An integrative analysis of SARS-CoV 2 during the first and second waves of COVID-19 in Salta, Argentina

Abstract

Wastewater surveillance has been applied to provide information about SARS-CoV-2 circulation in the community. However, applicability is limited in regions lackingsewerage infrastructure or with insufficient coverage. During the COVID-19 pandemic,from July 2020 to September 2021, comprehensive epidemiological dataencompassing positive, recovered, and deceased cases were collected alongsideprecipitation records. Additionally, wastewater samples from 13 main sewersheds andriver water from two points (up- and downstream the main WWTP), in the city of Salta,were gathered. A total of 452 water samples were analysed for quantitative detection ofSARS-CoV-2 using RT-qPCR. Across the 62-week study period, two distinct waves ofCOVID-19 were identified. The dynamics of deceased cases showed peaks 10 and 28days after the peaks of positive cases in the first and second waves, respectively.Downstream river water exhibited higher faecal contamination than the upstreamsamples, evincing the impact of the WWTP discharges. Viral concentration in riverwaters mirrored those from wastewater, reflecting the progression of cases. Despitethe lower reported number of cases during the first wave compared to the second(5420 vs. 8516 cases at the respective peaks), higher viral concentrations weredetected in water (1.97×107 vs. 2.36×106 gc/L, respectively), suggestingunderreporting during the first wave, and highlighting the benefit of vaccination duringthe second. To the best of our knowledge, this is the first study that simultaneously andsystematically analyzed surface water and wastewater over a prolonged period andcompared the findings with epidemiological information. Environmental surveillancewas demonstrated to be a great tool to obtain valuable information about the circulationpatterns of SARS-CoV-2, especially under resource constraints to massively test thepopulation, thus, underreporting cases. Furthermore, the methodology employedherein can be easily expanded to the community-level surveillance of other pathogensexcreted in urine and feces, encompassing viruses, bacteria, and protozoa.