The study attributes increased transmissibility of Monkeypox Clade IIb to genomic accordions

The study attributes increased transmissibility of Monkeypox Clade IIb to genomic accordions

In a recent study published in bioRxiv * Server: Researchers conducted a genomic study of confirmed cases of Monkeypox virus (MPXV) diagnosed in Spain between May 18 and July 14, 2022.

Lernen: Genomische Akkordeons könnten der Schlüssel zur erhöhten Übertragbarkeit von Monkeypox Clade IIb sein. Bildquelle: FOTOGRIN/Shutterstock

*Important NOTE:bioRxiv publishes preliminary scientific reports that are not peer-reviewed and therefore should not be considered conclusive, intended to guide clinical practice/health-related behavior, or treated as established information.

background

In the current outbreak, the number of disseminated MPXV transmissions has remained consistently low, and person-to-person transmission (PTP) appears to occur after a primary localized rash appears. If the latter mode is responsible for MPXV transmission, it should also be reflected at the genomic level. To date, all genomic studies have focused on describing the evolutionary history of MPXV and tracking its introduction into the virus in Western countries.

These studies revealed that the 2022 MPXV cluster diverges from the corresponding 2016-2019 MPXVs by an average of 50 single nucleotide polymorphisms (SNPs), with approximately 24 nonsynonymous mutations, ~18 synonymous mutations, and some intergenic differences. They attributed the mutation bias mainly to the action of apolipoprotein B mRNA-editing catalytic polypeptide-like 3 enzymes (APOBEC3). In addition, they described genetic variations of MPXV, including deletion of immunomodulatory genes. Until now, the host exerted selective pressure, and the loss of genes that interact with the virus was the driver of MPXV evolution.

Retrospective evolutionary studies have demonstrated the unique adaptive strategies of MPXV; However, these studies failed to resolve genomic regions with many repeats, particularly the low complexity regions (LCRs). LCRs are not randomly located in the genome and may be associated with adaptive changes related to differences in MPXV transmissibility. They have different levels of complexity, such as dinucleotide, trinucleotide or more complex palindromic repeats. Previous studies have shown that genomic accordions provide a rapid route to adaptation of poxviruses during serial passage. There is an urgent need to examine these genomic features in the context of MPXV evolutionary adaptation.

About the study

In the present study, researchers examined the effects of LCRs, including all short tandem repeats (STRs) and homopolymer changes, in the MPXV genome. They compared the distribution of LCRs between different key functional groups in the MPXV genome. In addition, the researchers assessed the extent of intra-host and inter-host variations in LCR.

The team first obtained a high-quality genome from an unpassaged vesicular fluid from an MPXV case in Spain. They then used a conventional validated MPXV nested polymerase chain reaction (PCR) targeting the transferrin (TFN) receptor gene to confirm the presence of MPXV in swabs from skin lesions. Next, they combined three sequencing technologies, NovaSeq, MiSeq and nanopore sequencing, to read the entire genome.

Study results

Only two genome samples, 353R and 349R, provided high-quality viral measurements for comparison of allele frequencies in most LCR areas. While LCR8 and LCR9 showed no variation, LCR7 and LCR10/11 showed significant within-host variation and differences in the predominant allele between samples. Based on whole-genome heterozygosity, the magnitude and magnitude of variations were significantly higher for LCR than for SNPs, and the same also occurred within the host.

Four samples belonged to B.1.1, defined by an amino acid mutation in OPG094 R194H. They identified one sample as B.1.3, defined by the amino acid mutation R84K, corresponding to position G190.660A, and the remaining samples belonged to B1 clade IIb. Among group IIb, the B1 strains consistently showed 16 repeats. The A.1 strain was polymorphic, A.2 strains showed 23, 25 and 26 repeats, while older lineage A strains had 32, 43, 53 and 71 repeats. Although the researchers discovered additional clusters among the Spanish isolates defined by some SNP changes; However, they only found an epidemiological connection in one case.

Since the current study results showed a limited association between SNP changes and viral epidemiology, a potential convergence effect has likely occurred for this class of viruses, necessitating a change in focus in their genomic epidemiology studies. The researchers identified 21 LCRs, 13 STRs and eight homopolymers. Comparison of the diversity level between the 21 identified LCRs with SNP variability revealed eight LCR regions (1/4, 2, 3, 5, 6, 7, 10/11, 21) with obvious signs of variation within host and between samples.

Five LCRs were colocalized in two regions of the MPXV genome, with LCRs 5, 6, and 7 located in the core of the MPXV genome. LCRs 3 and 21 were located in the immunomodulatory region, and the other three LCRs were located within the putative translated region of the MPXV genes OPG153 (A26L), OPG204 (B16R), and OPG208 (B19R). The changes in repeat number observed in LCR3 and LCR21 followed the same pattern by expanding the N-terminal region of an immunomodulatory open reading frame (ORF). Given the unusually long repetitive stretch of LCR3, clade IIb MPXV may require large amounts of tyrosine: translational ribonucleic acid (tRNA) to translate the OPG208 gene. This may represent another potential method by which viral tandem repeat sequences adapt to a new environment by modulating ORF expression.

The researchers found that the changes associated with LCR21/OPG204 were subtle. They did not observe changes in the number of repeats, but rather in mutations. Therefore, most clade IIb viruses exhibited multiple alternative starts followed by a lysine amino acid that was always encoded by the rarest codon. The most intriguing area of ​​variability observed in the ORF involved the OPG153 gene, which is an essential factor in OPXV transmission and virulence. For example, it is the core gene that was most frequently “lost” during the evolution of the smallpox virus. The LCR7 repeat region, located in the central domain of OPG153, encodes an unstructured polyaspartic acid (poly-D) region that is conserved among OPXVs; however, its length varies greatly. Interestingly, class IIa MPXV strains have a poly-D extended by 21 amino acids.

Conclusions

The study results expanded the concept of genome accordions in MPXV evolution. The study showed that LCRs of the genome, currently unresolved in genomic studies, could be crucial for managing changes in host range or virulence and contain important transmission information. Therefore, there is a need to establish a new standardized approach to generate and analyze the sequencing data that prioritizes these regions. Further functional studies are urgently needed to complement this comparative genomic study.

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

Reference:

• Vorläufiger wissenschaftlicher Bericht.
  Sara Monzon, Sarai Varona, Anabel Negredo, et al. (2022). Genomische Akkordeons könnten der Schlüssel zur erhöhten Übertragbarkeit von Monkeypox Clade IIb sein. bioRxiv. doi: https://doi.org/10.1101/2022.09.30.510261 https://www.biorxiv.org/content/10.1101/2022.09.30.510261v2

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