Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City
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Abstract
Recombination is an evolutionary process by which many pathogens generate diversity and acquire novel functions. Although a common occurrence during coronavirus replication, detection of recombination is only feasible when genetically distinct viruses contemporaneously infect the same host. Here, we identify an instance of SARS-CoV-2 superinfection, whereby an individual was infected with two distinct viral variants: Alpha (B.1.1.7) and Epsilon (B.1.429). This superinfection was first noted when an Alpha genome sequence failed to exhibit the classic S gene target failure behavior used to track this variant. Full genome sequencing from four independent extracts reveals that Alpha variant alleles comprise around 75% of the genomes, whereas the Epsilon variant alleles comprise around 20% of the sample. Further investigation reveals the presence of numerous recombinant haplotypes spanning the genome, specifically in the spike, nucleocapsid, and ORF 8 coding regions. These findings support the potential for recombination to reshape SARS-CoV-2 genetic diversity.
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SciScore for 10.1101/2022.01.18.22269300: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Rolling circle amplification and Sanger sequencing of the clones were performed by GeneWiz (New Jersey). GeneWizsuggested: (GENEWIZ, RRID:SCR_003177)Major and minor variant calling: We used the Galaxy SARS-CoV-2 variant calling pipeline for paired-end Illumina ARTIC amplicon data 21. Galaxysuggested: (Galaxy, RRID:SCR_006281)Briefly, the workflow performs quality control, masks primer sites, maps reads to reference using BMA-mem, calls variants using lofreq, annotates them using SNPEff, and outputs tabular variant call files, thresholded on minimum allele frequency of 0.05. SNPEffsuggested:…SciScore for 10.1101/2022.01.18.22269300: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Rolling circle amplification and Sanger sequencing of the clones were performed by GeneWiz (New Jersey). GeneWizsuggested: (GENEWIZ, RRID:SCR_003177)Major and minor variant calling: We used the Galaxy SARS-CoV-2 variant calling pipeline for paired-end Illumina ARTIC amplicon data 21. Galaxysuggested: (Galaxy, RRID:SCR_006281)Briefly, the workflow performs quality control, masks primer sites, maps reads to reference using BMA-mem, calls variants using lofreq, annotates them using SNPEff, and outputs tabular variant call files, thresholded on minimum allele frequency of 0.05. SNPEffsuggested: (SnpEff, RRID:SCR_005191)We tested 15 multiple sequence alignments, each containing all observed unique read fragment sequences spanning the S-gene (12 fragments) and N-gene (3 fragments) with three different four gamete tests: (1) the PHI test (implemented in RDP5 23,36) which considers sites with more than two alternative nucleotide states and uses a permutation-based test to determine whether detected site pairs displaying all four gametes display a degree of spatial clustering along the sequence that is significantly higher than would be expected in the absence of recombination; (2) the MCL recombination detection test (implemented in the pairwise component of the LDHat package; 24) which uses an approximate maximum likelihood method to infer the population scaled recombination rate needed to explain the observed numbers of site pairs with four gametes and then tests for significant deviation of the inferred recombination rate from zero using a permutation test, and (3) the RvsDist test (implemented in pairwise component of LDHat) which determines the correlation between the R2 measure of linkage disequilibrium between site pairs with four gametes with the physical distance in nucleotides between the site pairs 24 and uses a permutation test to detect significant deviations from the expected degree of correlation in the absence of recombination. LDHatsuggested: (LDHAT, RRID:SCR_006298)These genomes were aligned to the Wuhan-Hu-1 reference genome (Genbank accession NC_045512.2) using MAFFT v7.453 (options --auto --keeplength -- addfragments) 33. MAFFTsuggested: (MAFFT, RRID:SCR_011811)Results from OddPub: Thank you for sharing your data.
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
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- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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