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1.
Viruses ; 15(8)2023 08 19.
Artículo en Inglés | MEDLINE | ID: mdl-37632111

RESUMEN

Although domestic cats are susceptible to infection with SARS-CoV-2, the role of the virus in causing feline disease is less well defined. We conducted a large-scale study to identify SARS-CoV-2 infections in UK pet cats, using active and passive surveillance. Remnant feline respiratory swab samples, submitted for other pathogen testing between May 2021 and February 2023, were screened using RT-qPCR. In addition, we appealed to veterinarians for swab samples from cats suspected of having clinical SARS-CoV-2 infections. Bespoke testing for SARS-CoV-2 neutralising antibodies was also performed, on request, in suspected cases. One RT-qPCR-positive cat was identified by active surveillance (1/549, 0.18%), during the Delta wave (1/175, 0.57%). Passive surveillance detected one cat infected with the Alpha variant, and two of ten cats tested RT-qPCR-positive during the Delta wave. No cats tested RT-qPCR-positive after the emergence of Omicron BA.1 and its descendants although 374 were tested by active and eleven by passive surveillance. We describe four cases of SARS-CoV-2 infection in pet cats, identified by RT-qPCR and/or serology, that presented with a range of clinical signs, as well as their SARS-CoV-2 genome sequences. These cases demonstrate that, although uncommon in cats, a variety of clinical signs can occur.


Asunto(s)
COVID-19 , SARS-CoV-2 , Animales , Gatos , SARS-CoV-2/genética , COVID-19/diagnóstico , COVID-19/veterinaria , Anticuerpos Antivirales , Reino Unido/epidemiología
2.
Sci Rep ; 12(1): 16308, 2022 09 29.
Artículo en Inglés | MEDLINE | ID: mdl-36175536

RESUMEN

Farm animals may harbor viral pathogens, some with zoonotic potential which can possibly cause severe clinical outcomes in animals and humans. Documenting the viral content of dust may provide information on the potential sources and movement of viruses. Here, we describe a dust sequencing strategy that provides detailed viral sequence characterization from farm dust samples and use this method to document the virus communities from chicken farm dust samples and paired feces collected from the same broiler farms in the Netherlands. From the sequencing data, Parvoviridae and Picornaviridae were the most frequently found virus families, detected in 85-100% of all fecal and dust samples with a large genomic diversity identified from the Picornaviridae. Sequences from the Caliciviridae and Astroviridae familes were also obtained. This study provides a unique characterization of virus communities in farmed chickens and paired farm dust samples and our sequencing methodology enabled the recovery of viral genome sequences from farm dust, providing important tracking details for virus movement between livestock animals and their farm environment. This study serves as a proof of concept supporting dust sampling to be used in viral metagenomic surveillance.


Asunto(s)
Pollos , Polvo , Animales , Granjas , Humanos , Metagenoma , Metagenómica
3.
Microbiol Resour Announc ; 10(8)2021 Feb 25.
Artículo en Inglés | MEDLINE | ID: mdl-33632868

RESUMEN

We report the genome sequence of a Minacovirus strain identified from a fecal sample from a farmed mink (Neovison vison) in The Netherlands that was tested negative for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using real-time PCR (RT-PCR). The viral genome sequence was obtained using agnostic deep sequencing.

4.
Microbiol Resour Announc ; 9(47)2020 Nov 19.
Artículo en Inglés | MEDLINE | ID: mdl-33214312

RESUMEN

We report seven chicken megrivirus genome sequences identified in chicken fecal samples from a broiler farm in The Netherlands. The sequences were determined using metagenomic sequencing and would expand our understanding of the genome diversity of megriviruses.

5.
Viruses ; 12(1)2020 01 16.
Artículo en Inglés | MEDLINE | ID: mdl-31963174

RESUMEN

A majority of emerging infectious diseases are of zoonotic origin. Metagenomic Next-Generation Sequencing (mNGS) has been employed to identify uncommon and novel infectious etiologies and characterize virus diversity in human, animal, and environmental samples. Here, we systematically reviewed studies that performed viral mNGS in common livestock (cattle, small ruminants, poultry, and pigs). We identified 2481 records and 120 records were ultimately included after a first and second screening. Pigs were the most frequently studied livestock and the virus diversity found in samples from poultry was the highest. Known animal viruses, zoonotic viruses, and novel viruses were reported in available literature, demonstrating the capacity of mNGS to identify both known and novel viruses. However, the coverage of metagenomic studies was patchy, with few data on the virome of small ruminants and respiratory virome of studied livestock. Essential metadata such as age of livestock and farm types were rarely mentioned in available literature, and only 10.8% of the datasets were publicly available. Developing a deeper understanding of livestock virome is crucial for detection of potential zoonotic and animal pathogens and One Health preparedness. Metagenomic studies can provide this background but only when combined with essential metadata and following the "FAIR" (Findable, Accessible, Interoperable, and Reusable) data principles.


Asunto(s)
Ganado/virología , Metagenómica , Virus/genética , Animales , Bovinos , Enfermedades Transmisibles Emergentes/virología , Reservorios de Enfermedades , Granjas , Genoma Viral , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Metagenoma , Salud Única , ARN Viral , Virosis , Zoonosis
6.
Emerg Infect Dis ; 25(1): 119-122, 2019 01.
Artículo en Inglés | MEDLINE | ID: mdl-30561298

RESUMEN

We compared viral load of emerging recombinant norovirus GII.P16-GII.2 with those for pandemic GII.Pe-GII.4 and epidemic GII.P17-GII.17 genotypes among inpatients in Hong Kong. Viral load of GII.P16-GII.2 was higher than those for other genotypes in different age groups. GII.P16-GII.2 is as replication competent as the pandemic genotype, explaining its high transmissibility and widespread circulation.


Asunto(s)
Infecciones por Caliciviridae/epidemiología , Enfermedades Transmisibles Emergentes/epidemiología , Gastroenteritis/epidemiología , Norovirus/genética , Pandemias , Adolescente , Adulto , Infecciones por Caliciviridae/virología , Niño , Preescolar , Enfermedades Transmisibles Emergentes/virología , Femenino , Gastroenteritis/virología , Genotipo , Hong Kong/epidemiología , Humanos , Lactante , Masculino , Persona de Mediana Edad , Carga Viral , Adulto Joven
7.
Emerg Infect Dis ; 24(4)2018 Apr 17.
Artículo en Inglés | MEDLINE | ID: mdl-29369754

RESUMEN

We report emerging subtropical bimodal seasonality and alternating predominance of norovirus GII.4 and non-GII.4 genotypes in Hong Kong. GII.4 predominated in summer and autumn months and affected young children, whereas emergent non-GII.4 genotypes predominated in winter months and affected all age groups. This highly dynamic epidemiology should inform vaccination strategies.

8.
Emerg Infect Dis ; 23(11): 1852-1855, 2017 11.
Artículo en Inglés | MEDLINE | ID: mdl-29048294

RESUMEN

A new recombinant norovirus GII.P16-GII.2 outnumbered pandemic GII.4 as the predominant GII genotype in the winter of 2016-2017 in Hong Kong, China. Half of hospitalized case-patients were older children and adults, including 13 young adults. This emergent norovirus targets a wider age population compared with circulating pandemic GII.4 strains.


Asunto(s)
Enfermedades Transmisibles Emergentes/epidemiología , Brotes de Enfermedades , Gastroenteritis/epidemiología , Norovirus/genética , Adolescente , Adulto , Anciano , Infecciones por Caliciviridae/epidemiología , Infecciones por Caliciviridae/virología , Niño , Preescolar , Enfermedades Transmisibles Emergentes/virología , Femenino , Gastroenteritis/virología , Genotipo , Hong Kong/epidemiología , Humanos , Lactante , Masculino , Persona de Mediana Edad , Norovirus/aislamiento & purificación , Filogenia , Virus Reordenados , Estaciones del Año , Adulto Joven
9.
Emerg Infect Dis ; 23(8): 1359-1354, 2017 08.
Artículo en Inglés | MEDLINE | ID: mdl-28726618

RESUMEN

Analysis of complete capsid sequences of the emerging norovirus GII.17 Kawasaki 308 from 13 countries demonstrated that they originated from a single haplotype since the initial emergence in China in late 2014. Global spread of a sublineage SL2 was identified. A new sublineage SL3 emerged in China in 2016.


Asunto(s)
Infecciones por Caliciviridae/epidemiología , Infecciones por Caliciviridae/virología , Gastroenteritis/epidemiología , Gastroenteritis/virología , Norovirus/clasificación , Infecciones por Caliciviridae/historia , Infecciones por Caliciviridae/transmisión , Proteínas de la Cápside/genética , Análisis por Conglomerados , Gastroenteritis/historia , Genotipo , Salud Global , Historia del Siglo XXI , Humanos , Norovirus/genética , Filogenia , Análisis de Secuencia de ADN
10.
J Infect Dis ; 216(1): 97-104, 2017 07 01.
Artículo en Inglés | MEDLINE | ID: mdl-28510725

RESUMEN

Background: We examined associations between single-nucleotide polymorphisms (SNPs) of IFITM3, TLR3, and CD55 genes and influenza clinical outcomes in Chinese. Methods: A multicenter study was conducted on 275 adult cases of avian (H7N9) and pandemic (H1N1pdm09) influenza. Host DNA was extracted from diagnostic respiratory samples; IFITM3 rs12252, TLR3 rs5743313, CD55 rs2564978, and TLR4 rs4986790/4986791 were targeted for genotyping (Sanger sequencing). The primary outcome analyzed was death. Results: IFITM3 and TLR3 SNPs were in Hardy-Weinberg equilibrium; their allele frequencies (IFITM3/C-allele 0.56, TLR3/C-allele 0.88) were comparable to 1000 Genomes Han Chinese data. We found over-representation of homozygous IFITM3 CC (54.5% vs 33.2%; P = .02) and TLR3 CC (93.3% vs 76.9%; P = .04) genotypes among fatal cases. Recessive genetic models showed their significant independent associations with higher death risks (adjusted hazard ratio [aHR] 2.78, 95% confidence interval [CI] 1.29-6.02, and aHR 4.85, 95% CI 1.11-21.06, respectively). Cumulative effects were found (aHR 3.53, 95% CI 1.64-7.59 per risk genotype; aHR 9.99, 95% CI 1.27-78.59 with both). Results were consistent for each influenza subtype and other severity indicators. The CD55 TT genotype was linked to severity. TLR4 was nonpolymorphic. Conclusions: Host genetic factors may influence clinical outcomes of avian and pandemic influenza infections. Such findings have important implications on disease burden and patient care in at-risk populations.


Asunto(s)
Antígenos CD55/genética , Gripe Humana/genética , Proteínas de la Membrana/genética , Proteínas de Unión al ARN/genética , Receptor Toll-Like 3/genética , Adulto , Anciano , Pueblo Asiatico , China/epidemiología , Femenino , Frecuencia de los Genes , Predisposición Genética a la Enfermedad , Técnicas de Genotipaje , Humanos , Subtipo H1N1 del Virus de la Influenza A , Subtipo H7N9 del Virus de la Influenza A , Gripe Humana/epidemiología , Masculino , Persona de Mediana Edad , Polimorfismo de Nucleótido Simple , Modelos de Riesgos Proporcionales
11.
Genome Announc ; 5(20)2017 May 18.
Artículo en Inglés | MEDLINE | ID: mdl-28522708

RESUMEN

A new recombinant norovirus, GII.P16-GII.2, emerged in the winter of 2016-2017. Here, we report the complete genome of this strain (Hu/GII/HK/2016/GII.P16-GII.2/CUHK-NS-1082), which was collected from a patient hospitalized with gastroenteritis in September 2016 in Hong Kong, China, and sequenced using next-generation sequencing. This genome had a 95.2% nucleotide identity to the closest sequence in GenBank.

12.
J Clin Microbiol ; 55(5): 1408-1415, 2017 05.
Artículo en Inglés | MEDLINE | ID: mdl-28202801

RESUMEN

Hepatitis E virus (HEV) causes substantial morbidity and mortality in developing countries and is considered an emerging foodborne pathogen in developed countries in which it was previously not endemic. To investigate genetic association between human HEV infection and HEV-contaminated high-risk food in Hong Kong, we compared local virus strains obtained from hepatitis E patient sera with those surveyed from high-risk food items during 2014 to 2016. Twenty-four cases of laboratory-confirmed human HEV infections were identified from January 2014 to March 2016 in our hospitals. Five types of food items at risk of HEV contamination were purchased on a biweekly basis from April 2014 to March 2016 in two local market settings: supermarkets (lamb, oyster, and pig liver) and wet markets (oyster, pig blood curd, pig large intestine, and pig liver). HEV RNA detection was performed by a real-time reverse transcription-PCR assay. HEV RNA was detected in pig liver, pig intestine, and oyster samples with prevalences of 1.5%, 0.4%, and 0.2%, respectively. Neighbor-joining phylogenetic inference showed that all human and swine HEV strains belonged to genotype 4. HEV subtype distributions in humans and swine were highly comparable: subtype 4b predominated, while subtype 4d was the minority. Local human and swine HEV genotype 4 strains shared over 95% nucleotide identity and were genetically very similar, implicating swine as an important foodborne source of autochthonous human HEV infections in Hong Kong. Action should be taken to raise the awareness among public and health care professionals of hepatitis E as an emerging foodborne disease.


Asunto(s)
Enfermedades Transmitidas por los Alimentos/virología , Virus de la Hepatitis E/genética , Hepatitis E/epidemiología , Hepatitis E/veterinaria , Hígado/virología , Porcinos/virología , Animales , Femenino , Genotipo , Hepatitis E/transmisión , Hepatitis E/virología , Virus de la Hepatitis E/clasificación , Virus de la Hepatitis E/aislamiento & purificación , Hong Kong , Humanos , Intestinos/virología , Masculino , Carne/virología , Persona de Mediana Edad , Epidemiología Molecular , Ostreidae/virología , ARN Viral/genética , Reacción en Cadena en Tiempo Real de la Polimerasa , Ovinos/virología , Enfermedades de los Porcinos/virología
14.
J Clin Microbiol ; 54(6): 1650-1652, 2016 06.
Artículo en Inglés | MEDLINE | ID: mdl-27030486

RESUMEN

Two commonly used norovirus enzyme immunoassays have reduced diagnostic performance, with clinical sensitivities ranging from 11% to 35% for the detection of the recently emerging genogroup II genotype 17 (GII.17) Kawasaki 2014 variant that caused the majority of infections in Asia during the winter of 2014 to 2015. False-negative results can compromise infection control and patient management.


Asunto(s)
Antígenos Virales/análisis , Infecciones por Caliciviridae/diagnóstico , Técnicas de Laboratorio Clínico/métodos , Reacciones Falso Negativas , Genotipo , Técnicas para Inmunoenzimas/métodos , Norovirus/aislamiento & purificación , Adolescente , Adulto , Anciano , Asia , Niño , Preescolar , Femenino , Humanos , Masculino , Persona de Mediana Edad , Norovirus/clasificación , Norovirus/genética , Sensibilidad y Especificidad , Adulto Joven
15.
Nat Commun ; 6: 10061, 2015 Dec 02.
Artículo en Inglés | MEDLINE | ID: mdl-26625712

RESUMEN

Norovirus genogroup II genotype 4 (GII.4) has been the predominant cause of viral gastroenteritis since 1996. Here we show that during the winter of 2014-2015, an emergent variant of a previously rare norovirus GII.17 genotype, Kawasaki 2014, predominated in Hong Kong and outcompeted contemporary GII.4 Sydney 2012 in hospitalized cases. GII.17 cases were significantly older than GII.4 cases. Root-to-tip and Bayesian BEAST analyses estimate GII.17 viral protein 1 (VP1) evolves one order of magnitude faster than GII.4 VP1. Residue substitutions and insertion occur in four of five inferred antigenic epitopes, suggesting immune evasion. Sequential GII.4-GII.17 infections are noted, implicating a lack of cross-protection. Virus bound to saliva of secretor histo-blood groups A, B and O, indicating broad susceptibility. This fast-evolving, broadly recognizing and probably immune-escaped emergent GII.17 variant causes severe gastroenteritis and hospitalization across all age groups, including populations who were previously less vulnerable to GII.4 variants; therefore, the global spread of GII.17 Kawasaki 2014 needs to be monitored.


Asunto(s)
Infecciones por Caliciviridae/virología , Evolución Molecular , Gastroenteritis/virología , Norovirus/genética , Norovirus/aislamiento & purificación , Adolescente , Adulto , Anciano , Australia/epidemiología , Infecciones por Caliciviridae/epidemiología , Niño , Preescolar , Brotes de Enfermedades , Femenino , Gastroenteritis/epidemiología , Genotipo , Hong Kong/epidemiología , Humanos , Masculino , Persona de Mediana Edad , Datos de Secuencia Molecular , Norovirus/clasificación , Filogenia , Estaciones del Año , Proteínas Virales/genética , Adulto Joven
16.
Genome Announc ; 3(6)2015 Nov 12.
Artículo en Inglés | MEDLINE | ID: mdl-26564051

RESUMEN

The complete genome sequence of a novel recombinant GII.Pe_GII.17 norovirus strain, tentatively named GII.17 Hong Kong 2015, was determined. RNA-dependent RNA polymerase has 95.6% and 98.4% and viral protein 1 has 90.6% and 95.9% identity at the nucleotide and amino acid levels, respectively, to the closest sequences in GenBank.

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