Genomic Sequencing and Phylogenomics of Cowpox Virus

Diana Diaz-Cánova; Carla Mavian; Annika Brinkmann; Andreas Nitsche; Ugo Moens; Malachy Ifeanyi Okeke

doi:10.3390/v14102134

Genomic Sequencing and Phylogenomics of Cowpox Virus

Viruses. 2022 Sep 28;14(10):2134. doi: 10.3390/v14102134.

Authors

Diana Diaz-Cánova¹, Carla Mavian², Annika Brinkmann³, Andreas Nitsche³, Ugo Moens¹, Malachy Ifeanyi Okeke⁴

Affiliations

¹ Molecular Inflammation Research Group, Department of Medical Biology, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway.
² Emerging Pathogens Institute, Department of Pathology, College of Medicine, University of Florida, Gainesville, FL 32610, USA.
³ Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, 1335 Berlin, Germany.
⁴ Section of Biomedical Sciences, Department of Natural and Environmental Sciences, School of Arts and Sciences, American University of Nigeria, Yola PMB 2250, Nigeria.

Abstract

Cowpox virus (CPXV; genus Orthopoxvirus; family Poxviridae) is the causative agent of cowpox, a self-limiting zoonotic infection. CPXV is endemic in Eurasia, and human CPXV infections are associated with exposure to infected animals. In the Fennoscandian region, five CPXVs isolated from cats and humans were collected and used in this study. We report the complete sequence of their genomes, which ranged in size from 220-222 kbp, containing between 215 and 219 open reading frames. The phylogenetic analysis of 87 orthopoxvirus strains, including the Fennoscandian CPXV isolates, confirmed the division of CPXV strains into at least five distinct major clusters (CPXV-like 1, CPXV-like 2, VACV-like, VARV-like and ECTV-Abatino-like) and can be further divided into eighteen sub-species based on the genetic and patristic distances. Bayesian time-scaled evolutionary history of CPXV was reconstructed employing concatenated 62 non-recombinant conserved genes of 55 CPXV. The CPXV evolution rate was calculated to be 1.65 × 10^-5 substitution/site/year. Our findings confirmed that CPXV is not a single species but a polyphyletic assemblage of several species and thus, a reclassification is warranted.

Keywords: Fennoscandian; cowpox virus; molecular clock; orthopoxvirus; phylodynamics; phylogenetic; poxviridae.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Bayes Theorem
Cowpox virus
Cowpox* / veterinary
Genomics
Humans
Orthopoxvirus* / genetics
Phylogeny

Grants and funding

This research was funded by UiT—The Arctic University of Norway, grant number A212100108 and the National Graduate School in Infection Biology and Antimicrobials, grant number 249062. The APC was funded by UiT—The Arctic University of Norway.