Variations in regions of low complexity in the monkeypox genome were found to influence virus transmissibility

Variations in regions of low complexity in the monkeypox genome were found to influence virus transmissibility

In a recently published study bioRxiv * Preprint servers, researchers examined whether low-complexity regions (LCRs) are more likely to be responsible for the current outbreak of the 2022 IIb clade monkeypox (MPX) virus (MPXV) than single-nucleotide polymorphisms (SNPs).

Lernen: Änderungen in einem neuen Typ von genomischem Akkordeon können die Paletten für eine erhöhte Übertragbarkeit von Affenpocken öffnen. Bildnachweis: MIA Studio/Shutterstock

*Important NOTE:bioRxiv publishes preliminary scientific reports that have not been peer-reviewed and therefore should not be considered conclusive, guide clinical practice/health behavior, or be treated as established information.

background

The ongoing MPXV outbreak is due to infection with the IIb subclass MPXV. In contrast to Clade I and Clade IIa MPXV-caused MPX cases, the current outbreak prognosis is largely favorable despite significantly more efficient human-to-human MPXV transmission. MPXV has evolved due to selective pressure from hosts and gene losses upon interaction with the host. To date, there have been unsatisfactory genomic explanations for SNPs responsible for the increased transmissibility of MPXV.

About studying

The present study investigated whether LCR variations are primarily responsible for MPXV genomic alterations and the unexpected epidemiology of the MPXV-2022 outbreak.

The II subclade B.1 MPXV lineage sequences were assembled de novo using a mapping method that included the use of shotgun metagenomics and short reads sequencing of ribonucleic acid (RNA) and deoxyribonucleic acid (DNA) extracted from swabs of vesicular lesions from MPX patients diagnosed between May 18 and July 14, 2022 in Spain.

LCR resolution was performed based on reference genome mapping, and in silico analyzes were performed. Results were applied to publicly available MPXV NCBI (National Center for Biotechnology Information) SRA (Sequence Read Archive) datasets (n=35) of single-molecule raw reads. A combination of different sequencing strategies was used to determine the actual LCR sequence.

The LCR distribution between different functional protein orthologous poxvirus gene (OPG) groups and the extent of diversity among the 21 identified LCRs were compared. For all LCRs across all data samples, allele frequencies were characterized and comparatively assessed.

Results

An MPXV genome HQS 353R, which represented the current MPXV outbreak in 2022, was pinpointed based on LCR variations with significant STR variations in the LCRs. In the MPXV genome, LCR entropy was significantly higher than SNP entropy. In silico analyzes showed that the expression, translation, stability or function of MPXV OPGs 153, 204 and 208 could be influenced by the genomic evolutionary accord with rhythmic genome expansions and contractions.

A total of 48 MPXV genome sequences were determined with ≥10x read depth and 39,697,742 HQ reads for each swab. One contig, two contigs, three contigs, and one contig belonged to MPXV with 101%, 97%, and 97% coverage of the MPXV M5312_HM12_Rivers sequence, respectively. A total of 21 LCRs were identified, with LCR pairs 10/11 and 1/4 having similar copies in the reverse complementary formations.

LCR3 contained a TR with the ATAT [ACATTATAT]n sequence, and analysis showed that n = 52. None of the publicly available MPXV orthopoxvirus genome sequences had a similar long TR. Four MPXV genome sequences of the IIb clade B.1 lineage of the current MPXV outbreak in 2022 showed n = 54 to 62 LCR3 repeats, and the number of STRs distinguished the sequences from the IIb subclade A lineage genome sequences (12 to 42 STRs in LCR3 regions). , indicating high genetic variability in LCR3.

Likewise, lineage-specific STR differences of the IIb subclass MPXV were detected in the 1/4 LCR pair. The pair contained an STR with the [AACTAACTTATGACTT]n sequence, and the analysis results showed that n = 16. LCR3 appeared to be longer since viral spillover, whereas the length of the 1/4 LCR pair appeared to have decreased and behaved like a genomic accordion over time.

The genomic sequences of the II subclade B.1 line MPXV_USA_2022_MA001 and 353R had 67 SNPs compared to the reference isolation sequences of the II subclade A line. Additionally, the 353R HQS contained two additional SNP pairs on inverted repeats (ITRs) right and left, resulting in an OPG015 gene stop codon. The MPXV_USA_2022_MA001 and 353R sequences also differed by two indels (insertions-deletions) of bases located at positions 077,133 and 273,173, corresponding to the differences of the LCR2 region and the LCR5 region, respectively.

The 353R-HQS differed by 1,338 base pairs (bp) and 1,342 bp in genomic length compared to the MPXV M5312_HM12_Rivers and MPXV_USA_2022_MA001 sequences, respectively. MPXV LCRs were distributed nonrandomly, with significant purifying power of selection against introduction of LCR into central conserved sites. In 353R HQS, LCR regions 2, 5, 7, 10, 11, and 21 showed intrahost genomic diversity with entropy values ​​between 0.2 and 1.7, with significantly greater diversity in LCRs compared to those in SNPs. The average Euclidean distance between samples for LCRs was between 0.1 (LCR21) and 0.7 (LCR2), and the LCR differences showed statistical significance.

The LCR 10/11 pair and LCR7 showed considerable within-host variation and predominant allelic differences between samples. LCRs 5, 6, and 7 were located at a defined central conserved site of the MPXV genome between genome positions 130,000 and 138,000, and the site included OPGs-152, 153, and 154. LCR7 was located at a functional ORF center, while LCR3 and 21 were located in the promoter/start site, which is likely ORF's starting point changed. The region between positions 170,000 and 180,000 included LCRs 2, 3, 19, 20, and 21 and was another site of functional impact.

Overall, the study results showed that most of the MPXV genome variability occurred in LCRs. Therefore, research focusing on MPXV phenotypic differences should focus on LCR variations rather than SNP variations.

*Important NOTE:bioRxiv publishes preliminary scientific reports that have not been peer-reviewed and therefore should not be considered conclusive, guide clinical practice/health behavior, or be treated as established information.

Reference:

• Vorläufiger wissenschaftlicher Bericht.
  Sara Monzonet al. (2022). Änderungen in einem neuen Typ von genomischem Akkordeon können die Paletten für eine erhöhte Übertragbarkeit von Affenpocken öffnen. bioRxiv. doi: https://doi.org/10.1101/2022.09.30.510261 https://www.biorxiv.org/content/10.1101/2022.09.30.510261v3

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