Dataset Information

Retrospective Genotyping and Whole Genome Sequencing of a Canine Parvovirus Outbreak in Bangladesh.

ABSTRACT: Canine parvovirus 2 (CPV-2) outbreaks in close quarters such as kennels or shelters can cause substantial case fatality. Thirteen dead Labradors from a secluded kennel of security dogs presented with typical clinical signs and gross pathology of parvovirus infection. Whole genome shotgun sequencing from tissue-extracted genomic DNA detected new CPV-2a as the contributing antigenic variant. Further genotyping using polymerase chain reaction coupled with high-resolution melt assays (PCR-HRM) confirmed new CPV-2a infection in all deceased dogs. PCR-HRM of additional thirty-four clinically suspected dogs suggested that this variant is in wider community circulation, at least in the southeastern part of Bangladesh. We present complete genome sequence of the new CPV-2a variant circulating in the domestic canine population of Bangladesh.

SUBMITTER: Rakib TM

PROVIDER: S-EPMC8619975 | biostudies-literature | 2021 Oct

REPOSITORIES: biostudies-literature

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Retrospective Genotyping and Whole Genome Sequencing of a Canine Parvovirus Outbreak in Bangladesh.

Rakib Tofazzal Md TM Nath Babu Kanti BK Das Tridip T Yadav Saroj Kumar SK Raidal Shane R SR Das Shubhagata S

Pathogens (Basel, Switzerland) 20211024 11

Canine parvovirus 2 (CPV-2) outbreaks in close quarters such as kennels or shelters can cause substantial case fatality. Thirteen dead Labradors from a secluded kennel of security dogs presented with typical clinical signs and gross pathology of parvovirus infection. Whole genome shotgun sequencing from tissue-extracted genomic DNA detected new CPV-2a as the contributing antigenic variant. Further genotyping using polymerase chain reaction coupled with high-resolution melt assays (PCR-HRM) confi ...[more]

PMID: 34832529

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Project description:AimThis study aimed to detect and characterize current genotypes of canine parvovirus (CPV) in Egypt during 2018.Materials and methodsA total of 50 fecal swabs were collected from clinically infected domestic dogs of 2-5 months of age, suspected to suffer from CPV infection, from Cairo and Giza Governorates. The samples were subjected to qualitative antigen detection using the rapid test, followed by isolation on Madin-Darby Canine Kidney (MDCK) cells, molecular characterization with partial amplification of VP2 gene using polymerase chain reaction (PCR), followed by sequencing and phylogenetic analysis.ResultsOut of 50 fecal samples, 20 samples were positive (40%) by Rapid CPV/canine coronavirus Ag Test Kit. These positive samples were cultured successfully on MDCK cells. Nine randomly chosen samples out of 30 apparently negative samples were amplified using PCR with primers Hfor and Hrev to yield a typical 630 bp fragment. Then, six randomly chosen samples out of nine were amplified using PCR with primers Pbs and Pbas to yield a typical 427 bp fragment. Sequencing, BLAST analysis and assembly of the two fragments (630 bp and 427 bp) to produce 912 bp fragments, in the six samples, revealed two serotypes CPV-2b and CPV-2c. The obtained strains were submitted to GenBank and given accession numbers MK642272, MK642273, MK642274, MK642275, MK642276, and MK642277. Phylogenetic analysis of the Egyptian strains serotype 2b illustrated that they were closely related to Thailand strains (accession numbers KP715709, KP715694, KP715701, and KP715700); while Egyptian strains serotype 2c was closely related to Thailand strains (accession numbers MH711894 and MH711902), Taiwanese strain (KU244254), Chinese strain (MF467242), and Vietnamese strain (accession number LC216910).ConclusionThe current research recommends further epidemiological studies to assess the extent of the occurrence of different serotypes of CPV in Egypt and the efficiency of imported and locally produced vaccines in protection against CPV infection.

Project description:BACKGROUND: Understanding Mycobacterium tuberculosis (Mtb) transmission is essential to guide efficient tuberculosis control strategies. Traditional strain typing lacks sufficient discriminatory power to resolve large outbreaks. Here, we tested the potential of using next generation genome sequencing for identification of outbreak-related transmission chains. METHODS AND FINDINGS: During long-term (1997 to 2010) prospective population-based molecular epidemiological surveillance comprising a total of 2,301 patients, we identified a large outbreak caused by an Mtb strain of the Haarlem lineage. The main performance outcome measure of whole genome sequencing (WGS) analyses was the degree of correlation of the WGS analyses with contact tracing data and the spatio-temporal distribution of the outbreak cases. WGS analyses of the 86 isolates revealed 85 single nucleotide polymorphisms (SNPs), subdividing the outbreak into seven genome clusters (two to 24 isolates each), plus 36 unique SNP profiles. WGS results showed that the first outbreak isolates detected in 1997 were falsely clustered by classical genotyping. In 1998, one clone (termed "Hamburg clone") started expanding, apparently independently from differences in the social environment of early cases. Genome-based clustering patterns were in better accordance with contact tracing data and the geographical distribution of the cases than clustering patterns based on classical genotyping. A maximum of three SNPs were identified in eight confirmed human-to-human transmission chains, involving 31 patients. We estimated the Mtb genome evolutionary rate at 0.4 mutations per genome per year. This rate suggests that Mtb grows in its natural host with a doubling time of approximately 22 h (400 generations per year). Based on the genome variation discovered, emergence of the Hamburg clone was dated back to a period between 1993 and 1997, hence shortly before the discovery of the outbreak through epidemiological surveillance. CONCLUSIONS: Our findings suggest that WGS is superior to conventional genotyping for Mtb pathogen tracing and investigating micro-epidemics. WGS provides a measure of Mtb genome evolution over time in its natural host context.

Dataset Information

Retrospective Genotyping and Whole Genome Sequencing of a Canine Parvovirus Outbreak in Bangladesh.

Publications

Retrospective Genotyping and Whole Genome Sequencing of a Canine Parvovirus Outbreak in Bangladesh.

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