Multiplex PCR and multiplex RT-PCR for inclusive detection of major swine DNA and RNA viruses in pigs with multiple infections

AbstractLactoferrin is part of the innate immune system, with antiviral activity against numerous DNA and RNA viruses. Rhinoviruses, the leading cause of the common cold, are associated with exacerbation of respiratory illnesses such as asthma. Here, we explored the effect of bovine lactoferrin (BLf) on RV-B14 infectivity. Using different assays, we show that the effect of BLf is strongest during adhesion of the virus to the cell and entry. Tracking the internalisation of BLf and virus revealed a degree of colocalisation, although their interaction was only confirmed in vitro using empty viral particles, indicating a possible additional influence of BLf on other infection steps.

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Detection of multiple enteric virus strains within a foodborne outbreak of gastroenteritis: an indication of the source of contamination

Epidemiology and Infection ◽

10.1017/s0950268804003218 ◽

2004 ◽

Vol 133 (1) ◽

pp. 41-47 ◽

Cited By ~ 55

Author(s):

C. I. GALLIMORE ◽

C. PIPKIN ◽

H. SHRIMPTON ◽

A. D. GREEN ◽

Y. PICKFORD ◽

...

Keyword(s):

Arabian Gulf ◽

Enteric Virus ◽

Multiple Infections ◽

Rt Pcr ◽

Chain Reaction ◽

Epidemiological Analysis ◽

Viral Aetiology ◽

Polymerase Chain ◽

Most Probable Explanation ◽

Virus Strains

An outbreak of acute gastroenteritis of suspected viral aetiology occurred in April 2003 in the British Royal Fleet Auxillary ship (RFA) Argus deployed in the Northern Arabian Gulf. There were 37 cases amongst a crew of 400 personnel. Of 13 samples examined from cases amongst the crew, six enteric viruses were detected by reverse transcriptase polymerase chain reaction (RT–PCR). Five different viruses were identified including, three norovirus genotypes, a sapovirus and a rotavirus. No multiple infections were detected. A common food source was implicated in the outbreak and epidemiological analysis showed a statistically significant association with salad as the source of the outbreak, with a relative risk of 3·41 (95% confidence interval of 1·7–6·81) of eating salad on a particular date prior to the onset of symptoms. Faecal contamination of the salad at source was the most probable explanation for the diversity of viruses detected and characterized.

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VirusTaxo: Taxonomic classification of virus genome using multi-class hierarchical classification by k-mer enrichment

10.1101/2021.04.29.442004 ◽

2021 ◽

Author(s):

Rajan Saha Raju ◽

Abdullah Al Nahid ◽

Preonath Shuvo ◽

Rashedul Islam

Keyword(s):

Genome Sequence ◽

Rna Viruses ◽

Hierarchical Classification ◽

Classification Problem ◽

Virus Genome ◽

Taxonomic Classification ◽

Dna Viruses ◽

Dna And Rna ◽

Full Length Genome

AbstractTaxonomic classification of viruses is a multi-class hierarchical classification problem, as taxonomic ranks (e.g., order, family and genus) of viruses are hierarchically structured and have multiple classes in each rank. Classification of biological sequences which are hierarchically structured with multiple classes is challenging. Here we developed a machine learning architecture, VirusTaxo, using a multi-class hierarchical classification by k-mer enrichment. VirusTaxo classifies DNA and RNA viruses to their taxonomic ranks using genome sequence. To assign taxonomic ranks, VirusTaxo extracts k-mers from genome sequence and creates bag-of-k-mers for each class in a rank. VirusTaxo uses a top-down hierarchical classification approach and accurately assigns the order, family and genus of a virus from the genome sequence. The average accuracies of VirusTaxo for DNA viruses are 99% (order), 98% (family) and 95% (genus) and for RNA viruses 97% (order), 96% (family) and 82% (genus). VirusTaxo can be used to detect taxonomy of novel viruses using full length genome or contig sequences.AvailabilityOnline version of VirusTaxo is available at https://omics-lab.com/virustaxo/.

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