Whole-genome sequencing of parvoviruses from wild and domestic animals in Brazil provides new insights into parvovirus distribution and diversity

Souza, William Marciel de; Dennis, Tristan; Fumagalli, Marcílio Jorge; Araújo, Jansen de; Santos, Gilberto Sabino dos; Maia, Felipe Gonçalves Motta; Acrani, Gustavo Olszanski; Carrasco, Adriano de Oliveira Torres; Romeiro, Marília Farignoli; Modha, Sejal; Vieira, Luiz Carlos; Ometto, Tatiana; Queiroz, Luzia Helena; Durigon, Edison Luiz; Nunes, Márcio Roberto Teixeira; Figueiredo, Luíz Tadeu Moraes; Gifford, Robert J.

doi:10.1101/268219

Cited by 5 publications

(3 citation statements)

References 40 publications

(44 reference statements)

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“…The infection rate of bovine parvovirus (BPV) is about 83% to 100% worldwide [6,19]. The bovine viral diarrhea virus (BVDV) is a key pathogenic factor in bovine diarrhea [7,11].…”

Section: Discussionmentioning

confidence: 99%

“…Then, BL-21 competent cells were transferred with the recombinant plasmids of DNA/PCR products and pMD18-T at 37 overnight. The recombinant plasmids were extracted using the EasyPureR Plasmid MiniPrep Kit 5 and sequenced 6 . The sequences homology of the recombinant plasmids was compared with those of NCBI Genbank after they were sequenced by Shanghai Sangon Biotec, Shanghai, China.…”

Section: Construction Of Standard Plasmids and Copiesmentioning

confidence: 99%

“…Bovine parvovirus (BPV) and bovine viral diarrhea virus (BVDV) are key pathogenic factors causing viral diarrhea of calves [2]. The genome of BPV comprises of single-stranded DNA [6,23] and possesses three ORFs. ORF3 encodes VP1 and VP2 capsid viral proteins which share a C-terminal end [3].…”

Section: Introductionmentioning

confidence: 99%

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Synchronous Detection of BPV and BVDV with Duplex Taqman qPCR Method

Gong

Shen

Liang

et al. 2019

Acta Scientiae. Vet.

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Background: Bovine parvovirus (BPV) and bovine viral diarrhea virus (BVDV) are commonly etiologies causing diarrhea in dairy herds. BPV is a member of bocaparvovirus genus with a non-enveloped capsid. BVDV, belonging to Pestivirus genus in Flaviviridae, possesses a single-stranded RNA, and is classified into BVDV-1 and BVDV-2 genotypes according to the 5’UTR sequence. 21 genetic groups of BVDV-1 and four groups of BVDV-2 have been found. Diagnosis of viral diarrhea is often relied on virus detection by isolation or detection of serum antibody. The main objective of the present study was to establish a duplex real time PCR (qPCR) based on Taqman probe to detect synchronously BPV and BVDV. Materials, Methods & Results: TaqMan probe and primers were designed and synthesized from the sequences of conserved 5′ - untranslated regions (5′ UTR) of Haden strain of BPV and NADL strain of BVDV. The cDNAs were transcribed in vitro to make standard curves before optimizing the assay. DNA/PCR products were ligated into pMD18-T vector, and then used to transfer BL-21 competent cells to acquire the recombinant plasmids of pMD18-T-BPV and pMD18-T-BVDV. Optimum reaction conditions were comparatively selected. The sensitivity, specificity and reproducibility of TaqMan probe qRT-PCR were evaluated respectively. The results showed the concentrations of pMD18-T-BPV or pMD18-T-BVDV were 2.0 × 1010 DNA copies/μL, respectively. A duplex Taqman qPCR method was developed by optimizing the amplification conditions to simultaneously detect BPV and BVDV. The assay targets at highly conserved VP2 gene of BPV and 5′ UTR gene of BVDV. This qPCR assay was assessed for specificity and sensitivity using DNA of BPV and cDNA of BVDV. For clinical validation, 308 samples were tested from clinically diarrhea calves. The results showed that optimum annealing temperature was achieved in 43.2 ℃ fro duplex BPV and BPIV. Dynamic curves and standard curves were created following amplification of recombinant plasmids using the optimized duplex Taqman BPV and BVDV, with an amplification efficiency of 95.69%. Duplex Taqman qPCR could only detect DNA of BPV and cDNA of BVDV with a strong specificity. The detection limitation was as low as 2.0 × 102 copies/μL of pMD18-T-BPV plasmid and 2.0 × 101 copies/μL for pMD18-T-BVDV plasmid, respectively. Sensitivity of detection was 100-fold higher than conventional PCR. Duplex Taqman qPCR had excellent repeatability or stability with less than 1.2% of intra-assay and inter-assay. 35 and 47 positive feces samples were identified using duplex Taqman qPCR in comparison to 30 and 42 positives for universal PCR, respectively. Discussion: The bovine viral diarrhea virus (BVDV) is a key pathogenic factor in bovine diarrhea. Currently, few effective measures are available for the treatment or prevention for BVDV and BPV infections in animals. The technique was proven to be repeatable and linear over a range of at least 5 magnitudes, from 101 to 105 RNA/DNA copies, thus ensuring an accurate measurement of BPV DNA and BVDV RNA loads in clinical samples. In conclusion, a duplex Taqman qPCR was established for detecting simultaneously BPV and BVDV. Taqman qPCR method was rapid and specific assay. This assay was 100-fold sensitive than conventional PCR. It will be propitious to rapidly and differentially diagnose pathogens of viral diarrhea of dairy farms. Taqman qPCR method was rapid and specific assay and had a sensitivity of 2.0 copies/μL.

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“…The infection rate of bovine parvovirus (BPV) is about 83% to 100% worldwide [6,19]. The bovine viral diarrhea virus (BVDV) is a key pathogenic factor in bovine diarrhea [7,11].…”

Section: Discussionmentioning

confidence: 99%

Section: Construction Of Standard Plasmids and Copiesmentioning

confidence: 99%

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Synchronous Detection of BPV and BVDV with Duplex Taqman qPCR Method

Gong

Shen

Liang

et al. 2019

Acta Scientiae. Vet.

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Metagenomic Identification of Novel Eukaryotic Viruses with Small DNA Genomes in Pheasants

Kaszab,

Bali,

Marton

et al. 2024

Animals

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A panel of intestinal samples collected from common pheasants (Phasianus colchicus) between 2008 and 2017 was used for metagenomic investigation using an unbiased enrichment protocol and different bioinformatic pipelines. The number of sequence reads in the metagenomic analysis ranged from 1,419,265 to 17,507,704 with a viral sequence read rate ranging from 0.01% to 59%. When considering the sequence reads of eukaryotic viruses, RNA and DNA viruses were identified in the samples, including but not limited to coronaviruses, reoviruses, parvoviruses, and CRESS DNA viruses (i.e., circular Rep-encoding single-stranded DNA viruses). Partial or nearly complete genome sequences were reconstructed of at least three different parvoviruses (dependoparvovirus, aveparvovirus and chaphamaparvovirus), as well as gyroviruses and diverse CRESS DNA viruses. Generating information of virus diversity will serve as a basis for developing specific diagnostic tools and for structured epidemiological investigations, useful to assess the impact of these novel viruses on animal health.

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Emerging and Novel Viruses in Passerine Birds

Williams,

Sánchez-Llatas,

Doménech

et al. 2023

Microorganisms

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There is growing interest in emerging viruses that can cause serious or lethal disease in humans and animals. The proliferation of cloacal virome studies, mainly focused on poultry and other domestic birds, reveals a wide variety of viruses, although their pathogenic significance is currently uncertain. Analysis of viruses detected in wild birds is complex and often biased towards waterfowl because of the obvious interest in avian influenza or other zoonotic viruses. Less is known about the viruses present in the order Passeriformes, which comprises approximately 60% of extant bird species. This review aims to compile the most significant contributions on the DNA/RNA viruses affecting passerines, from traditional and metagenomic studies. It highlights that most passerine species have never been sampled. Especially the RNA viruses from Flaviviridae, Orthomyxoviridae and Togaviridae are considered emerging because of increased incidence or avian mortality/morbidity, spread to new geographical areas or hosts and their zoonotic risk. Arguably poxvirus, and perhaps other virus groups, could also be considered “emerging viruses”. However, many of these viruses have only recently been described in passerines using metagenomics and their role in the ecosystem is unknown. Finally, it is noteworthy that only one third of the viruses affecting passerines have been officially recognized.

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Whole-genome sequencing of parvoviruses from wild and domestic animals in Brazil provides new insights into parvovirus distribution and diversity

Cited by 5 publications

References 40 publications

Synchronous Detection of BPV and BVDV with Duplex Taqman qPCR Method

Synchronous Detection of BPV and BVDV with Duplex Taqman qPCR Method

Metagenomic Identification of Novel Eukaryotic Viruses with Small DNA Genomes in Pheasants

Emerging and Novel Viruses in Passerine Birds

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