First report of natural recombination of monkeypox virus genome

In a recent study posted to the medRxiv* preprint server, researchers analyzed monkeypox (MPX) virus (MPXV) sequences during the current 2022 outbreak to investigate whether MPXV is adapting for improved survival and viral transmission among humans.

Background

The ongoing 2022 MPXV outbreak has represented MPXVA transmission in non-endemic areas beyond the western and central parts of Africa. MPXV was detected in the UK (United Kingdom) in May of 2022, and case counts increased rapidly after that in Europe, Asia, Africa, Oceania, and northern and southern parts of America.

Subsequently, on 23 July 2022, MPX was declared by the World Health Organization (WHO) as an international public health emergency, and MPXV has impacted several nations to date. Most of the viral sequences obtained from the ongoing MPXV outbreak have been reported to be B.1 MPXV clade sequences. Data on the natural recombination of MPXV are lacking.

About the study

In the present study, researchers analyzed 415 B.1 clade MPXV sequences from the national center for biotechnology information (NCBI) database between 1 January and 20 July 2022 globally by studying linkage disequilibrium [LD, a single nucleotide variant (SNV)-based analysis] and tandem repeats (TRs), with emphasis on exploring MPXV genomic variability through recombination for determining the probable risks of novel MPXV strains.

MPX recombination was assessed by analyzing tandem repeats (TRs), and LD analysis was performed to detect novel MPXV lineages and viral recombination in the ongoing 2022 outbreak MPXV genome. The viral populations were categorized into six groups based on the TR numbers (TRNs) of TRA/E. Subsequently, single nucleotide polymorphism (SNPs) analysis was performed.

Results

The analysis findings showed that the ongoing 2022 outbreak MPXV population has diverged into four and 11 lineages and subgroups, respectively, and four lineages based on the TRs and CNs (copy numbers). In addition, the LD analysis findings indicated that MPXV has evolved into three novel lineages. The team identified six, one, and one novel recombinant MPXV from Slovenia, Italy, and Australia, respectively by analyzing TRs and two and one MPXV recombinants from Germany and Spain, respectively by LD analysis.

Six TRs with varying copy numbers were identified, TR A/E had identical 16 base-pair (bp) sequences with inverted TRs at both MPXV genomic ends. In total, 378 cases (91%) and 14 cases (three percent) comprised TRNs 7.9 and 16, respectively, obtained from the United States of America (USA), the Czech Republic, and Belgium.

One case with TRN values of six, four, and three was detected in the United Kingdom (UK). The team identified 21 cases of mismatch with differing TRN values between TRs E and A. The findings indicated that genetic diversity could be categorized based on TR polymorphisms in the current MPXV outbreak populations. TR B, TR C, TR D, and TR F were found to be direct repeats situated at the inter-genic areas or 3’ terminal (inverted) TRs. TR F and TR C comprised three and one 5’-TATGATGGA-3’ bp sequence copies, respectively.

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While most of the viral sequences contained TR F (97%, TRN value of 3.5), 51% and 48% of the viral samples comprised TR C, having TRN values of 10 and eight, respectively. Based on the TR C/F patterns, MPXV populations could be categorized into four lineages (M, U, I and uncategorized lineages with 210, 193, and one case, respectively.

Further, in conjunction with TR A/E and TR C/F TRNs, the team divided MPXV populations under 11 viral subdivisions. TR D contained the nine bp 5’-ATATCATT-3’ sequence with varying CNs and TRNs ranging between 2.0 and 55, respectively. Of interest, viral sequences with higher TR D TRNs (TRN greater than 30) also contained more TR A/E TRNs (20 cases with TRN greater than 16) in the U group, indicative of greater TR diversity in the U lineage than other MPXV lineages.

Using TR polymorphisms, eight genomes of MPXV with recombinant viral crossovers were identified. Case ON755039 (FVG-ITA-01) of Italy could have originated from parental M, and I group sequences. Case ON631963 (VIDRL01) of Australia came from parental U and M group viral sequences, as did six Slovenia cases (ON631241, ON838178, ON754986, ON754985, ON609725, and ON754987). The findings also indicated that the six cases from Slovenia could have given rise to a novel lineage.

The LD analysis showed five pairs of SNP situated at G148421A/G34305A, G74357A/C22736T, C188379T/G186153A (eight cases), G189246A/G148421A, and G189246A/G34305A, with high LOD (log of odds, greater than 10) values and strong LD. G74357A /C22736T SNPs were detected in 28 MPX cases, inclusive of 25 cases, one case, one case, and one case in Germany, Austria, Portugal and the UK, respectively.

SNP pairs of C188379T/G186153A were detected in eight cases in Germany. Fourteen cases in Canada comprised G148421A/G189246A/G34305A SNPs. The findings were indicative of MPXV evolution into ≥3 novel lineages. Moreover, for the SNP pairs G5592A/G78031A and C25641T/C70777T, the upper 95% confidence interval (CI) limits were 0.9 and 0.3, respectively, strongly indicative of MPXV recombination. The findings indicated that two cases in Germany (ON637939 and ON959149) and one case in Spain (ON720849) gained mutations already through recombination.

Conclusion

Overall, the study findings showed that the TRs frequently diverged during natural transmission in the B.1 clade and that the MPXV genome is evolving and expanding rapidly during the current 2022 outbreak. Further, combined with genomic surveillance, LD and TR analyses are valuable techniques for monitoring and tracking MPXV phylogenetic recombination transmission dynamics.

*Important notice

medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Written by

Pooja Toshniwal Paharia

Dr. based clinical-radiological diagnosis and management of oral lesions and conditions and associated maxillofacial disorders.