Quasi-species prevalence and clinical impact of evolving SARS-CoV-2 lineages in European COVID-19 cohorts, January 2020 to February 2022

Abstract

BackgroundEvolution of SARS-CoV-2 is continuous.AimBetween 01/2020 and 02/2022, we studied SARS-CoV-2 variant epidemiology, evolution and association with COVID-19 severity.MethodsIn nasopharyngeal swabs of COVID-19 patients (n = 1,762) from France, Italy, Spain, and the Netherlands, SARS-CoV-2 was investigated by reverse transcription-quantitative PCR and whole-genome sequencing, and the virus variant/lineage (NextStrain/Pangolin) was determined. Patients' demographic and clinical details were recorded. Associations between mild/moderate or severe COVID-19 and SARS-CoV-2 variants and patient characteristics were assessed by logistic regression. Rates and genomic locations of mutations, as well as quasi-species distribution (≥ 2 heterogeneous positions, ≥ 50× coverage) were estimated based on 1,332 high-quality sequences.ResultsOverall, 11 SARS-CoV-2 clades infected 1,762 study patients of median age 59 years (interquartile range (IQR): 45-73), with 52.5% (n = 925) being male. In total, 101 non-synonymous substitutions/insertions correlated with disease prognosis (severe, n = 27; mild-to-moderate, n = 74). Several hotspots (mutation rates ≥ 85%) occurred in Alpha, Delta, and Omicron variants of concern (VOCs) but none in pre-Alpha strains. Four hotspots were retained across all study variants, including spike:D614G. Average number of mutations per open-reading-frame (ORF) increased in the spike gene (average < 5 per genome in January 2020 to > 15 in 2022), but remained stable in ORF1ab, membrane, and nucleocapsid genes. Quasi-species were most prevalent in 20A/EU2 (48.9%), 20E/EU1 (48.6%), 20A (38.8%), and 21K/Omicron (36.1%) infections. Immunocompromised status and age (≥ 60 years), while associated with severe COVID-19 or death irrespective of variant (odds ratio (OR): 1.60-2.25; p ≤ 0.014), did not affect quasi-species' prevalence (p > 0.05).ConclusionSpecific mutations correlate with COVID-19 severity. Quasi-species potentially shaping VOCs' emergence are relevant to consider.

Keywords: France; Genome evolution; Italy; ORCHESTRA; RNA secondary structure; SNV; Spain; The Netherlands; coronavirus; deletions; insertions; mutation rate; mutations; quasi-species.

Figure 1

Flowchart illustrating steps to include patients and samples in the study in four European countries^a, January 2020–February 2022 (n = 2,099 patients screened)

Figure 2

(A) Distribution of infecting SARS-CoV-2 variants, (B, C) COVID-19 severity by patients’ demographic characteristics and variant, and (D) viral loads by variant in patients from four European countries^a, January 2020–February 2022 (n = 1,762 patients)

Figure 3

Evolution of the SARS-CoV-2 genome based on viral genetic sequences derived from patients from four European countries^a, January 2020–February 2022 (n = 1,332)

Figure 4

Mutation rates at different positions across the SARS-CoV-2 genome, January 2020–February 2022 (n = 1,332)

Figure 5

Association of non-synonymous mutations in the SARS-CoV-2 genome and COVID-19 severity, January 2020—February 2022 (n = 1,332 sequences)