Genomic Sequencing and Analysis of a Novel Human Cowpox Virus With Mosaic Sequences From North America and Old World Orthopoxvirus

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

doi:10.3389/fmicb.2022.868887

Genomic Sequencing and Analysis of a Novel Human Cowpox Virus With Mosaic Sequences From North America and Old World Orthopoxvirus

Front Microbiol. 2022 May 3:13:868887. doi: 10.3389/fmicb.2022.868887. eCollection 2022.

Authors

Diana Diaz-Cánova¹, Ugo L Moens¹, Annika Brinkmann², Andreas Nitsche², Malachy Ifeanyi Okeke³

Affiliations

¹ Molecular Inflammation Research Group, Department of Medical Biology, UiT - The Arctic University of Norway, Tromsø, Norway.
² 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, Berlin, Germany.
³ Section of Biomedical Sciences, Department of Natural and Environmental Sciences, School of Arts and Sciences, American University of Nigeria, Yola, Nigeria.

Abstract

Orthopoxviruses (OPXVs) not only infect their natural hosts, but some OPXVs can also cause disease in humans. Previously, we partially characterized an OPXV isolated from an 18-year-old male living in Northern Norway. Restriction enzyme analysis and partial genome sequencing characterized this virus as an atypical cowpox virus (CPXV), which we named CPXV-No-H2. In this study, we determined the complete genome sequence of CPXV-No-H2 using Illumina and Nanopore sequencing. Our results showed that the whole CPXV-No-H2 genome is 220,276 base pairs (bp) in length, with inverted terminal repeat regions of approximately 7 kbp, containing 217 predicted genes. Seventeen predicted CPXV-No-H2 proteins were most similar to OPXV proteins from the Old World, including Ectromelia virus (ECTV) and Vaccinia virus, and North America, Alaskapox virus (AKPV). CPXV-No-H2 has a mosaic genome with genes most similar to other OPXV genes, and seven potential recombination events were identified. The phylogenetic analysis showed that CPXV-No-H2 formed a separate clade with the German CPXV isolates CPXV_GerMygEK938_17 and CPXV_Ger2010_MKY, sharing 96.4 and 96.3% nucleotide identity, respectively, and this clade clustered closely with the ECTV-OPXV Abatino clade. CPXV-No-H2 is a mosaic virus that may have arisen out of several recombination events between OPXVs, and its phylogenetic clustering suggests that ECTV-Abatino-like cowpox viruses form a distinct, new clade of cowpox viruses.

Keywords: Fennoscandian; Norway; phylogenetics; poxvirus; recombination.