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Abstract

Background

Evolution of SARS-CoV-2 is continuous.

Aim

Between 01/2020 and 02/2022, we studied SARS-CoV-2 variant epidemiology, evolution and association with COVID-19 severity.

Methods

In 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.

Results

Overall, 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).

Conclusion

Specific mutations correlate with COVID-19 severity. Quasi-species potentially shaping VOCs’ emergence are relevant to consider.

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This work is licensed under a Creative Commons Attribution 4.0 International License.
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2025-03-17
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Quasi-species prevalence and clinical impact of evolving SARS-CoV-2 lineages in European COVID-19 cohorts, January 2020 to February 2022
<p class="citation"> <span>Citation style for this article:</span> <span class="meta-value authors"> <a href="/search?value1=Matilda+Berkell&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Berkell Matilda</a>, <a href="/search?value1=Anna+G%C3%B3rska&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Górska Anna</a>, <a href="/search?value1=Mathias+Smet&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Smet Mathias</a>, <a href="/search?value1=Delphine+Bachelet&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Bachelet Delphine</a>, <a href="/search?value1=Elisa+Gentilotti&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Gentilotti Elisa</a>, <a href="/search?value1=Mariana+Guedes&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Guedes Mariana</a>, <a href="/search?value1=Anna+Maria+Franco-Yusti&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Franco-Yusti Anna Maria</a>, <a href="/search?value1=Fulvia+Mazzaferri&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Mazzaferri Fulvia</a>, <a href="/search?value1=Erley+Lizarazo+Forero&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Forero Erley Lizarazo</a>, <a href="/search?value1=Veerle+Matheeussen&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Matheeussen Veerle</a>, <a href="/search?value1=Benoit+Visseaux&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Visseaux Benoit</a>, <a href="/search?value1=Zaira+R.+Palacios-Baena&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Palacios-Baena Zaira R.</a>, <a href="/search?value1=Natascia+Caroccia&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Caroccia Natascia</a>, <a href="/search?value1=Aline-Marie+Florence&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Florence Aline-Marie</a>, <a href="/search?value1=Charlotte+Charpentier&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Charpentier Charlotte</a>, <a href="/search?value1=Coretta+van+Leer&option1=author&noRedirect=true" class="nonDisambigAuthorLink">van Leer Coretta</a>, <a href="/search?value1=Maddalena+Giannella&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Giannella Maddalena</a>, <a href="/search?value1=Alex+W.+Friedrich&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Friedrich Alex W.</a>, <a href="/search?value1=Jes%C3%BAs+Rodr%C3%ADguez-Ba%C3%B1o&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Rodríguez-Baño Jesús</a>, <a href="/search?value1=Jade+Ghosn&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Ghosn Jade</a>, <a href="/search?value1=ORCHESTRA+working+group&option1=author&noRedirect=true" class="nonDisambigAuthorLink">ORCHESTRA working group</a>, <a href="/search?value1=Samir+Kumar-Singh&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Kumar-Singh Samir</a>, <a href="/search?value1=Cedric+Laou%C3%A9nan&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Laouénan Cedric</a>, <a href="/search?value1=Evelina+Tacconelli&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Tacconelli Evelina</a>, <a href="/search?value1=Surbhi+Malhotra-Kumar&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Malhotra-Kumar Surbhi</a></span>. Quasi-species prevalence and clinical impact of evolving SARS-CoV-2 lineages in European COVID-19 cohorts, January 2020 to February 2022. <a href="/content/ecdc">Euro Surveill.</a> 2025;30(10):pii=2400038. <a href="https://doi.org/10.2807/1560-7917.ES.2025.30.10.2400038" title="doi link" target="_blank">https://doi.org/10.2807/1560-7917.ES.2025.30.10.2400038</a> <span class="ES_Article_citation"> <span class="generated">Received</span>: 16 Jan 2024;&nbsp;&nbsp; <span class="generated">Accepted</span>: 05 Sept 2024 </span> </p>
/content/10.2807/1560-7917.ES.2025.30.10.2400038
/content/10.2807/1560-7917.ES.2025.30.10.2400038
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