Contact tracing has played a crucial role in understanding SARS-CoV-2 transmission dynamics since the pandemic’s inception. In this context, the analysis of quasispecies through intra-host single nucleotide variants (iSNVs) has proven to be a particularly helpful instrument for outbreak investigations. This article presents a study conducted in Brescia Civic Hospital to understand the virus transmission chain among patients. Through procedures such as phylogenetic analysis and estimation of the transmission bottleneck size, a method for conducting contact tracing was developed that utilizes a genomic approach based on iSNVs analysis.
During the COVID-19 pandemic, coupling contact tracing with molecular testing was found to be key in containing the virus spread and break transmission chains. Notably, Next Generation Sequencing (NGS) technology was of immense help in this regard, allowing for the tracking of SARS-CoV-2 transmission between individuals. This transformed high-resolution genomic epidemiology into an effective tool for public health surveillance.
Understanding transmission chains in specific clinical units hosting patients at high risk for severe COVID-19 outcomes is essential for developing strategies to prevent and contain viral spreading. Quasispecies analysis has proven helpful for accurately tracking person-to-person transmission for different RNA viruses. Thus, molecular tracing and analysis of quasispecies are more useful than consensus sequences for finely tuning SARS-CoV-2 spread during an outbreak.
For the subject study, 13 nasopharyngeal specimens were collected from patients and tested for SARS-CoV-2 positivity using FLOQSwabs (Copan). The RNA extraction and genome sequencing were done using QIAamp DSP Virus Kit® (Qiagen) and Paragon Genomics’ CleanPlex multiplex PCR Research and Surveillance Panel, respectively. A consensus sequence was reconstructed by mapping the reads to the SARS-CoV-2 reference sequence NC_045512 using Bowtie2 in high sensitivity-local mode. Lineage assessment was conducted using the Phylogenetic Assignment of Named Global Outbreak LINeages tool (Pangolin).
From this, two transmission clusters were identified in the cardiology unit. This resulted in tracking the SARS-CoV-2 transmission chain among infected patients accurately. Important lessons were drawn for infection prevention and virus containment, especially in a hospital setting hosting vulnerable patients.
Source: https://virologyj.biomedcentral.com/articles/10.1186/s12985-024-02609-2