Surveillance of SARS-CoV-2, rotavirus, norovirus genogroup II, and human adenovirus in wastewater as an epidemiological tool to anticipate outbreaks of COVID-19 and acute gastroenteritis in a city without a wastewater treatment plant in the Peruvian Highlands

The coronavirus disease 2019 (COVID-19) pandemic has demonstrated that Wastewater Based Epidemiology is a fast and economical alternative for monitoring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the community level in high-income countries. In the present study, wastewater from a city in the Peruvian Highlands, which lacks a wastewater treatment plant, was monitored for one year to assess the relationship between the concentration of SARS-CoV-2 and the reported cases of COVID-19 in the community. Additionally, we compared the relationship between rotavirus (RV), norovirus genogroup II (NoV GGII), and human adenovirus (HAdV) with the number of reported cases of acute gastroenteritis. Before commencing the analysis of the samples, the viral recovery efficacy of three processing methods was determined in spiked wastewater with SARS-CoV-2. This evaluation demonstrated the highest recovery rate with direct analysis (72.2 %), as compared to ultrafiltration (50.8 %) and skimmed milk flocculation (5.6 %). Wastewater monitoring revealed that 72 % (36/50) of the samples tested positive for SARS-CoV-2, with direct analysis yielding the highest detection frequency and quantification of SARS-CoV-2. Furthermore, a strong correlation was observed between the concentration of SARS-CoV-2 in wastewater and the reported cases of COVID-19, mainly when we shift the concentration of SARS-CoV-2 by two weeks, which allows us to anticipate the onset of the fourth and fifth waves of the pandemic in Peru up to two weeks in advance. All samples processed using the skimmed milk flocculation method tested positive and showed high concentrations of RV, NoV GGII, and HAdV. In fact, the highest RV concentrations were detected up to four weeks before outbreaks of acute gastroenteritis reported in children under four years of age. In conclusion, the results of this study suggest that periodic wastewater monitoring is an excellent epidemiological tool for surveillance and can anticipate outbreaks of infectious diseases, such as COVID-19, in low- and middle-income countries.

Comparison of Skimmed Milk and Lanthanum Flocculation for Concentration of Pathogenic Viruses in Water

Concentration of viruses in water is necessary for detection and quantification of the viruses present, in order to evaluate microbiological barriers in water treatment plants and detect pathogenic viruses during waterborne outbreaks, but there is currently no standardised procedure. In this study, we implemented a previously described fast and simple lanthanum-based protocol for concentration of norovirus genogroup I (GI), genogroup II (GII) and hepatitis A virus (HAV) in drinking and surface water. We compared the results with those of a widely used skimmed milk flocculation method, followed by nucleic acid extraction and RT-qPCR detection. Three seeding levels, with intended concentrations 5 × 10³, 5 × 10⁴ and 5 × 10⁵ genome copies/10 L, were added to drinking water or surface water. All seed levels were detected with both flocculation methods. Samples extracted with skimmed milk flocculation had on average 1.82, 1.86 and 1.38 times higher measured concentration of norovirus GI, GII and HAV, respectively, than those extracted with lanthanum flocculation, across all seeding levels and water types tested. Mengovirus was used as a positive process control. Mengovirus recovery was higher for skimmed milk (40.7% in drinking water, 26.0% in surface water) than for lanthanum flocculation (24.4% in drinking water, 9.7% in surface water). Together, this indicates that skimmed milk flocculation provides higher viral recovery than lanthanum flocculation. However, lanthanum-based flocculation can be performed much faster than skimmed milk flocculation (1.5 h versus 16 h flocculation time) and thus could be a good alternative for rapid monitoring of viruses in water.

Evaluation of low-cost viral concentration methods in wastewaters: Implications for SARS-CoV-2 pandemic surveillances

In the pandemic of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) many strategies have been performed in order to control viral spread in the population and known the real-time situation about the number of infected persons. In this sense, Wastewater Based Epidemiology (WBE) has been applied as an excellent tool to evaluate the virus circulation in a population. In order to obtain reliable results, three low-cost viral concentration methods were evaluated in this study, polyethylene glycol (PEG) precipitation, skimmed milk flocculation (SM) and Aluminum polychloride flocculation, for Pseudomonas aeruginosa bacteriophage PP7 as a surrogate for non-enveloped viruses and Bovine Coronavirus (BCoV) as a surrogate for enveloped virus, with emphasis for SARS- CoV-2. Our results suggest that PEG precipitation for viral concentration, for both enveloped and non-enveloped virus from wastewater is an appropriate approach since it was more sensitive compared to SM flocculation and Aluminum polychloride flocculation. This methodology can be used for WBE studies in order to follow the epidemiology of the SARS-CoV-2 pandemic, mainly in developing countries where the economic resources are frequently limited.