Monitoring the spread of SARS-CoV-2 via wastewater genome sequencing

Abstract

Introduction. Studying the genetic SARS-CoV-2 makeup and tracking its mutations are essential for understanding the course of the pandemic and preparing effective responses to public health threats. Wastewater-based surveillance, followed by genome sequencing, has emerged as a valuable tool for generating evidence to inform public health decisions. In densely populated areas, wastewater monitoring provides an efficient approach to studying both the epidemiology and genomic diversity of the virus, thus supporting the development of targeted strategies and reinforcing efforts to prevent future outbreaks. Since SARS-CoV- 2 can spread before the onset of symptoms, this method offers a significant advantage by allowing early detection and the ability to predict potential future outbreaks. Purpose of the study. The study aimed to monitor wastewater-based genomic surveillance, as well as to identify circulating SARS-CoV-2 variants, thereby improving both epidemiological tracking and public health emergency response. Material and methods. A retrospective descriptive study was conducted at the National Public Health Agency's reference laboratory for genomic sequencing. The study analyzed a total of 24 samples, including 23 wastewater samples collected from the Chișinău wastewater treatment plant between September and November 2024, as well as a single biological sample from a confirmed COVID-19 patient being included as a positive control. Genetic sequencing was performed on the Illumina MiSeq platform to identify genetic variants and mutation types. The resulting data were analyzed using bioinformatics software. Results. Analysis of SARS-CoV-2 isolates from wastewater revealed 32 genetic lineages based on the Pango classification system. The variants B.1.177.66, B.1.1.243, B.1.160.32, and B.1.1.305 were the most prevalent. Further analysis showed that the B.1.177.66 sulineage was dominant across multiple samples, suggesting its widespread circulation in Chișinău. Conclusions. This study emphasizes the importance of using wastewater-based wholegenome sequencing to characterize the diversity of circulating SARS-CoV-2 strains in the studied community. This approach could serve as a valuable supplement to traditional epidemiological surveillance tool or be used in situations when sequencing human biospecimens is not feasible.