Emergence, phylogeography, and adaptive evolution of mpox virus

Haifei Guan; Ijaz Gul; Chufan Xiao; Shuyue Ma; Yingshan Liang; Dongmei Yu; Ying Liu; Hong Liu; Can Yang Zhang; Juan Li; Peiwu Qin

doi:10.1016/j.nmni.2023.101102

Emergence, phylogeography, and adaptive evolution of mpox virus

New Microbes New Infect. 2023 Mar:52:101102. doi: 10.1016/j.nmni.2023.101102. Epub 2023 Feb 18.

Authors

Haifei Guan^{1

2}, Ijaz Gul^{1

2}, Chufan Xiao^{1

2}, Shuyue Ma^{1

2}, Yingshan Liang¹, Dongmei Yu³, Ying Liu⁴, Hong Liu⁴, Can Yang Zhang¹, Juan Li⁵, Peiwu Qin^{1

2}

Affiliations

¹ Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China.
² Tsinghua-Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China.
³ School of Mechanical, Electrical & Information Engineering, Shandong University, Weihai, Shandong, 264209, China.
⁴ Food Inspection & Quarantine Center, Shenzhen Custom, Shenzhen, Guangdong, 518060, China.
⁵ Advanced Research Institute for Multidisciplinary Science, Beijing Institute of Technology, Beijing, 100081, China.

Abstract

Mpox (Monkeypox) is a zoonotic disease caused by mpox virus (MPXV). A multi-country MPXV outbreak in non-endemic demographics was identified in May 2022. A systematic evaluation of MPXV evolutionary trajectory and genetic diversity could be a timely addition to the MPXV diagnostics and prophylaxis. Herein, we integrated a systematic evolution analysis including phylogenomic and phylogeographic, followed by an in-depth analysis of the adaptive evolution and amino acid variations in type I interferon binding protein (IFNα/βBP). Mutations in IFNα/βBP protein may impair its binding capacity, affecting the MPXV immune evasion strategy. Based on the equilibrated data, we found an evolutionary rate of $7.75 \times 10^{- 5}$ substitutions/site/year, and an earlier original time (2021.25) of the clade IIb. We further discovered significant genetic variations in MPXV genomes from different regions and obtained six plausible spread trajectories from its intricate viral flow network, implying that North America might have acted as a bridge for the spread of MPXV from Africa to other continents. We identified two amino acids under positive selection in the Rifampicin resistance protein and extracellular enveloped virus (EEV) type-I membrane glycoprotein, indicating a role in adaptive evolution. Our research sheds light on the emergence, dispersal, and adaptive evolution of MPXV, providing theoretical support for mitigating and containing its expansion.

Keywords: Evolution; IFNα/βBP; Mpox virus; Orthopoxvirus; Phylogeographic.