Comparative analysis of within-host diversity among vaccinated COVID-19 patients infected with different SARS-CoV-2 variants

Al-Khatib, Hebah A.; Smatti, Maria K.; Ali, Fatma; Al-Jighefee, Hadeel; Thomas, Swapna; Ahmed, Muna; kahlout, Reham A. El; Bader, Mashael A. Al; Elgakhlab, Dina; Coyle, Peter; Abu‐Raddad, Laith J.; Thani, Asma Al; Yassine, Hadi M.

doi:10.1016/j.isci.2022.105438

Cited by 9 publications

(7 citation statements)

References 51 publications

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“…All five patients had mutations S255F on the S gene and I376V, N4969S, and S5339F on the ORF1a/b. S255F is an important mutation previously identified in the S gene, with immune escape properties 1 , 4 , however, the I376V, N4969S, and S5339F are all unique to the non-vaccinated patients and have not been reported previously ( Fig. 5A ).…”

Section: Resultsmentioning

confidence: 82%

“…SNP analysis gives insight into the regions and domains affected, and SARS-CoV-2 genomic positions and protein domains associated with virulence. For example, mutations such as S255F 8 , 52 , confer reduced neutralization by monoclonal antibodies and have the potential for immune escape 1 , 53 , 54 . In this study we identify unique SNPs, in the context of vaccination status Some mutations of interest include S255F, which occurred in a group of patients who had previously unreported SNPs in their ORF1a/b and showed a different pattern of recombination events compared to other non-vaccinated individuals.…”

Section: Discussionmentioning

confidence: 99%

“…Previous studies have implicated both minimal and significant increase in the intrahost diversity of viruses with vaccination 1 – 3 . Vaccination is a critical mitigation factor in controlling the COVID-19 pandemic and in Kenya it began with adults in March 2021 and later proceeded to teenagers in November 2021 4 .…”

Section: Introductionmentioning

confidence: 99%

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Characterization of SARS-CoV-2 genetic evolution in vaccinated and non-vaccinated patients from the Kenyan population

Oyola

2023

Preprint

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Vaccination is a key control measure of COVID-19 by preventing severe effects of disease outcomes, reducing hospitalization rates and death, and increasing herd immunity. However, vaccination can affect the evolution and adaptation of SARS-CoV-2, largely through vaccine-induced immune pressure. Here we investigated the recombination events and single nucleotide polymorphisms (SNPs) on SARS-CoV-2 genome in non-vaccinated and vaccinated patients in the Kenyan population. We identified recombination hotspots in the S, N, and ORF1a/b genes and showed the genetic evolution landscape of SARS-CoV-2 by comparing within-wave and inter-wave recombination events from the beginning of the pandemic (June 2020) to (October 2022) in Kenya. An in-depth analysis of (SNPs) on the S, ORf1a/b, and N genes identified previously unreported mutations. We detected a minority variant in non-vaccinated patients in Kenya, that contained immune escape mutation S255F of the spike gene and showing a differential recombination pattern within the non-vaccinated patients. Detailed analysis of recombination between waves suggested an association between increased population immunity and declining risk of emergence of variants of concern. Overall, this work identified unique mutations in SARS-CoV-2 which could have significant implications for virus evolution, virulence, and immune escape.

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Section: Resultsmentioning

confidence: 82%

Section: Discussionmentioning

confidence: 99%

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Characterization of SARS-CoV-2 genetic evolution in vaccinated and non-vaccinated patients from the Kenyan population

Oyola

2023

Preprint

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“…Nevertheless, one myth that has since been dispelled is that vaccination can increase the likelihood of new variants evolving within the host. According to data published by Al-Khatib et al [47], the number of quasispecies detected in vaccinated patients with breakthrough infections was almost identical, if not lower than, in unvaccinated patients with homologous infection with the same SARS-CoV-2 strain. Similarly, analysis of the number of intra-host variants in patients with infections by different SARS-CoV-2 strains did not reveal significant differences between unvaccinated and vaccinated individuals.…”

Section: Sars-cov-2 Evolutionmentioning

confidence: 85%

SARS-CoV-2: An Update on the Biological Interplay with the Human Host

Lippi,

Sanchis-Gomar,

Mattiuzzi

et al. 2023

COVID

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Coronavirus Disease 2019 (COVID-19) is an infectious respiratory illness caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The disease, first identified in the Chinese city of Wuhan in November 2019, has since spread worldwide, is the latest human pandemic and has officially infected over 800 million people and has caused nearly seven million deaths to date. Although SARS-CoV-2 belongs to the large family of coronaviruses, it has some unique biological characteristics in its interplay with the human host. Therefore, this narrative review aims to provide an up-to-date overview of the structure of the virus, incubation and shedding in the human host, infectivity and biological evolution over time, as well as the main mechanisms for invading human host cells and replicating within. We also proffer that ongoing epidemiological surveillance of newly emerged variants must always be accompanied by biological studies aimed at deciphering new advantageous traits that may contribute to increasing virulence and pathogenicity, such that the most appropriate strategies for establishing a (relatively) safe coexistence with the human host can be implemented.

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“…Along the pandemic course, Severe Acute Respiratory Syndrome COronaVirus 2 (SARS-CoV-2) has evolved rapidly, accumulating single nucleotide polymorphisms (SNPs) and generating new variants characterized by different transmissibility, virulence, and immune evasion 1 – 8 . Some of these have been declared by WHO to be of particular concern due to their high transmissibility and impact on the general population.…”

Section: Introductionmentioning

confidence: 99%

Molecular characterization of SARS-CoV-2 Omicron clade and clinical presentation in children

Scutari,

Fox,

Fini

et al. 2024

Sci Rep

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Since its emergence, SARS-CoV-2 Omicron clade has shown a marked degree of variability and different clinical presentation compared with previous clades. Here we demonstrate that at least four Omicron lineages circulated in children since December 2021, and studied until November 2022: BA.1 (33.6%), BA.2 (40.6%), BA.5 (23.7%) and BQ.1 (2.1%). At least 70% of infections concerned children under 1 year, most of them being infected with BA.2 lineages (n = 201, 75.6%). Looking at SARS-CoV-2 genetic variability, 69 SNPs were found to be significantly associated in pairs, (phi < − 0.3 or > 0.3 and p-value < 0.001). 16 SNPs were involved in 4 distinct clusters (bootstrap > 0.75). One of these clusters (A23040G, A27259C, T23617G, T23620G) was also positively associated with moderate/severe COVID-19 presentation (AOR [95% CI] 2.49 [1.26–4.89] p-value: 0.008) together with comorbidities (AOR [95% CI] 2.67 [1.36–5.24] p-value: 0.004). Overall, these results highlight the extensive SARS-CoV-2 Omicron circulation in children, mostly aged < 1 year, and provide insights on viral diversification even considering low-abundant SNPs, finally suggesting the potential contribution of viral diversification in affecting disease severity.

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Comparative analysis of within-host diversity among vaccinated COVID-19 patients infected with different SARS-CoV-2 variants

Cited by 9 publications

References 51 publications

Characterization of SARS-CoV-2 genetic evolution in vaccinated and non-vaccinated patients from the Kenyan population

Characterization of SARS-CoV-2 genetic evolution in vaccinated and non-vaccinated patients from the Kenyan population

SARS-CoV-2: An Update on the Biological Interplay with the Human Host

Molecular characterization of SARS-CoV-2 Omicron clade and clinical presentation in children

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