Spatiotemporal Surveillance of SARS-CoV-2 in the Sewage of Three Major Urban Areas in Peru: Generating Valuable Data Where Clinical Testing Is Extremely Limited

Abstract

Peru has been severely affected by the COVID-19 pandemic. By January 2022, Peru had surpassed 200 000 COVID-19 deaths, constituting the highest death rate per capita worldwide. Peru has had several limitations during the pandemic: insufficient testing access, limited contact tracing, a strained medical infrastructure, and many economic hurdles. These limitations hindered the gathering of accurate information about infected individuals with spatial resolution in real time, a critical aspect of effectively controlling the pandemic. Wastewater monitoring for SARS-CoV-2 RNA offered a promising alternative for providing needed population-wide information to complement health care indicators. In this study, we demonstrate the feasibility and value of implementing a decentralized SARS-CoV-2 RNA wastewater monitoring system to assess the spatiotemporal distribution of COVID-19 in three major cities in Peru: Lima, Callao, and Arequipa. Our data on viral loads showed the same trends as health indicators such as incidence and mortality. Furthermore, we were able to identify hot spots of contagion within the surveyed urban areas to guide the efforts of health authorities. Viral decay in the sewage network of the cities studied was found to be negligible (<2%). Overall, our results support wastewater monitoring for SARS-CoV-2 as a valuable and cost-effective tool for monitoring the COVID-19 pandemic in the Peruvian context.

Presence of SARS-CoV-2 in urban effluents in south-east Buenos Aires, Argentina, May 2020 to March 2022

“…Indeed, for such countries, wastewater epidemiology may be the only feasible means of effective population surveillance ( 9 ). Similar successful experiences have been reported in the Americas regions, such as in other areas of Argentina ( 23 , 28 , 30 , 33 , 34 ), Brazil ( 35 ), and Peru ( 16 ).…”

Evaluation of low-cost SARS-CoV-2 RNA purification methods for viral quantification by RT-qPCR and next-generation sequencing analysis: Implications for wider wastewater-based epidemiology adoption

“…Wastewater samples were obtained from Sewer Treatment Plants (STPs) and Sewer Network (SN) manholes located across 3 major urban areas in Peru: Lima, the capital; Callao, located in close proximity to Lima; and Arequipa, the second largest city in Peru (see Ref. [ 12 ]). In total, 137 untreated wastewater samples, 49 from STPs and 88 from SN, collected between May 2021 and October 2021, were used in the study (see Supplementary Information 1 to 4).…”

“…By default, total RNA was obtained from filtered wastewater samples using the NucleoSpin® RNA stool isolation kit following manufacturer's instructions, with minor modifications (see Ref. [ 12 ]). For instance, to improve RNA recovery, membranes were soaked in 1 mL rather than 860 μL (660 μL RST1 and 200 μL Nucleozol buffers) and the volume of reagents used in subsequent steps was adjusted to keep proportions constant (see Ref.…”

“…While wastewater monitoring has been used before, i. e. to survey health and habits of contributing populations [ [3] , [4] , [5] , [6] , [7] ], the COVID-19 pandemic validated wastewater monitoring as a powerful tool to complement health system's efforts [ [8] , [9] , [10] ]. This was particularly the case in developing countries [ 11 , 12 ] where suboptimal disease surveillance, diagnostic and healthcare infrastructure exist [ 13 , 14 ]. Furthermore, with current advances in analytical capacities, WBE is becoming a necessary tool to address emerging epidemiological concerns, as well as the attainment of sustainable development goals [ 1 , 2 ].…”

“…For viral outbreaks in particular, wastewater monitoring can provide population-wide estimates of viral prevalence in real-time at a relatively low-cost, compared to full clinical testing [ 9 , 15 ]. WBE can be carried out to provide centralized information (i. e. sampling at sewage treatment plants), and decentralized information (i. e. sampling within the sewage network) for early warnings [ 16 , 17 ] and to identify hot-spots [ 11 , 12 , 18 ]. In either case, robust, sensitive and cost-effective methods must be in place.…”