Surveillance of SARS-COV-2 Variants of Concern (VOC) from wastewater samples
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Project Overview
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19 pandemic, affected millions of people across the globe and resulted in more than three million deaths. Further, the emergence of new severe SARS-CoV-2 variants of concern (VOC) poses a major threat on public health worldwide. These variants have altered viral phenotypes such as virulence, transmissibility, and ability to evade host response giving rise to greater challenge to diagnostic and clinical management. In this project, you will first learn about the current variants of concern (VOC) of SARS-COV-2. Subsequently, you will learn about the approach to study and analyze VOCs in the samples. Briefly, you will learn how to find and download data to study VOCs. Next, you will learn how to perform multiple sequence alignment and phylogenetic analysis using NGS data employing the T-Bioinfo server. Subsequently, you will learn how to interpret MSA and phylogenetic results to derive biological significance and understand the evolutionary relationship between samples. Further, you will learn how to analyze variants of concern (VOCs) in given samples.
Objectives of Project
Learn about Variants of Concern of SARS-COV-2
Learn how to extract Data to Study VOC
Methods & Approach to study Variants of Concern
Dataset
Since, the Wastewater-based epidemiology (WBE) of human viruses represents a useful tool for population-scale monitoring of SARS-CoV-2 prevalence and epidemiology to help prevent further spread of the disease. Here, we have extracted data from the BioProject PRJEB42191 (
https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJEB42191 ). It contains sewage samples from the UK. In the original study, authors performed a longitudinal analysis (March-July, 2020) of SARS-CoV-2 RNA prevalence in sewage across six major urban centres in the UK by q(RT-) PCR and viral genome sequencing. Their results demonstrated that levels of SARS-CoV-2 RNA generally correlated with the abundance of clinical cases recorded within the community, with a marked decline in SARS-CoV-2 RNA abundance following the implementation of lockdown measures. In their study, authors shown that the genetic diversity of SARS-CoV-2 from wastewater suggests that multiple genetically distinct clusters were co-circulating in the local populations covered by their sample sites, and that the genetic variants observed in wastewater reflect similar SNPs observed in contemporaneous samples from cases tested in clinical diagnostic laboratories.Here, for this project, we have taken 10 samples for this project. We downloaded raw data from SRA (Note: we download SRA run table)
