Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

Alm, Erik; Broberg, Eeva; Connor, Thomas R.; Hodcroft, Emma B.; Komissarov, Andrey; Maurer‐Stroh, Sebastian; Melidou, Angeliki; Neher, Richard A.; O’Toole, Áine; Pereyaslov, Dmitriy

doi:10.2807/1560-7917.es.2020.25.32.2001410

Cited by 228 publications

(254 citation statements)

References 12 publications

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“…The discrepancy in the GR clade abundance between the set of 115 Polish sequences collected between March and mid-June, and the European reference sequences collected until April 9th was mostly due to the contribution of Polish sequences collected after April 9th; the frequency of Polish isolates collected until April 9th was much closer to that in the European dataset. Indeed, the recent study on the SARS-CoV-2 geographical and temporal distribution in Europe, encompassing the period from January to mid-June (Alm et al 2020 ), has indicated that the frequency of the GR clade in April was ~ 30%, consistent with our calculations based on the manual analysis of the GISAID data. However, early in June, the GR clade frequency in Europe overtook that of the other clades, and since then is on the constant rise.…”

Section: Discussionsupporting

confidence: 91%

European context of the diversity and phylogenetic position of SARS-CoV-2 sequences from Polish COVID-19 patients

et al. 2021

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To provide a comprehensive analysis of the SARS-CoV-2 sequence diversity in Poland in the European context. All publicly available (n = 115; GISAID database) whole-genome SARS-Cov-2 sequences from Polish samples, including those obtained during coronavirus testing performed in our COVID-19 Lab, were examined. Multiple sequence alignment of Polish isolates, phylogenetic analysis (ML tree), and multidimensional scaling (based on the pairwise DNA distances) were complemented by the comparison of the coronavirus clades frequency and diversity in the subset of over 5000 European GISAID sequences. Approximately seventy-seven percent of isolates in the European dataset carried frequent and ubiquitously found haplotypes; the remaining haplotype diversity was population-specific and resulted from population-specific mutations, homoplasies, and recombinations. Coronavirus strains circulating in Poland represented the variability found in other European countries. The prevalence of clades circulating in Poland was shifted in favor of GR, both in terms of the diversity (number of distinct haplotypes) and the frequency (number of isolates) of the clade. Polish-specific haplotypes were rare and could be explained by changes affecting common European strains. The analysis of the whole viral genomes allowed detection of several tight clusters of isolates, presumably reflecting local outbreaks. New mutations, homoplasies, and, to a smaller extent, recombinations increase SARS-CoV-2 haplotype diversity, but the majority of these variants do not increase in frequency and remains rare and population-specific. The spectrum of SARS-CoV-2 haplotypes in the Polish dataset reflects many independent transfers from a variety of sources, followed by many local outbreaks. The prevalence of the sequences belonging to the GR clade among Polish isolates is consistent with the European trend of the GR clade frequency increase.

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Section: Discussionsupporting

confidence: 91%

European context of the diversity and phylogenetic position of SARS-CoV-2 sequences from Polish COVID-19 patients

et al. 2021

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“…The first SARS-CoV-2 infected patient was identified in Poland on 4 th March 2020, and since then, the genetic drift of the virus was monitored. The phylogenetic analysis led to the conclusion that the diversity of the virus is similar to the one observed worldwide [ 6 ]. The virus was introduced to the population of Poland from different sources, as hallmarks of different clades are present; virtually all genetic clades identified thus far were present [ 6 ].…”

Section: Resultsmentioning

confidence: 99%

The SARS-CoV-2 ORF10 is not essential in vitro or in vivo in humans

Pancer¹,

Milewska

Owczarek

et al. 2020

PLoS Pathog

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SARS-CoV-2 genome annotation revealed the presence of 10 open reading frames (ORFs), of which the last one (ORF10) is positioned downstream of the N gene. It is a hypothetical gene, which was speculated to encode a 38 aa protein. This hypothetical protein does not share sequence similarity with any other known protein and cannot be associated with a function. While the role of this ORF10 was proposed, there is growing evidence showing that the ORF10 is not a coding region. Here, we identified SARS-CoV-2 variants in which the ORF10 gene was prematurely terminated. The disease was not attenuated, and the transmissibility between humans was maintained. Also, in vitro, the strains replicated similarly to the related viruses with the intact ORF10. Altogether, based on clinical observation and laboratory analyses, it appears that the ORF10 protein is not essential in humans. This observation further proves that the ORF10 should not be treated as the protein-coding gene, and the genome annotations should be amended.

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“…We prepared libraries from these 4000 bp-long amplicons using Illumina TruSeq adapter sequences and sequenced them on an Illumina MiSeq System (Paired-end sequencing, 2x 251 cycle). The phylogenetic relationship between the consensus sequence of 681 samples from this collection has been previously analyzed as part of the subset of GISAID data available for Switzerland until July 10, 2020 in [24] and results based on the consensus sequences of the full dataset are presented in [45]. Here we focus on the raw reads directly and analyse the deep sequencing data to uncover within host diversity.…”

Section: Methodsmentioning

confidence: 99%

“…The sequences generated are largely deposited in data repositories such as the sequence read archive (SRA) and GISAID [19]. The availability of these sequences has allowed for platforms such as Nextstrain [20] to continually update and track viral evolution and spread, and to illuminate the viral genetic diversity among carriers [21–24].…”

Section: Introductionmentioning

confidence: 99%

Within-patient genetic diversity of SARS-CoV-2

Kuipers

Batavia

Jablonski

et al. 2020

Preprint

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SARS-CoV-2, the virus responsible for the current COVID-19 pandemic, is evolving into different genetic variants by accumulating mutations as it spreads globally. In addition to this diversity of consensus genomes across patients, RNA viruses can also display genetic diversity within individual hosts, and co-existing viral variants may affect disease progression and the success of medical interventions. To systematically examine the intra-patient genetic diversity of SARS-CoV-2, we processed a large cohort of 3939 publicly-available deeply sequenced genomes with specialised bioinformatics software, along with 749 recently sequenced samples from Switzerland. We found that the distribution of diversity across patients and across genomic loci is very unbalanced with a minority of hosts and positions accounting for much of the diversity. For example, the D614G variant in the Spike gene, which is present in the consensus sequences of 67.4% of patients, is also highly diverse within hosts, with 29.7% of the public cohort being affected by this coexistence and exhibiting different variants. We also investigated the impact of several technical and epidemiological parameters on genetic heterogeneity and found that age, which is known to be correlated with poor disease outcomes, is a significant predictor of viral genetic diversity.

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Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

Abstract: Investigator group: The members of the WHO European Region sequencing laboratories and GISAID EpiCoV group are listed at the end of the article

Cited by 228 publications

References 12 publications

European context of the diversity and phylogenetic position of SARS-CoV-2 sequences from Polish COVID-19 patients

European context of the diversity and phylogenetic position of SARS-CoV-2 sequences from Polish COVID-19 patients

The SARS-CoV-2 ORF10 is not essential in vitro or in vivo in humans

Within-patient genetic diversity of SARS-CoV-2

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