been reported in China, but the causative agent has not been detected in the country. SMS outbreaks occurred in multiple provinces in 2020. A total of 44 brain samples from minks associated with SMS were collected from Heilongjiang, Liaoning and Shandong provinces of which 28 samples (63.3%) were SMS-astrovirus (SMS-AstV)-positive by reverse transcription PCR. Histopathological examination revealed non-suppurative encephalitis in three minks. Moreover, the complete coding region sequences (CDSs, 6559 bp) of a sample collected from a 2-month-old mink (termed SMS-AstV-H1, GSA accession No. SAMC816786) were amplified by PCR and Sanger sequencing. The complete CDS and open reading frame 2 sequences of SMS-AstV-H1 were 94.3% and 96.4% identical to an SMS-AstV strain (GenBank accession number: GU985458). Phylogenetically, SMS-AstV-H1 was closely related to an SMS-AstV strain (GU985458). Based on the above results, we describe SMS-AstV-associated encephalitis in farmed minks in China. Future studies need to focus on epidemiology, virus isolation and potential interspecies transmission of SMS-AstV.

Comparison of gut viral communities in diarrhoea and healthy dairy calves.

Calf diarrhoea has been a major cause of economic losses in the global dairy industry. Many factors, including multiple pathogen infections, can directly or indirectly cause calf diarrhoea. This study compared the faecal virome between 15 healthy calves and 15 calves with diarrhoea. Significantly lower diversity of viruses was found in samples from animals with diarrhoea than those in the healthy ones, and this feature may also be related to the age of the calves. Viruses belonging to the families Astroviridae and Caliciviridae that may cause diarrhoea in dairy calves have been characterized, which revealed that reads of caliciviruses and astroviruses in diarrhoea calves were much higher than those in healthy calves. Five complete genomic sequences closely related to Smacoviridae have been identified, which may participate in the regulation of the gut virus community ecology of healthy hosts together with bacteriophages. This research provides a theoretical basis for further understanding of known or potential enteric pathogens related to calf diarrhoea.

Molecular detection and characterization reveals circulation of multiple genotypes of porcine astrovirus in Haryana, India.

Porcine astrovirus (PAstV) is distributed worldwide and has been reported to cause diarrhea in pigs. PAstV belongs to the family Astroviridae and genus Mamastrovirus. PAstVs are divided into five diverse genotypes (PAstV1-PAstV5) on the basis of phylogenetic analysis of a part of the RNA-dependent RNA polymerase (RdRp) gene and the capsid gene. However, knowledge regarding the clinical significance and molecular characteristics of PAstV in Haryana, India, is limited. In this study, we investigated the presence of PAstV by RT-PCR of the partial RdRp gene in 110 rectal swabs collected from diarrheic pigs in different parts of Haryana, India. Of these, 35 samples (31.8%) tested positive for PAstV, with the highest positivity observed among weaning piglets 3 to 9 weeks of age (47.7%, 21/44), followed by fattening pigs 9 to 24 weeks of age (28.5%, 8/28). Phylogenetic analysis of the partial RdRp gene revealed circulation of four different genotypes (PAstV1, PAstV2, PAstV4, and PAstV5) in Haryana, with PAstV1 being the predominant genotype. To the best of our knowledge, this is the first report of the presence of PAstV1 and PAstV5 in the pig population of India. The PAstV sequences revealed high genetic variability and genetic heterogeneity in a relatively confined area.

Phylogenetic analysis of kobuviruses and astroviruses from Korean wild boars: 2016-2018.

Between 2016 and 2018, the prevalence of porcine kobuvirus (PKoV) and porcine astrovirus (PAstV) in Korean wild boars (n = 845) was 28.0% and 10.7%, respectively. Coinfection by both viruses was detected in 5.1% of boars. Phylogenetic analysis revealed that 134 PKoV isolates belonged to diverse lineages within the species Aichivirus C; however, one strain (WKoV16CN-8627) clustered with bovine kobuvirus (Aichivirus B). Forty-seven PAstVs belonged to lineage PAstV4, and only one strain (WAst17JN-10931) was a novel addition to lineage PAstV2. The two viruses were more prevalent in boars weighing ≤ 60 kg than in boars weighing > 61 kg.

Human Astrovirus 1-8 Seroprevalence Evaluation in a United States Adult Population.

Human astroviruses are an important cause of viral gastroenteritis globally, yet few studies have investigated the serostatus of adults to establish rates of previous infection. Here, we applied biolayer interferometry immunosorbent assay (BLI-ISA), a recently developed serosurveillance technique, to measure the presence of blood plasma IgG antibodies directed towards the human astrovirus capsid spikes from serotypes 1-8 in a cross-sectional sample of a United States adult population. The seroprevalence rates of IgG antibodies were 73% for human astrovirus serotype 1, 62% for serotype 3, 52% for serotype 4, 29% for serotype 5, 27% for serotype 8, 22% for serotype 2, 8% for serotype 6, and 8% for serotype 7. Notably, seroprevalence rates for capsid spike antigens correlate with neutralizing antibody rates determined previously. This work is the first seroprevalence study evaluating all eight classical human astrovirus serotypes.

Molecular and clinical epidemiological features of human astrovirus infections in children with acute gastroenteritis in Shandong province, China.

Human astrovirus (HAstV) is one of the most common causative agents of acute gastroenteritis in children with an infection rate estimated to range from 2% to 9% worldwide. This study was aimed at investigating the molecular and clinical epidemiological features of human astrovirus infections in children under 5 years old with acute gastroenteritis in Shandong province, China from July 2017 to June 2018. In total, 376 fecal samples and the corresponding clinical information were collected and analyzed. HAstV infections were detected in all age groups with an overall positive rate of 8.51%. In addition to acute diarrhea, the main clinical manifestations were fever, abdominal pain, vomiting, and dehydration, in which fever was the most common complication. Infections could be seen throughout the year with a peak in the colder season. Four genotypes were detected in which HAstV-1 was the most prevalent genotype with a prevalence of 78.12%, followed by HAstV-5 (9.38%), MLB-1 (9.38%), and MLB-2 (3.12%). HAstV-1 strains were classified as lineage 1a, 1b, and 1d, in which lineage 1a strains were the most prevalent followed by lineage 1b and lineage 1d strains. All HAstV-5 strains were classified as lineage 5b and no other lineages were detected. The results showed that HAstV infection was an important cause of acute gastroenteritis among children under 5 years old in Shandong province. Given that their disease spectrum had been broadened, HAstVs should be paid more attention, not only as a causative agent of acute gastroenteritis but also as a potential pathogen of unexpected diseases.

First Detection of Bat Astroviruses (BtAstVs) among Bats in Poland: The Genetic BtAstVs Diversity Reveals Multiple Co-Infection of Bats with Different Strains.

BACKGROUND: Astroviruses (AstVs) are common pathogens of a wide range of animal hosts, including mammals and avians, causing gastrointestinal diseases, mainly gastroenteritis and diarrhea. They prompt a significant health problem in newborns and young children and economic losses in the poultry sector and mink farms. Recent studies revealed a growing number of bat species carrying astroviruses with a noticeable prevalence and diversity. Here, we demonstrate the first detection of bat astroviruses (BtAstVs) circulating in the population of insectivorous bats in the territory of Poland. RESULTS: Genetically diverse BtAstVs (n = 18) were found with a varying degree of bat species specificity in five out of 15 bat species in Poland previously recognized as BtAstV hosts. Astroviral RNA was found in 12 out of 98 (12.2%, 95% CI 7.1-20.2) bat intestines, six bat kidneys (6.1%, 95% CI 2.8-12.7) and two bat livers (2.0%, 95% CI 0.4-7.1). Deep sequencing of the astroviral RNA-dependent RNA polymerase (RdRp) region revealed co-infections in five single bat individuals with highly distinct astrovirus strains. CONCLUSIONS: The detection of highly distinct bat astroviruses in Polish bats favors virus recombination and the generation of novel divergent AstVs and creates a potential risk of virus transmission to domestic animals and humans in the country. These findings provide a new insight into molecular epidemiology, prevalence of astroviruses in European bat populations and the risk of interspecies transmission to other animals including humans.

Identification of Novel Astroviruses in the Gastrointestinal Tract of Domestic Cats.

Astroviruses, isolated from numerous avian and mammalian species including humans, are commonly associated with enteritis and encephalitis. Two astroviruses have previously been identified in cats, and while definitive evidence is lacking, an association with enteritis is suggested. Using metagenomic next-generation sequencing of viral nucleic acids from faecal samples, we identified two novel feline astroviruses termed Feline astrovirus 3 and 4. These viruses were isolated from healthy shelter-housed kittens (Feline astrovirus 3; 6448 bp) and from a kitten with diarrhoea that was co-infected with Feline parvovirus (Feline astrovirus 4, 6549 bp). Both novel astroviruses shared a genome arrangement of three open reading frames (ORFs) comparable to that of other astroviruses. Phylogenetic analysis of the concatenated ORFs, ORF1a, ORF1b and capsid protein revealed that both viruses were phylogenetically distinct from other feline astroviruses, although their precise evolutionary history could not be accurately determined due to a lack of resolution at key nodes. Large-scale molecular surveillance studies of healthy and diseased cats are needed to determine the pathogenicity of feline astroviruses as single virus infections or in co-infections with other enteric viruses.

Molecular epidemiology of astrovirus in children with gastroenteritis in southwestern Nigeria.

Human astrovirus (HAstV) is recognized as one of the major causative agents of acute gastroenteritis in children worldwide. Data on the genetic diversity of HAstV in Nigeria are limited. The aim of this study was to determine the prevalence and molecular epidemiology of classical HAstV in children under 5 years of age with acute gastroenteritis in Ogun State, Nigeria. Fecal samples (331) as well as socio-demographic and clinical data were collected across the three senatorial districts of the state from February 2015 to April 2017. One hundred seventy-five samples were randomly selected and analyzed for the presence of HAstV using RT-PCR. PCR amplicons from positive samples were sequenced, and phylogenetic analysis was done to determine genotypes and lineages. The overall prevalence rate was 19.4% (34), with the highest occurrence observed in 2015 (41.4%). Viral coinfections were detected in 13 cases (38.2%). HAstV infection occurred throughout the year and in all age groups, mainly in the age group of 0-12 months. There was significant association between prevalence rate and collection year; however, no association was observed with gender, age, symptoms or risk factors. HAstV-5 was the predominant genotype (76.5%) circulating throughout the study period, followed by HAstV-1 (23.5%), which circulated only in the first 2 years of the study. Phylogenetic analysis showed that all HAstV-5 strains detected belonged to the 5a lineage, while HAstV-1 strains were grouped into lineage 1b. This study, to the best of our knowledge, is the first comprehensive report on molecular characterization of classical HAstV among children with gastroenteritis in the country, and this will serve as baseline information for implementing appropriate infection control practices.

Complete genome of a novel recombinant human astrovirus and its quasispecies in patients following hematopoietic stem cell transplantation.

Human astroviruses (HAstVs) were first identified in 1975 and can be classified into three clades: classic HAstVs (HAstV 1-8), MLB (MLB1-3) and VA (VA1-5), with MLB and VA were newly identified. Recombination and a high mutation rate make HAstV as one of the rapidly evolving infectious agents. This study reported a novel identified recombinant human astrovirus (Y/1-CHN) and its long existence in two immunocompromised patients with diarrhea following allogeneic hematopoietic stem cell transplantation (allo-HSCT). The identified Yu/1-CHN genome contains 6801 base pairs encoding three open reading frames, with ORF1a best hit to the HAstV1 (Pune strain, 97 % nucleotide identity), while ORF1b and ORF2 best hit to HAstV-5 (DL30 strain, 99 % nucleotide identity). Possible recombination breakpoint was predicted to be located in the boundary of ORF1a and ORF1b. Different quasispecies were found in the host, and the dN/dS ratios of the S and P domains were determined to be 1.189 and 1.444, respectively, suggesting a positive selection existed. Fecal samples collected in different clinical phases from the two patients were all positive for Yu/1-CHN, suggesting a long existence of the virus in the host. It was indicated that immunocompromised patients may a reservoir for astrovirus, their excreta should be monitored even after discharge from hospital.

Classical human astroviruses in symptomatic and asymptomatic children of Goiás, Brazil: Positivity rates, viral loads, and molecular characterization.

Classical human astroviruses (HAstV) are agents of nonbacterial acute gastroenteritis (AGE), being predominant among children. There are only a few studies reporting HAstV loads in samples from patients with AGE, data are even scarcer regarding asymptomatic patients. The aim of this study was to evaluate the occurrence and estimate the viral load of HAstV and to perform molecular characterization of positive samples obtained from children, up to 6 years old, with and without AGE. One fecal sample was obtained from each of the 250 children enrolled in the study, from May 2014 to April 2015. Real-time reverse transcription-polymerase chain reaction (RT-qPCR TaqMan) was performed, followed by a conventional RT-PCR directed to ORF2, region C, of the positive samples. Then, these amplicons were sequenced and a phylogenetic analysis was performed to determine the HAstV-1 lineages. A global positivity index of 3.2% (8 of 250) was observed for HAstV with a similar frequency (50%) in both symptomatic and asymptomatic group. Viral loads ranged from 2.8 × 105 to 1.6 × 1011 genome copy/mL Four samples were characterized as HAstV-1, lineage 1a and two as HAstV-4, lineage 4c. Our findings show similar HAstV positivity rates for children with and without AGE, providing evidence of HAstV-1a and HAstV-4c lineage cocirculation in the Central West region of Brazil. Data contributes to the molecular epidemiology of these agents in the region.

Identification and Characterization of a Novel Recombinant Porcine Astrovirus from Pigs in Anhui, China.

Porcine astroviruses (PAstVs) have wide distribution in swine herds worldwide. At present, five porcine astrovirus genotypes have been identified. In this study, using viral metagenomics, a novel PAstV strain (designated as Ahast) was identified in fecal samples from pigs in Anhui of China, and the complete genomic sequence of Ahast was obtained by assembling and PCR amplification. Genomic structural analysis indicated that Ahast had a typical ribosomal frameshifting signal, and some conserve amino acid motifs were also found in virally encoded proteins. Phylogenetic analysis and sequence comparison indicated that this virus belonged to porcine astrovirus genotype 4 (PAstV4), which formed a clade clustered with other PAstV4. Multiple recombinant events were confirmed by recombination analysis and indicated that Ahast was a potential recombinant. Epidemiological investigation indicated that PAstV4 has a 10.7% prevalence in this pig farm. The new recombinant identified in this study will be beneficial to comprehend the origin, genetic diversity, and evolution of porcine astroviruses in Anhui of China.

Evaluation of the RIDA®GENE RT-PCR assays for detection of sapovirus, astrovirus, adenovirus, and rotavirus in stool samples of adults in Switzerland.

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 (n = 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 (n = 9), RoV (n = 6), AstV (n = 3) or SaV (n = 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.

Molecular epidemiology and viremia of porcine astrovirus in pigs from Guangxi province of China.

BACKGROUND: Porcine astroviruses (PAstVs) are common in pigs worldwide. There are five distinct lineages with each lineage representing a different ancestral origin. Recently, multiple reports have demonstrated the evidence of extra-intestinal infection of PAstVs, but little is known about viremia. RESULTS: In this study, a total of 532 fecal samples and 120 serum samples from healthy pigs were collected and tested from 2013 to 2015 in Guangxi province, China; of these 300/532 (56.4%) and 7/120 (5.8%) of fecal samples tested positive for PAstVs, respectively. Our study revealed that there was wide genetic diversity and high prevalence of the virus in the pig population. All five of the known PAstVs genotypes (1-5) prevailed in the pig population of Guangxi province and were distributed in all age groups of pigs, from suckling piglets to sows, with PAstV2 (47.7%), PAstV1 (26.2%) and PAstV5 (21.5%) seen predominantly. Phylogenetic analysis of partial ORF1b and partial capsid sequences from fecal and serum samples revealed that they were divided into the five lineages. Among these genotypes, based on partial ORF2 genes sequencing 23 strains were grouped as PAstV1, including 6 serum-derived strains, and were regarded as the causative agents of viremia in pigs. CONCLUSIONS: Due to the information regarding the types of PAstV in blood is limit. This is the first report for the presence of PAstV1 in blood and PAstV3 in the feces of nursery pigs of China. This study provides a reference for understanding the prevalence and genetic evolution of PAstVs in pigs in Guangxi province, China. It also provides a new perspective for understanding of the extra-intestinal infection of PAstVs in pigs.

Genetic diversity of human adenovirus and human astrovirus in children with acute gastroenteritis in Northwest Ethiopia.

Human adenovirus (HAdV) and human astrovirus (HAstV) are common causes of gastroenteritis. Data on the prevalence and diversity of enteric viruses are important for control and preventive measures. However, epidemiological information regarding HAdV and HAstV infections in Ethiopia are limited. Fecal specimens were collected from 450 outpatient diarrheic infants and young children in Gondar and Bahir Dar from November 2015 to April 2016. Socio-demographic information was recorded. All fecal specimens were screened for the presence of HAdV and classical HAstV using PCR. Genotyping was performed by sequencing and phylogenetic analysis. Human HAdV and HAstV were detected in 144 (32%) and 16 (3.6%) of the children, respectively. Overall, 182 different adenovirus genotypes were detected, including mixed infections. Species F adenoviruses (HAdV-40, HAdV-41) were less common than other adenoviruses (HAdV-1, -2, -3, -5,-12, -16, -31, species D types) with a frequency of 32 versus 150, respectively. The HAstV genotypes were classified as HAstV-8 (n = 10), HAstV-1 (n = 3), HAstV-2 (n = 3), and HAstV-3 (n = 1). HAstV was detected only in Gondar. Thirty-eight coinfections HAdV and one HAstV coinfections were detected. There was no significant difference in the detection rate of HAdV and HAstV between boys and girls. The detection rates also did not differ between children from rural and urban areas. Children under 6 months of age, were less often infected with both viruses. These findings suggest that HAdV and HAstV are common in children with diarrhea in Ethiopia.

First whole genome characterization of porcine astrovirus detected in swine faeces in Italy.

Porcine astroviruses (PoAstV) are found in the gastrointestinal tract of healthy and diseased pigs worldwide. However, their role in causing enteric disease in pigs and other animals has not been elucidated. In the present report, we describe for the first time in Italy, the identification and genetic characterization, through whole genome sequencing, of a PoAstV2 in pigs in Northeast Italy in 2015. This instance is the first detection of PoAstV2 in pigs in Italy. The phylogenetic analysis of the complete ORF2 segment highlights the high similarity of this virus to those circulating that same year in Japan. There are very few full astrovirus genomes available, and the present data represent an important contribution towards a better understanding of the characteristics and evolution of these viruses.

High genetic diversity and recombination events of porcine astrovirus strains identified from ill and asymptomatic pigs in 2017, Hunan Province, China.

Astroviruses (AstV) are associated with enteric and systemic disease in mammals and birds. Astroviruses have received increased attention recently as they have been found to be associated with sporadic neurologic disease in mammals including humans. In pigs, porcine astrovirus (PoAstV) can be widely detected and has been grouped in five genotypes (PoAstV1 to PoAstV5). In the present study, we detected multiple PoAstVs in serum samples, nasal swabs, and fecal swabs collected from pigs suffering from respiratory disease or diarrhea but also from asymptomatic pigs, indicating a wide tissue tropism of the identified PoAstV genotypes. Coinfection of different genotypes in the same pig was commonly observed, and within an individual pig a high genetic diversity was observed for viruses belonging to the same PoAstV genotype. Two complete genomes of PoAstV2-WG-R2/2017 and PoAstV4-WG-R2/2017 were successfully obtained and characterized, with genome sizes of 6396 and 6643 nucleotides, respectively. The PoAstV2-WG-R2/2017 genome showed identities of 67.2-77.4% to other known PoAstV2 genomes, and the PoAstV4-WG-R2/2017 genome showed identities of 72.8-80.5% to other known PoAstV4 genomes. The predicted spike domain of open reading frame 2 (ORF2) of these strains showed the highest genetic heterogeneity, with amino acid identities of 13.7-70.9% for PoAstV2-WG-R2/2017 to other known PoAstV2 strains, and identities of 24.4-63.3% for the PoAstV4-WG-R2/2017 to other known PoAstV4 strains. Possible recombination events were identified in each of the two sequences. Two subclades of PoAstV2 and three subclades of PoAstV4 were defined in the present analyses. The obtained data provide further evidence for extraintestinal infectivity of PoAstVs, and confirmed the high genetic diversity of PoAstVs and the coinfection potential of different PoAstV types in a single pig.

Molecular Evolution of Classic Human Astrovirus, as Revealed by the Analysis of the Capsid Protein Gene.

Classic human astroviruses (HAstV) are major global viral agents for gastroenteritis, but the molecular characteristics of classic HAstVs are not well understood. Here, we presented the molecular evolution of all classic HAstV serotypes by the analysis of the capsid protein sequences. Our results show that classic HAstVs can be divided into four groups with the most recent common ancestor (TMRCA) of 749. The overall evolutionary rate of classic HAstVs on the capsid gene was 4.509×10-4 substitutions/site/year, and most of the serotypes present a clock-like evolution with an amino acid accumulation of mutations over time. The mean effective population size of classic HAstVs is in a downward trend, and some positive and more than 500 negative selection sites were determined. Taken together, these results reveal that classic HAstVs evolve at the intra-serotype level with high genetic heterogeneity and are driven by strong purifying selection. Long-term surveillance of classic HAstVs are needed to enrich the genomic data for further analysis.

Novel Human Astroviruses: Prevalence and Association with Common Enteric Viruses in Undiagnosed Gastroenteritis Cases in Spain.

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.