Co-variation of viral recombination with single nucleotide variants during virus evolution revealed by CoVaMa

Abstract

Adaptation of viruses to their environments occurs through the acquisition of both novel Single-Nucleotide Variants (SNV) and recombination events including insertions, deletions, and duplications. The co-occurrence of SNVs in individual viral genomes during their evolution has been well-described. However, unlike covariation of SNVs, studying the correlation between recombination events with each other or with SNVs has been hampered by their inherent genetic complexity and a lack of bioinformatic tools. Here, we expanded our previously reported CoVaMa pipeline (v0.1) to measure linkage disequilibrium between recombination events and SNVs within both short-read and long-read sequencing datasets. We demonstrate this approach using long-read nanopore sequencing data acquired from Flock House virus (FHV) serially passaged in vitro. We found SNVs that were either correlated or anti-correlated with large genomic deletions generated by nonhomologous recombination that give rise to Defective-RNAs. We also analyzed NGS data from longitudinal HIV samples derived from a patient undergoing antiretroviral therapy who proceeded to virological failure. We found correlations between insertions in the p6Gag and mutations in Gag cleavage sites. This report confirms previous findings and provides insights on novel associations between SNVs and specific recombination events within the viral genome and their role in viral evolution.

Generation and Functional Analysis of Defective Viral Genomes during SARS-CoV-2 Infection

“…We used ViReMa to identify DVGs, as this algorithm has been developed and validated to faithfully identify recombination events in a range of plant viruses ( 65 – 67 ), insect viruses ( 68 , 69 ), arthropod-borne viruses (arboviruses) ( 70 – 72 ), human pathogens (influenza virus [ 73 ], reovirus [ 74 ], MERS-CoV, and SARS-CoV-2 [ 17 , 75 ]), and retroviruses (human immunodeficiency virus [HIV]) ( 76 ). It has also been validated independently by Alnaji et al ( 77 ) and Boussier et al ( 78 ) who provided a series of condition and parameter optimizations using simulated and experimental data to map RNA recombination events in DVGs of influenza A and B.…”

ViReMa: A Virus Recombination Mapper of Next-Generation Sequencing data characterizes diverse recombinant viral nucleic acids

“…ViReMa has been independently validated by Alnaji et al (33) and Boussier et al (34) who provided a series of condition and parameter optimizations using simulated and experimental data to map RNA recombination events in DVGs of influenza A and B. ViReMa has been used and validated to study viral recombination in range a of plant viruses (Polygonum ringspot virus (PolRSV) (35), Tomato yellow leaf curl virus (TYLCV) (36), Potato X Virus (37)), insect viruses (Flock House virus (FHV) (38), Cricket Paralysis virus (CrPV) (39)), arboviruses virus (Zika virus (ZIKV) (40), Chikungunya virus (CHIKV) (41, 42)), human pathogens (Influenza virus (43), Reovirus (44), MERS-CoV and SARS-CoV-2 (45, 46)), and retroviruses (Human Immunodeficiency Virus (HIV) (7)).…”

“…Simple duplications of the viral genome are frequently observed during the intra-host diversification of HIV during anti-retroviral treatments. These duplications include short 9-21 AA stretches near the protease cleavage sites of GAG that result in altered processing kinetics of GAG by the HIV protease in the presence of protease inhibitors (7–11).…”