Study on SARS-CoV-2 strains in Iran reveals potential contribution of co-infection with and recombination between different strains to the emergence of new strains

Abstract

We aimed to describe SARS-CoV-2 strains in Iranians from nine distributed cities infected during two months expanding late 2020 and early 2021 by genotyping known informative single nucleotide in five PCR amplicons. Two variants associated with haplotype H1 (clade G) and nine additional variants associated with other haplotypes were genotyped, respectively, in RNA isolates of 244 and 85 individuals. The variants associated with the H1a (GR) and H1b (GH) haplotypes were most prevalent, indicating a significant change in infection pattern with passage of time. The most important findings were that recombinant genomes and co-infection, respectively, were surmised in 44.7% and 12.9% of the samples extensively genotyped. Partners of many of the recombinations were relatively common strains. Co-existing viruses were among those currently circulating in Iran. In addition to random mutations, co-infection with different existing strains and recombination between their genomes may significantly contribute to the emergence of new SARS-CoV-2 strains.

Distribution of SARS-CoV-2 Lineages in the Czech Republic, Analysis of Data from the First Year of the Pandemic

“…This finding raises the question about the limitations of de novo assembly approach regarding the detection of eventual superinfection events. Recently, there emerged several reports of superinfection with two strains of SARS-CoV-2 [ 24 , 25 , 26 ]. Our sequencing data showed that ~10% of the samples examined (23 of 229 samples) had two SARS-CoV-2 variants present, with a similar frequency (12.8%) observed in an independent Iranian cohort [ 25 ].…”

“…Recently, there emerged several reports of superinfection with two strains of SARS-CoV-2 [ 24 , 25 , 26 ]. Our sequencing data showed that ~10% of the samples examined (23 of 229 samples) had two SARS-CoV-2 variants present, with a similar frequency (12.8%) observed in an independent Iranian cohort [ 25 ]. Whether superinfection contributed to one of the highest rates of COVID-19 and the high number of COVID-related deaths during the first year of the pandemic in the Czech Republic remains unknown.…”

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

“…Recognition of recombination between SARS-CoV-2 viruses requires co-infection with viruses with distinct sequences. Co-infection with different SARS-CoV-2 strains has been documented [ 113 – 115 ]. With increased frequencies of infections worldwide, at least partly due to the emergence of strains with higher transmissibility, it is expected that the frequency of co-infections will also rise.…”

“…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 ].…”

“…Although strains with large numbers of variations may have evolved by accumulation of sequential mutations and subsequent expansion due to stochastic events or selection, an alternative scenario is that they are products of one or more recombination events between virus strains that each contained a subset of the variations. It is to be noted that coinfection and recombination are most likely to occur between locally or globally dominant strains [ 26 , 115 ]. In a recent study in which SARS-CoV-2 genome sequences in various cities of a single country were analyzed using non-conventional protocols, notably high frequencies of co-infection as well as sequences that were probable products of recombination events between locally or globally dominant strains were indeed observed [ 115 ].…”