Rapid detection of inter-clade recombination in SARS-CoV-2 with Bolotie

Abstract

The ability to detect recombination in pathogen genomes is crucial to the accuracy of phylogenetic analysis and consequently to forecasting the spread of infectious diseases and to developing therapeutics and public health policies. However, in case of the SARS-CoV-2, the low divergence of near-identical genomes sequenced over a short period of time makes conventional analysis infeasible. Using a novel method, we identified 225 anomalous SARS-CoV-2 genomes of likely recombinant origins out of the first 87,695 genomes to be released, several of which have persisted in the population. Bolotie is specifically designed to perform a rapid search for inter-clade recombination events over extremely large datasets, facilitating analysis of novel isolates in seconds. In cases where raw sequencing data was available, we were able to rule out the possibility that these samples represented co-infections by analyzing the underlying sequence reads. The Bolotie software and other data from our study are available at https://github.com/salzberg-lab/bolotie.

Pandemic-Scale Phylogenomics Reveals Elevated Recombination Rates in the SARS-CoV-2 Spike Region

“…Our extensively optimized implementation of RIPPLES allows it to search the entire phylogenetic tree and detect recombination both within and between SARS-CoV-2 lineages without a priori defining a set of lineages or clade-defining mutations. This is a key advantage of our approach relative to other methods that cope with the scale of SARS-CoV-2 datasets by reducing the search space for possible recombination events (e.g., (9,10,14)). RIPPLES discovers 239 recombination events within branches of the same Pango lineages.…”

Ongoing Recombination in SARS-CoV-2 Revealed through Genealogical Reconstruction

“…A number of more recent reports have utilized methods based on classifying sequences into clades, and searching for those that appear to carry a mix of mutations characteristic to more than one clade. VanInsberghe et al (2021) identified 1,175 possible recombinants out of 537,000 analyzed sequences; Varabyou et al (2021) identified 225 possible recombinants out of 88,000; Jackson et al (2021) have identified a small number of putative recombinants circulating in the United Kingdom. These methods are sensitive to the classification of sequences into clades, do not allow for the detection of intra-clade recombinants (thus underestimating the overall extent of recombination), and do not incorporate a framework for quantifying how likely it is that an observed pattern of incompatibilities has arisen through recombination rather than recurrent mutation.…”

Evolution of the SARS-CoV-2 genome and emergence of variants of concern

“…Genome replication infidelity [ 98 ], intra-host viral evolution in prolonged infections, which predominantly occurs in immunocompromised individuals [ 54 , 99 – 102 ], host RNA-editing systems [ 103 ], and within-host recombination events occurring subsequently to co- or super-infection with different circulating strains [ 104 ] are considered the potential sources of SARS-CoV-2 genome sequence variability. Random mutations account for the majority of genomic variations [ 103 , 105 ]. Although most immunocompromised persons effectively clear SARS-CoV-2 infection, accelerated viral evolution in persistently infected immunocompromised individuals has been reported [ 54 , 103 , 106 ].…”

“…To the best of our knowledge, the first report of recombination between SARS-CoV-2 strains was published in August of 2020 [ 104 ]. In a few subsequent studies, recombination events between SARS-CoV-2 strains were surmised on the basis of defining markers of major clades or sequence variations in locally circulating strains [ 26 , 105 , 115 – 117 ]. It is not unlikely that some recombinant genomes have not been recognized because of technical issues in sequence analysis [ 105 ].…”

“…In a few subsequent studies, recombination events between SARS-CoV-2 strains were surmised on the basis of defining markers of major clades or sequence variations in locally circulating strains [ 26 , 105 , 115 – 117 ]. It is not unlikely that some recombinant genomes have not been recognized because of technical issues in sequence analysis [ 105 ]. In light of the importance of recombination vis a vis the emergence of novel virus strains with a large number of mutations, efforts must be made to resolve these impediments [ 54 , 106 ].…”