Detection of influenza D virus in bovine respiratory disease samples, UK

Dane, Hannah; Duffy, Catherine; Guelbenzu-Gonzalo, Maria; Hause, Ben M.; Fee, S.; Forster, Fiona; McMenamy, Michael; Lemon, Ken

doi:10.1111/tbed.13273

Cited by 43 publications

(42 citation statements)

References 14 publications

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“…Several epidemiological and serological studies have reported the isolation of IDV in cattle from many geographic areas (Canada, the United Kingdom, Japan, the United States, Mexico, Luxemburg, Ireland, France and China), suggesting that cattle may be a primary natural reservoir for the virus [6][7][8][9][10][11][12][13][14][15][16][17][18]. In addition, two studies have suggested that IDV has circulated among beef cattle since at least 2003/2004 [9,13].…”

Section: Introductionmentioning

confidence: 99%

Influenza D Virus: Serological Evidence in the Italian Population from 2005 to 2017

Trombetta

Marchi

Manini

et al. 2019

Viruses

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Influenza D virus is a novel influenza virus, which was first isolated from an ailing swine in 2011 and later detected in cattle, suggesting that these animals may be a primary natural reservoir. To date, few studies have been performed on human samples and there is no conclusive evidence on the ability of the virus to infect humans. The aim of this serological study was to assess the prevalence of antibodies against influenza D virus in human serum samples collected in Italy from 2005 to 2017. Serum samples were analysed by haemagglutination inhibition and virus neutralization assays. The results showed that the prevalence of antibodies against the virus increased in the human population in Italy from 2005 to 2017, with a trend characterized by a sharp increase in some years, followed by a decline in subsequent years. The virus showed the ability to infect and elicit an immune response in humans. However, prevalence peaks in humans appear to follow epidemics in animals and not to persist in the human population.

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Section: Introductionmentioning

confidence: 99%

Influenza D Virus: Serological Evidence in the Italian Population from 2005 to 2017

Trombetta

Marchi

Manini

et al. 2019

Viruses

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“…In Europe, IDV viruses have been detected and sequenced in France, Italy [14][15][16], Republic of Ireland and Northern Ireland (UK) [14][15][16]. D/OK is the most reported lineage circulating in Europe, even though two strains clustering separately have been reported in France and Ireland (D/bovine/France/2986/2012 and D/bovine/Ireland/07780/2014) [10,17]. In particular, since 2014, we have detected in Italy the circulation of a single genetic group within the D/OK lineage in swine and cattle population [15,16].…”

Section: Introductionmentioning

confidence: 99%

Detection of a New Genetic Cluster of Influenza D Virus in Italian Cattle

Chiapponi

Faccini

Fusaro

et al. 2019

Viruses

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Influenza D virus (IDV) has been increasingly reported all over the world. Cattle are considered the major viral reservoir. Based on the hemagglutinin-esterase (HEF) gene, three main genetic and antigenic clusters have been identified: D/OK distributed worldwide, D/660 detected only in the USA and D/Japan in Japan. Up to 2017, all the Italian IDV isolates belonged to the D/OK genetic cluster. From January 2018 to May 2019, we performed virological surveillance for IDV from respiratory outbreaks in 725 bovine farms in Northern Italy by RT-PCR. Seventy-four farms were positive for IDV. A full or partial genome sequence was obtained from 29 samples. Unexpectedly, a phylogenetic analysis of the HEF gene showed the presence of 12 strains belonging to the D/660 cluster, previously unreported in Europe. The earliest D/660 strain was collected in March 2018 from cattle imported from France. Moreover, we detected one viral strain with a reassortant genetic pattern (PB2, PB1, P42, HEF and NP segments in the D/660 cluster, whilst P3 and NS segments in the D/OK cluster). These results confirm the circulation of IDV in the Italian cattle population and highlight the need to monitor the development of the spreading of this influenza virus in order to get more information about the epidemiology and the ecology of IDV viruses.

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“…Influenza D virus (IDV) belongs to the Orthomyxoviridae, and is a single-stranded, enveloped, segmented and negative-sense RNA virus [11]. Since its discovery in swine in USA in 2011, IDV has been reported all over the world, and cattle are thought to be the natural host reservoir [10,12-12]. In addition to cattle and swine, IDV has been reported in sheep, goats, laboratory animals (ferrets and guinea pigs), and seropositivity has been detected in humans [14,16-16].…”

Section: Introductionmentioning

confidence: 99%

Assessment of metagenomic sequencing and qPCR for detection of influenza D virus in bovine respiratory tract samples

Zhang

Huang

Godson

et al. 2020

Preprint

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High throughput sequencing is currently re volutionizing the genomics field and 17 providing new approaches to the detection and characterization of microorganisms. The 18 objective of this study was to assess the detection of influenza D virus (IDV) in bovine 19 respiratory tract samples using two sequencing platforms (MiSeq and Nanopore 20 (GridION)), and species-specific qPCR. An IDV-specific qPCR was performed on 232 21 samples (116 nasal swabs and 116 tracheal washes) that had been previously subject to 22 virome sequencing using MiSeq. Nanopore sequencing was performed on 19 samples 23 positive for IDV by either MiSeq or qPCR. Nanopore sequence data was analyzed by two 24 bioinformatics methods: What's In My Pot (WIMP, on the EPI2ME platform), and an in-25 house developed analysis pipeline. The agreement of IDV detection between qPCR and 26 MiSeq was 82.3%, between qPCR and Nanopore was 57.9% (in-house) and 84.2% 27 (WIMP), and between MiSeq and Nanopore was 89.5% (in-house) and 73.7% (WIMP). 28 IDV was detected by MiSeq in 14 of 17 IDV qPCR-positive samples with Cq (cycle 29 quantification) values below 31, despite multiplexing 50 samples for sequencing. When 30 qPCR was regarded as the gold standard, the sensitivity and specificity of MiSeq sequence 31 detection were 28.3% and 98.9%, respectively. We conclude that both MiSeq and 32 Nanopore sequencing are capable of detecting IDV in clinical specimens with a range of Cq 33 values. Sensitivity may be further improved by optimizing sequence data analysis, 34 improving virus enrichment, or reducing the degree of multiplexing. 35

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Detection of influenza D virus in bovine respiratory disease samples, UK

Cited by 43 publications

References 14 publications

Influenza D Virus: Serological Evidence in the Italian Population from 2005 to 2017

Influenza D Virus: Serological Evidence in the Italian Population from 2005 to 2017

Detection of a New Genetic Cluster of Influenza D Virus in Italian Cattle

Assessment of metagenomic sequencing and qPCR for detection of influenza D virus in bovine respiratory tract samples

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