Molecular surveillance of SARS-CoV-2 in the province of Córdoba: monitoring of variants

Abstract

Abstract: 

The study of the SARS-CoV-2 genome allows to evaluate its evolutionary pattern, identify mutations, lineages and variants that may have an impact on public health. Variants of concern (VOC) and variants of interest (VOI), which have different biological characteristics, have been identified worldwide. The objective of this work is to describe the lineages and variants of SARS-CoV-2 circulating in Córdoba using different strategies.

Three strategies were implemented from positive SARS-CoV-2 RNA samples (Cts<30): 1)-whole genome sequencing (WGS) (ONT-MinION): 203 samples analysed from March 2020 to June 2021; 2)-partial sequencing of the Spike protein gene (Sanger): 54 samples analysed between February and April 2021 of travellers from abroad; and 3)-real time RT-PCR for detection of relevant VOC mutations (TaqMan™ SARS-CoV-2 Mutation Panel, Applied Biosystems): 816 samples analysed between May and June 2021.  

Results were the following: 1)-circulation of 7 lineages with a greater predominance of B.1.1.33.3 (N3) (40.5%) and B.1.499 (38.8%), between March 2020 and January 2021; and circulation of 12 lineages with presence of VOC [P.1 (Gamma, 28.4%), B.1.1.7 (Alpha, 6.9%)] and VOI [C.37 (Lambda, 20.6%), B.1.427 (Epsilon, 10.8%), P2 (Zeta, 2.9%), B.1.526 (Iota, 2%)], between February and June 2021; 2)-presence of VOC Alpha (26.4%) and Gamma (17%), and samples compatible with VOI Epsilon and Zeta; 3)-presence of VOC Gamma (56%) and Alpha (11%), and other variants which could not be typified by this methodology.

Results show the circulation of many SARS-CoV-2 lineages in Córdoba, which varied their distribution over time, according to the different introductions occurred, the population movement and the evolutionary advantages of some variants over others. In March 2021, the first VOC detections were realized in the province (Alpha and Gamma), being Gamma the one that mostly circulates at present. Although the WGS is the technique which provides more information, the other 2 strategies implemented were and are very useful tools for molecular epidemiological surveillance, obtaining the information in real time. Strategy 3 is a simpler, faster and more operative tool for molecular VOC screening.