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

## TL;DR

This study compares how different SARS-CoV-2 variants replicate in human cells, finding that Omicron replicates less efficiently and that RNA replication and nucleocapsid proteins play key roles.

## Contribution

The study reveals replication differences among SARS-CoV-2 variants linked to RNA replication and nucleocapsid protein expression.

## Key findings

- Omicron BA.1 showed the lowest replication capacity in human pulmonary cells.
- Differences in RNA replication sites and nucleocapsid proteoforms were observed among variants.
- RNA replication and nucleocapsid proteins influence replicative efficiency beyond initial virus entry.

## Abstract

The 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).

We 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.

We 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.

These 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.