Recombination shapes 2022 monkeypox outbreak

Abstract

Here we report the first evidence of recombination of monkeypox genome in natural transmission by analyzing six tandem repeats (TRs) among 415 sequences collected between January to July 2022. The 2022 monkeypox viral population has diverged into 11 subgroups based on various TRs and their copy numbers. Here we identify 8 new recombinants (six from Slovenia, one from Australia, one from Italy). Our results indicate that the monkeypox genome is evolving and expanding quickly during the 2022 pandemic (Zeng E = -1.65, Achaz Y=-2.52, p< 0.001). We conclude that, In combination with genomic surveillance, TR analysis is a useful tool to monitor and track phylogenetic dynamics of monkeypox transmission.

A comprehensive review of monkeypox virus and mpox characteristics

“…However, MPXV can inhibit host immune responses, although a recombinant VACV expressing the MPXV F3L gene did not inhibit host PKR activation ( Arndt et al., 2015 ), suggesting that MPXV has evolved to encode for yet undiscovered proteins that compensate for the missing N-terminal amino acids of F3 in limiting host antiviral activities. As previously mentioned, MPXV CCP ( D14L gene) is completely absent in Clade II isolates, whereas the Clade I strains are predicted to express CCP, albeit with a truncated fourth short consensus repeat ( Yeh and Contreras, 2022 ). Loss of expression of CCP/MOPICE limited the adaptive immune response against MPXV infection in rhesus macaques ( Estep et al., 2011 ).…”

“…The low clade supports are probably due to very low genetic variability among isolates (Scarpa et al, 2022). Polytomy within lineage B.1 could be an indication of uncertainty in the relatedness of isolates or the belief that those isolates evolved independently from a single origin (Slowinski, 2001;Phylogenetic pitchforks -Understanding Evolution, 2023), although recombination cannot be excluded (Yeh et al, 2022).…”

“…Gigante et al (Gigante et al, 2022) suggested the possibility of recombination in MPXV following observation of three sequences that showed a chimeric pattern in their genomes, although assembly errors could be a plausible explanation. Recently, tandem repeats and linkage disequilibrium analysis provided evidence of natural recombination in lineage B.1 (Yeh et al, 2022).…”

Adaptive changes in sexual behavior in the high‐risk population in response to human monkeypox transmission in Canada can help control the outbreak: Insights from a two‐group, two‐route epidemic model

“…This is an important distinction because we are still unsure about the precise transmission mechanisms, that is to say whether contagion is occurring through body fluids exchanged during sexual intercourse, or via contact with mucosal surfaces, scarification, or even respiratory exposures via droplets. 13 On the other hand, this new epidemiological trend seems to suggest that the monkeypox virus may have mutated, 14 adapted, and found a niche in high income countries among subjects with patterns of high frequencies of close, physical contact, like the MSM community. 15 Canada has become one of the most affected countries in the WHO Region of the Americas, reporting 1400 monkeypox cases (2.1% of all the cases worldwide), across 9 provinces or territories, 38 of which requiring hospitalization.…”

Monkeypox virus: an ongoing global outbreak hitting the non-endemic countries - a comprehensive review.

“…Like all orthopoxviruses, its genome comprises two terminal ends, called Telomeres. These contain identical but oppositely oriented adjacent repetitive nucleotide sequences, called Inverted Terminal Repeats (ITRs); they make up about 3% of monkeypox viral genome and are responsible for genetic variation and mutations (35). The monkeypox genome encodes several essential viral proteins that are categorized into three groups: i) Viral proteins that assist the virus to invade host cells by attaching to their glycoprotein receptors and enter via macropinocytosis; ii) viral proteins that liberate intracellularly proliferated viral replicas into the extracellular environment; iii) proteins that serve as immune modulators to host cell defenses.…”