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1.
Emerg Infect Dis ; 28(3): 713-716, 2022 Mar.
Article in English | MEDLINE | ID: covidwho-1770993

ABSTRACT

A rapid decrease in viral gastroenteritis during winter 2019-20 and a return of norovirus and rotavirus activity during winter 2020-21 were observed while multiple nonpharmaceutical interventions for coronavirus disease were in effect in Hong Kong. The initial collateral benefit of coronavirus disease countermeasures that reduced the viral gastroenteritis burden is not sustainable.


Subject(s)
COVID-19 , Caliciviridae Infections , Norovirus , Rotavirus Infections , Rotavirus , Caliciviridae Infections/epidemiology , Caliciviridae Infections/prevention & control , China/epidemiology , Feces , Humans , Infant , Norovirus/genetics , Rotavirus/genetics , Rotavirus Infections/epidemiology , Rotavirus Infections/prevention & control , SARS-CoV-2
2.
Commun Dis Intell (2018) ; 452021 Nov 30.
Article in English | MEDLINE | ID: covidwho-1543154

ABSTRACT

ABSTRACT: This report from the Australian Rotavirus Surveillance Network describes the circulating rotavirus genotypes identified in children and adults during the period 1 January - 31 December 2020. During this period, 229 faecal specimens were referred for rotavirus G- and P- genotype analysis, including 189 samples that were confirmed as rotavirus positive. Of these, 98/189 were wildtype rotavirus strains and 86/189 were identified as vaccine-like. A further five samples could not be determined as wildtype or vaccine-like due to poor sequence reads. Genotype analysis of the 98 wildtype rotavirus samples from both children and adults demonstrated that G3P[8] was the dominant genotype identified for the third consecutive year, identified in 27.6% of samples, followed by G2P[4] in 20.4% of samples. Forty-six percent of rotavirus positive samples received were identified as vaccine-like, highlighting the need to add caution in interpreting rotavirus positive results in children aged 0-8 months. This surveillance period was significantly impacted by the coronavirus disease 2019 ( COVID-19 ) pandemic. The reduction in rotavirus notifications reflected reduced healthcare-seeking behaviour and a decrease in community spread, with 'community lockdowns', school and day-care centre closure and improved compliance with hand hygiene. Fewer stool samples were collected throughout Australia during this period. There was a reluctance to store samples at collaborating laboratories and uncertainties regarding the safety and feasibility of the transport of samples to the central laboratory during the closure of state and territory borders. Systems have now been adapted to manage and send biological samples safely and confidently. Ongoing rotavirus surveillance is crucial to identify changes in genotypic patterns and to provide diagnostic laboratories quality assurance by reporting incidences of wildtype, vaccine-like, or false positive rotavirus results.


Subject(s)
COVID-19 , Gastroenteritis , Rotavirus Infections , Rotavirus Vaccines , Rotavirus , Adult , Australia/epidemiology , Child , Communicable Disease Control , Humans , Population Surveillance , Rotavirus/genetics , Rotavirus Infections/epidemiology , Rotavirus Infections/prevention & control , SARS-CoV-2
3.
PLoS One ; 16(6): e0252534, 2021.
Article in English | MEDLINE | ID: covidwho-1270459

ABSTRACT

Many recent disease outbreaks in humans had a zoonotic virus etiology. Bats in particular have been recognized as reservoirs to a large variety of viruses with the potential to cross-species transmission. In order to assess the risk of bats in Switzerland for such transmissions, we determined the virome of tissue and fecal samples of 14 native and 4 migrating bat species. In total, sequences belonging to 39 different virus families, 16 of which are known to infect vertebrates, were detected. Contigs of coronaviruses, adenoviruses, hepeviruses, rotaviruses A and H, and parvoviruses with potential zoonotic risk were characterized in more detail. Most interestingly, in a ground stool sample of a Vespertilio murinus colony an almost complete genome of a Middle East respiratory syndrome-related coronavirus (MERS-CoV) was detected by Next generation sequencing and confirmed by PCR. In conclusion, bats in Switzerland naturally harbour many different viruses. Metagenomic analyses of non-invasive samples like ground stool may support effective surveillance and early detection of viral zoonoses.


Subject(s)
Chiroptera/virology , Feces/virology , Metagenomics/methods , Virome/genetics , Viruses/genetics , Zoonoses/virology , Adenoviridae/classification , Adenoviridae/genetics , Animals , Chiroptera/classification , Disease Reservoirs/virology , Genetic Variation , Genome, Viral/genetics , Hepevirus/classification , Hepevirus/genetics , Humans , Middle East Respiratory Syndrome Coronavirus/classification , Middle East Respiratory Syndrome Coronavirus/genetics , Phylogeny , Rotavirus/classification , Rotavirus/genetics , Sequence Analysis, DNA/methods , Switzerland , Viruses/classification
4.
Sci Rep ; 11(1): 7430, 2021 04 01.
Article in English | MEDLINE | ID: covidwho-1162021

ABSTRACT

Bats are known to be reservoirs of several highly pathogenic viruses. Hence, the interest in bat virus discovery has been increasing rapidly over the last decade. So far, most studies have focused on a single type of virus detection method, either PCR, virus isolation or virome sequencing. Here we present a comprehensive approach in virus discovery, using all three discovery methods on samples from the same bats. By family-specific PCR screening we found sequences of paramyxoviruses, adenoviruses, herpesviruses and one coronavirus. By cell culture we isolated a novel bat adenovirus and bat orthoreovirus. Virome sequencing revealed viral sequences of ten different virus families and orders: three bat nairoviruses, three phenuiviruses, one orbivirus, one rotavirus, one orthoreovirus, one mononegavirus, five parvoviruses, seven picornaviruses, three retroviruses, one totivirus and two thymoviruses were discovered. Of all viruses identified by family-specific PCR in the original samples, none was found by metagenomic sequencing. Vice versa, none of the viruses found by the metagenomic virome approach was detected by family-specific PCRs targeting the same family. The discrepancy of detected viruses by different detection approaches suggests that a combined approach using different detection methods is necessary for virus discovery studies.


Subject(s)
Chiroptera/virology , Genome, Viral , Virome/genetics , Animals , Chlorocebus aethiops , Germany , High-Throughput Nucleotide Sequencing , Nairovirus/classification , Nairovirus/genetics , Orbivirus/classification , Orbivirus/genetics , Phylogeny , Polymerase Chain Reaction , Rotavirus/classification , Rotavirus/genetics , Vero Cells , Viruses/classification , Viruses/genetics
5.
mBio ; 12(1)2021 01 19.
Article in English | MEDLINE | ID: covidwho-1066819

ABSTRACT

Bats host many viruses pathogenic to humans, and increasing evidence suggests that rotavirus A (RVA) also belongs to this list. Rotaviruses cause diarrheal disease in many mammals and birds, and their segmented genomes allow them to reassort and increase their genetic diversity. Eighteen out of 2,142 bat fecal samples (0.8%) collected from Europe, Central America, and Africa were PCR-positive for RVA, and 11 of those were fully characterized using viral metagenomics. Upon contrasting their genomes with publicly available data, at least 7 distinct bat RVA genotype constellations (GCs) were identified, which included evidence of reassortments and 6 novel genotypes. Some of these constellations are spread across the world, whereas others appear to be geographically restricted. Our analyses also suggest that several unusual human and equine RVA strains might be of bat RVA origin, based on their phylogenetic clustering, despite various levels of nucleotide sequence identities between them. Although SA11 is one of the most widely used reference strains for RVA research and forms the backbone of a reverse genetics system, its origin remained enigmatic. Remarkably, the majority of the genotypes of SA11-like strains were shared with Gabonese bat RVAs, suggesting a potential common origin. Overall, our findings suggest an underexplored genetic diversity of RVAs in bats, which is likely only the tip of the iceberg. Increasing contact between humans and bat wildlife will further increase the zoonosis risk, which warrants closer attention to these viruses.IMPORTANCE The increased research on bat coronaviruses after severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) allowed the very rapid identification of SARS-CoV-2. This is an excellent example of the importance of knowing viruses harbored by wildlife in general, and bats in particular, for global preparedness against emerging viral pathogens. The current effort to characterize bat rotavirus strains from 3 continents sheds light on the vast genetic diversity of rotaviruses and also hints at a bat origin for several atypical rotaviruses in humans and animals, implying that zoonoses of bat rotaviruses might occur more frequently than currently realized.


Subject(s)
Chiroptera/virology , Rotavirus Infections/transmission , Rotavirus Infections/virology , Rotavirus/genetics , Zoonoses/transmission , Zoonoses/virology , Animals , COVID-19/transmission , COVID-19/virology , Diarrhea/virology , Genetic Variation , Genome, Viral , Genotype , Horses , Humans , Metagenomics , Middle East Respiratory Syndrome Coronavirus/isolation & purification , Phylogeny , SARS-CoV-2/isolation & purification
6.
J Med Virol ; 92(11): 2582-2592, 2020 11.
Article in English | MEDLINE | ID: covidwho-942384

ABSTRACT

Rotavirus infections have become one of the most common causes of infectious gastroenteritis in children. Although rotavirus infections have been intensively studied in infants and young children, the study in adults has been limited. As such, this study assessed the prevalence of rotaviruses and performed the molecular characterization of rotaviruses circulating in Thai adults experiencing acute gastroenteritis between January 2018 and December 2018. Group A human rotaviruses were detected in 100 feces samples by rapid immunochromatography. The peak incidence of infection occurred in February and began to decline in the summer months. From January 2018 to December 2018, there were 1344 acute gastroenteritis adult cases in the Hospital for Tropical Diseases, Bangkok, Thailand. Among these, 310 cases were rotavirus-suspected cases. Only 100 samples tested positive for rotavirus via an immunochromatography test. Twentynine out of the 100 rotavirus-positive samples were further characterized by real-time polymerase chain reaction. The G3[P8] strain was identified as the most prevalent (31.0%) followed by G1P[8], G8P[8] and G9P[8], and G2P[8], which accounted for 20.8%, 17.2%, and 13.8%, respectively. Because of the detection of rare rotavirus genotypes, such as G8, the surveillance of rotavirus epidemiology is crucial in monitoring new emergences of rotavirus strains, leading to a better understanding of the effects of strain variation for further vaccine development.


Subject(s)
Rotavirus Infections/epidemiology , Rotavirus Infections/virology , Rotavirus/genetics , Adolescent , Adult , Aged , Aged, 80 and over , Feces/virology , Female , Gastroenteritis/epidemiology , Gastroenteritis/virology , Genotype , Humans , Incidence , Male , Middle Aged , Molecular Epidemiology , Phylogeny , Prevalence , Rotavirus/classification , Rotavirus/isolation & purification , Seasons , Thailand/epidemiology , Young Adult
7.
Sci Rep ; 10(1): 20296, 2020 11 20.
Article in English | MEDLINE | ID: covidwho-938317

ABSTRACT

Bats are natural reservoirs for potential zoonotic viruses. In this study, next-generation sequencing was performed to obtain entire genome sequences of picornavirus from a picornavirus-positive bat feces sample (16BF77) and to explore novel viruses in a pooled bat sample (16BP) from samples collected in South Korea, 2016. Fourteen mammalian viral sequences were identified from 16BF77 and 29 from 16BP, and verified by RT-PCR. The most abundant virus in 16BF77 was picornavirus. Highly variable picornavirus sequences encoding 3Dpol were classified into genera Kobuvirus, Shanbavirus, and an unassigned group within the family Picornaviridae. Amino acid differences between these partial 3Dpol sequences were ≥ 65.7%. Results showed that one bat was co-infected by picornaviruses of more than two genera. Retrovirus, coronavirus, and rotavirus A sequences also were found in the BP sample. The retrovirus and coronavirus genomes were identified in nine and eight bats, respectively. Korean bat retroviruses and coronavirus demonstrated strong genetic relationships with a Chinese bat retrovirus (RfRV) and coronavirus (HKU5-1), respectively. A co-infection was identified in one bat with a retrovirus and a coronavirus. Our results indicate that Korean bats were multiply infected by several mammal viruses.


Subject(s)
Chiroptera/virology , Feces/virology , High-Throughput Nucleotide Sequencing/methods , Mouth/virology , RNA Viruses/genetics , Animals , Brain/virology , Coronavirus/classification , Coronavirus/genetics , Coronavirus/physiology , Geography , Host-Pathogen Interactions , Intestines/virology , Liver/virology , Lung/virology , Phylogeny , Picornaviridae/classification , Picornaviridae/genetics , Picornaviridae/physiology , RNA Viruses/classification , RNA Viruses/physiology , Republic of Korea , Retroviridae/classification , Retroviridae/genetics , Retroviridae/physiology , Rotavirus/classification , Rotavirus/genetics , Rotavirus/physiology
8.
Prev Vet Med ; 185: 105196, 2020 Dec.
Article in English | MEDLINE | ID: covidwho-894168

ABSTRACT

A total of 237 faecal specimens from diarrheic calves younger than two months were collected and submitted for diagnosis of enteropathogens over a two-year period (2017-2018) to a veterinary laboratory. Samples originated from 193 dairy and beef farms in 29 provinces distributed throughout Spain, and were tested for the occurrence of three target enteric pathogens by reverse transcription real-time PCR (RT-qPCR): bovine rotavirus A (RVA), Cryptosporidium parvum and bovine coronavirus (BCoV). RT-PCR and nucleotide sequencing analysis were used to determine the G (VP7 gene) and P (VP4 gene) genotypes of 26 specimens positive for RVA. A total of 188 specimens (79.3 %) were positive for at least one of the three target enteric pathogens, and 101 samples (42.6 %) harbored mixed infections. The individual prevalence was 57.8 %, 50.6 % and 23.6 % for C. parvum, RVA and BCoV, respectively. Molecular analysis of selected RVA strains revealed the presence of the G6, G10, G3, P[5] and P[11] genotypes, with the combinations G6P[5] and G6P[11] being the most prevalent. Alignments of nucleotide sequences of the VP7 and VP4 markers showed a high frequency of single nucleotide polymorphisms (SNPs), with up to 294 SNPs found in 869bp of sequence at the G6 genotype (0.338 SNPs/nt), which reveals the extensive genetic diversity of RVA strains. Phylogenetic analysis of the VP7 gene of the G6 strains revealed four distinct lineages, with most strains clustering in the G6-IV lineage. The discrepancies between the RVA genotypes circulating in the sampled cattle farms and the genotypes contained in commercial vaccines currently available in Spain are discussed. We believe that this is the first study on the molecular characterization of rotavirus infecting cattle in Spain.


Subject(s)
Cattle Diseases/virology , Diarrhea/veterinary , Rotavirus Infections/veterinary , Rotavirus/genetics , Animals , Cattle , Cattle Diseases/epidemiology , Coinfection , Coronavirus/isolation & purification , Coronavirus Infections/epidemiology , Coronavirus Infections/veterinary , Coronavirus Infections/virology , Cryptosporidiosis/complications , Cryptosporidiosis/epidemiology , Cryptosporidium parvum/isolation & purification , Diarrhea/epidemiology , Diarrhea/virology , Feces/virology , Genetic Variation , Genotype , Rotavirus Infections/epidemiology , Rotavirus Infections/virology , Spain/epidemiology
9.
Microb Pathog ; 138: 103814, 2020 Jan.
Article in English | MEDLINE | ID: covidwho-124709

ABSTRACT

Bovine rotavirus (BRoV) and bovine coronavirus (BCoV) are major enteric viral pathogens responsible for calve diarrhoea. They are widespread both in dairy and beef cattle throughout the world and causing huge economic losses. The diagnosis of these agents is very difficult due to non-specific nature of lesions and the involvement of some intrinsic and extrinsic risk factors. We performed postmortem of 45 calves, which was below three months of age. Out of 45 necropscid calves, three (6.66%) cases were positive for BRoV and four (8.88%) cases were found positive for BCoV, screened by reverse transcriptase polymerase chain reaction (RT-PCR). Further RT-PCR positive cases were confirmed by immunohistochemistry (IHC) in paraffin-embedded intestinal tissue sections. Three cases of enteritis caused by BRoV showed the hallmark lesions of the shortening and fusion of villi, denudation and infiltration of mononuclear cells in the lamina propria. The BRoV antigen distribution was prominent within the lining epithelium of the villi, peyer's patches in the ileum and strong immunoreactions in the lymphocytes and some macrophages of the mesenteric lymph nodes. Four cases in which BCoV was detected, grossly lesions characterized by colonic mucosa covered with thick, fibrinous and diphtheritic membrane. Histopathologically, jejunum showed skipping lesion of micro-abscesses in crypts. The BCoV antigen distribution was prominent within the necrotic crypts in the jejunum and cryptic micro-abscesses in the colon and ileum. It is the first report of BRoV and BCoV antigen demonstration in the jejunum, colon, ileum, Peyer's patches and mesenteric lymph nodes of naturally infected calves from India by using IHC.


Subject(s)
Cattle Diseases/virology , Coronavirus Infections/veterinary , Coronavirus, Bovine/physiology , Enteritis/veterinary , Rotavirus Infections/veterinary , Rotavirus/physiology , Animals , Cattle , Cattle Diseases/pathology , Coronavirus Infections/pathology , Coronavirus Infections/virology , Coronavirus, Bovine/genetics , Coronavirus, Bovine/isolation & purification , Enteritis/pathology , Enteritis/virology , Feces/virology , Immunohistochemistry , Intestines/pathology , Intestines/virology , Polymerase Chain Reaction , Rotavirus/genetics , Rotavirus/isolation & purification , Rotavirus Infections/pathology , Rotavirus Infections/virology
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