DETECTION AND MUTATIONAL ANALYSIS OF AN RNA VIRUS IN AN ENVIRONMENTAL SAMPLE

The major challenge regarding the detection and mutational analysis of RNA viruses (e.g. SARS-CoV-2) in environmental samples, such as wastewater, is the reduced stability of the viral RNA, RNA fragmentation and the minimum amount/concentration within the samples. Moreover, the analysis of clinical/patients samples introduces selection bias, due to asymptomatic carriers who are less likely to undergo testing and symptomatic patients avoiding testing, requiring large number of samples to be tested. Environmental samples (e.g. wastewater) analysis provide an innovative, cost-effective approach towards the establishment of an early-warning system for the global monitoring of RNA virus at community and population levels. The current invention describes the complete method for the detection and mutational analytics of an RNA virus (e.g. SARS-CoV-2) in an environmental sample (e.g. wastewater), which involves extraction of the total RNA from the sample, reverse transcription of the isolated RNA with random oligonucleotides, nested PCR using virus-specific primer pairs and finaly next-generation sequencing (NGS)