Insights on early mutational events in SARS-CoV-2 virus reveal founder effects across geographical regions

Abstract

Here we aim to describe early mutational events across samples from publicly available SARS-CoV-2 sequences from the sequence read archive repository. Up until March 27, 2020, we downloaded 53 illumina datasets, mostly from China, USA (Washington DC) and Australia (Victoria). Of 30 high quality datasets, 27 datasets (90%) contain at least a single founder mutation and most of the variants are missense (over 63%). Five-point mutations with clonal (founder) effect were found in USA sequencing samples. Sequencing samples from USA in GenBank present this signature with 50% allele frequencies among samples. Australian mutation signatures were more diverse than USA samples, but still, clonal events were found in those samples. Mutations in the helicase and orf1a coding regions from SARS-CoV-2 were predominant, among others, suggesting that these proteins are prone to evolve by natural selection. Finally, we firmly urge that primer sets for diagnosis be carefully designed, since rapidly occurring variants would affect the performance of the reverse transcribed quantitative PCR (RT-qPCR) based viral testing.

Temporal Increase in D614G Mutation of SARS-CoV-2 in the Middle East and North Africa: Phylogenetic and Mutation Analysis Study

“…In the aforementioned comprehensive study, Korber et al estimated the global prevalence of D614G at 71.0%, whereas our estimate in the MENA was 78.7%, which appears reasonable, bearing in mind the protracted duration of sequence collection in this study. The explanation for such an observation is most likely related to the association of D614G with a higher viral load and subsequent higher quantities of the virus shed by infected individuals, which increases the likelihood of infection by such a mutant, although an early founder effect of this variant cannot be ruled out (Deng et al, 2020;Farkas et al, 2020;Yurkovetskiy et al, 2020;Zhang et al, 2020).…”

Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmission

“…Next, we estimated the genetic complexity (S Finally, we analyzed the potential impact of iSNVs and SNPs on the probes and primers used for detection of SARS-CoV-2 (15,28). To evaluate this, we downloaded the set of probes and primers sequences available at the WHO website, as well as the Arctic primers.…”

Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa: Phylogenetic and mutation analysis study

“…In the aforementioned comprehensive study, Korber et al estimated the global prevalence of D614G at 71.0%, whereas our estimate in the MENA was 78.7%, which appears reasonable, bearing in mind the protracted duration of sequence collection in this study. The explanation for such an observation is most likely related to the association of D614G with a higher viral load and subsequent higher quantities of the virus shed by infected individuals, which increases the likelihood of infection by such a mutant, although an early founder effect of this variant cannot be ruled out (Deng et al, 2020;Farkas et al, 2020;Yurkovetskiy et al, 2020;Zhang et al, 2020).…”