THE IMPACT OF VACCINATION IMMUNITY ON VIRAL QUASISPECIES IN GOLDEN SYRIAN HAMSTERS EXPERIMENTALLY INFECTED WITH SARS-COV-2

TAIANA TAINÁ SILVA-PEREIRA; Marcelo Valdemir de Araujo; ANTÔNIO FRANCISCO DE SOUZA FILHO; Alex Junior Souza de Souza; Marcos Bryan Heinemann; Profa. Dra. Denise Morais da Fonseca; Paulo Eduardo Brandão; Ana Marcia de Sá Guimarães

Paper Title

Authors

TAIANA TAINÁ SILVA-PEREIRA
Marcelo Valdemir de Araujo
ANTÔNIO FRANCISCO DE SOUZA FILHO
Alex Junior Souza de Souza
Marcos Bryan Heinemann
Profa. Dra. Denise Morais da Fonseca
Paulo Eduardo Brandão
Ana Marcia de Sá Guimarães

Modality

Late Poster

Subject area

DNA and Genomics

Publishing Date

21/11/2024

Country of Publishing

Brazil | Brasil

Language of Publishing

Inglês

Paper Page

https://www.even3.com.br/anais/xmeeting-2024/860083-the-impact-of-vaccination-immunity-on-viral-quasispecies-in-golden-syrian-hamsters-experimentally-infected-with-s

ISBN

978-65-272-0843-3

Keywords

SARS-CoV-2, vaccination, viral quasispecies

Summary

The COVID-19 pandemic underescored the importance of understanding how SARS-CoV-2 evolves under various immune pressures. This study investigates the impact of adenovirus-vectored SARS-CoV-2 vaccines on the modulation of viral quasispecies in experimentally infected hamsters. Hamsters were divided into three groups: non-vaccinated (PBS), inoculated with vaccine #1, and inoculated with vaccine #2. Both vaccines express the whole Spike protein of SARS-CoV-2, but vaccine #2 also expresses an autophagy-inducing peptide. Thirty-five days following vaccination, animals were infected with SARS-CoV-2. Samples from lungs and nasal turbinates (NT) were collected on days 3 and 5 post-infection for SARS-CoV-2 deep sequencing (50,000X coverage) using ARTIC v.3 protocol in Illumina platform. Reads were assessed for quality, and SNP/indels were detected using a workflow with GATK variant caller. A higher number of mutations (n=15 in the lungs and n=14 in NT) was observed in the PBS group compared to vaccine groups (maximum n=7), indicating robust viral evolution in the absence of immune response. Exclusive mutations associated with each vaccine group were also detected (n=5 in lung and n=7 in NT of vaccine #1; n=7 in lung and n=4 in NT of vaccine #2), but no mutations were common only between these two groups. This finding suggest immune response-induced constraints on viral diversity specific of each vaccine formulation. At 3 days post-infection, lung samples revealed mutations predominantly in the S (Spike) and E (Envelope) genes with variable allele frequency (from 53% to 96%) in the PBS group only. In contrast, five days post-infection, distinct mutational patterns emerged between the PBS and vaccinated groups. Missense mutations in orf1ab, ORF3a, E, and ORF7a genes were detected in the PBS group, while high-impact mutations such as frameshift and nonsense variants in orf1ab and disruptive in-frame insertions in the M gene were detected in the vaccine #1 group. Vaccine #2 group displayed similar selective pressures, with frequent disruptive in-frame insertions in orf1ab. Three days post-infection, NT samples revealed mutations exclusively in the PBS group, specifically within the S, M (Membrane), ORF1ab, and ORF7a gene regions. Conversely, at five days post-infection, the PBS group exhibited a broader spectrum of mutations, including missense, synonymous, conservative inframe insertions, and disruptive inframe deletions. The vaccine groups 1 and 2 each displayed only a single mutation in the S gene and ORF1ab, respectively, indicating reduced genetic variability in these groups. At five days post-infection, missense and frameshift insertions in critical genes (e.g., S, orf1ab) were detected in NT of the PBS group, while disruptive mutations in the S gene and orf1ab were detected in the vaccine #1 and vaccine #2 groups, respectively. In conclusion, the vaccination constrained the genetic drift of SARS-CoV-2, with higher effect of the vaccine expressing the autophagy-induing peptide (vaccine #2). Mutations observed in breakthrough infections were more disruptive than those found in non-vaccinated animals. This aligns with the expected emergence of deleterious mutations associated with smaller effective population sizes due to pre-existing immunity. Future research should focus on the functional implications of these mutations and their roles in viral transmission and pathogenicity.

Title of the Event: 20º Congresso Brasileiro de Bioinformática: X-Meeting 2024
City of the Event: Salvador
Title of the Proceedings of the event: X-Meeting presentations
Name of the Publisher: Even3
Means of Dissemination: Meio Digital

How to cite

SILVA-PEREIRA, TAIANA TAINÁ et al.. THE IMPACT OF VACCINATION IMMUNITY ON VIRAL QUASISPECIES IN GOLDEN SYRIAN HAMSTERS EXPERIMENTALLY INFECTED WITH SARS-COV-2.. In: X-Meeting presentations. Anais...Salvador(BA) Hotel Deville Prime, 2024. Available in: https//www.even3.com.br/anais/xmeeting-2024/860083-THE-IMPACT-OF-VACCINATION-IMMUNITY-ON-VIRAL-QUASISPECIES-IN-GOLDEN-SYRIAN-HAMSTERS-EXPERIMENTALLY-INFECTED-WITH-S. Access in: 28/06/2025