AUTHOR=Corrêa Isadora Alonso , de Souza Marcos Romário Matos , da Silva Gustavo Peixoto Duarte , Pimentel Anna Beatriz Sampaio Vianna Macedo , Calil Pedro Telles , Cunha Marcela Sabino , Mariani Diana , Brindeiro Rodrigo de Moraes , Costa Sara Mesquita , Simas Maria Clara da Costa , Ota Victor Akira , Pereira Elisa Cavalcante , Siqueira Marilda Mendonça , Resende Paola Cristina , Galliez Rafael Mello , Faffe Debora Souza , Silva Rosane , Castiñeiras Terezinha Marta Pereira Pinto , Tanuri Amilcar , da Costa Luciana Jesus 

TITLE=Replication differences of SARS-CoV-2 lineages may arise from unique RNA replication characteristics and nucleocapsid protein expression

JOURNAL=Frontiers in Cellular and Infection Microbiology

VOLUME=Volume 15 - 2025

YEAR=2025

URL=https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2025.1582137

DOI=10.3389/fcimb.2025.1582137

ISSN=2235-2988

ABSTRACT=IntroductionThe COVID-19 pandemic was characterized by the sequential introduction and circulation of distinct SARS-CoV-2 variants, which presented differences in transmission capacity and pathogenicity. However, the relationship between these differences and the replicative capacity of these variants remains to be determined. Our research aimed to compare the biological traits of the SARS-CoV-2 lineages B.1.1.33, and variants Zeta (P.2), Gamma (P.1/P.1.*), Delta (B.1.617.2/AY.*), and Omicron (BA.1).MethodsWe employed three different cellular models susceptible to viral infection to demonstrated the differences in virus binding, entry and total RNA production through RT-qPCR assay and viral infectious progeny by plaque assay. The RNA replication was evaluated by dsRNA immunofluorescence and the viral protein production by western blotting analysis. NGS and RT-qPCR analysis were also used in competition experiments to verify the viral variants dynamic in cell culture.ResultsWe found that the differences in viral replication varied according to the cell type, with Omicron BA.1 exhibiting the lowest replication capacity in human pulmonary cells. Additionally, we demonstrated the occurrence of nucleocapsid proteoforms generated during infection and differences in size and number of sites of viral RNA replication for each virus.ConclusionThese data suggest that factors beyond the initial stages of virus entry influence the efficiency of viral replication among different SARS-CoV-2 variants. Thus, our study underscores the significance of RNA replication and the role of nucleocapsid proteins in shaping the replicative characteristics of SARS-CoV-2 variants.