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Use of Next Generation Sequencing to study two cowpox virus outbreaks
Markus H Antwerpen1, Enrico Georgi1, Alexandra Nikolic1
1Bundeswehr Institute of Microbiology, Munich, Germany.
Peerj
|March 9, 2019
Summary
Whole genome sequencing is crucial for accurately tracing cowpox virus (CPXV) outbreaks. Analyzing only the hemagglutinin gene can be insufficient for molecular traceback, especially with highly clonal strains.
Area of Science:
- Veterinary Virology
- Molecular Epidemiology
- Genomics
Background:
- Cowpox virus (CPXV) outbreaks in humans and cats linked to pet rats and veterinary clinics occurred between 2008-2011 and 2015.
- Identical hemagglutinin gene sequences suggested common sources, but epidemiological data required further investigation.
- Next-Generation Sequencing (NGS) was employed to re-evaluate these CPXV outbreaks.
Purpose of the Study:
- To investigate the genetic relatedness of CPXV isolates from distinct outbreaks.
- To determine the efficacy of hemagglutinin gene sequencing versus whole genome sequencing for molecular traceback.
- To confirm transmission routes in suspected CPXV outbreaks.
Main Methods:
- Virus isolation from clinical samples (lesions) of rats, cats, and humans.
- Whole genome sequencing of CPXV isolates and archived paraffin-embedded tissues.
- Phylogenetic analysis using MAFFT alignment, SNP-based distance matrix, and UPGMA dendrograms.
Main Results:
- The 2008-2011 pet rat-associated outbreak was caused by a single, highly clonal CPXV strain, with minimal genomic variation (≤3 SNPs).
- Genomic sequencing revealed that only three out of four suspected hospital-acquired feline CPXV cases involved transmission within the clinic.
- Hemagglutinin gene sequencing alone was insufficient to differentiate closely related CPXV strains or confirm transmission events accurately.
Conclusions:
- Whole genome sequencing is the definitive method for molecular traceback of CPXV outbreaks.
- NGS can be applied to various sample types, including ancient DNA from paraffin-embedded specimens.
- Relying solely on limited genetic markers like the hemagglutinin gene can lead to misinterpretations in outbreak investigations.
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