Comparative analysis of within-host diversity among vaccinated COVID-19 patients infected with different SARS-CoV-2 variants
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Date
2022-11-18Author
Hebah A., Al-KhatibSmatti, Maria K.
Ali, Fatma H.
Zedan, Hadeel T.
Thomas, Swapna
Ahmed, Muna N.
El-kahlout, Reham A.
Al Bader, Mashael A.
Elgakhlab, Dina
Coyle, Peter V.
Abu-Raddad, Laith J.
Al Thani, Asma A.
Yassine, Hadi M.
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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a rapidly evolving RNA virus that mutates within hosts and exists as viral quasispecies. Here, we evaluated the within-host diversity among vaccinated and unvaccinated individuals (n = 379) infected with different SARS-CoV-2 Variants of Concern. The majority of samples harbored less than 14 intra-host single-nucleotide variants (iSNVs). A deep analysis revealed a significantly higher intra-host diversity in Omicron samples than in other variants (p value < 0.05). Vaccination status and type had a limited impact on intra-host diversity except for Beta-B.1.315 and Delta-B.1.617.2 vaccinees, who exhibited higher diversity than unvaccinated individuals (p values: <0.0001 and <0.0021, respectively). Three immune-escape mutations were identified: S255F in Delta and R346K and T376A in Omicron-B.1.1.529. The latter 2 mutations were fixed in BA.1 and BA.2 genomes, respectively. Overall, the relatively higher intra-host diversity among vaccinated individuals and the detection of immune-escape mutations, despite being rare, suggest a potential vaccine-induced immune pressure in vaccinated individuals.
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