key: cord-0990991-fx029d7u authors: Iglesias, N. G.; Gebhard, L. G.; Carballeda, J. M.; Aiello, I.; Recalde, E.; Terny, G.; Ambrosolio, S.; L'Arco, G.; Konfino, J.; Brardinelli, J. I. title: SARS-CoV-2 surveillance in untreated wastewater: first detection in a low-resource community in Buenos Aires, Argentina. date: 2020-10-25 journal: nan DOI: 10.1101/2020.10.21.20215434 sha: 9682a1c1613d5cef1c81ff0870fdd30029bee711 doc_id: 990991 cord_uid: fx029d7u Recently, the World Health Organization (WHO) in a brief report about the status of environmental surveillance for SARS-CoV-2 indicated that 'approaches are needed that can be applied in lower-resource settings, where a greater proportion of the population is not connected to sewers and instead uses pit toilets or septic tanks. Possibilities include testing surface water contaminated by sewage'. In this study we measured SARS-CoV-2 RNA from a surface water source in a low-income settlement. We observe for this community that measurements of SARS-CoV-2 concentrations in surface water contaminated by sewage can be considered as an estimation of changes in COVID-19 prevalence on a population level. Wastewater-based epidemiology (WBE) provides comprehensive health information at the 26 community level [1] . The concept is mainly based on the detection and analysis of chemical 27 and biological compounds in sewage. WBE is an approach used to monitor the presence of 28 pathogens which may pose a public health concern [2]. During the current COVID-19 29 pandemic, sewage surveillance by analyzing for SARS-CoV-2 RNA traces in wastewater has 30 been reported in many locations around the world. All these reports have been conducted in 31 populations which have sewer networks and wastewater treatment facilities [3] [4] [5] [6] . However, 32 no study has been reported with this approach in low-resource settlements lacking these 33 facilities. 34 . CC-BY-NC-ND 4.0 International license It is made available under a perpetuity. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted October 25, 2020. ; https://doi.org/10.1101/2020. 10 confirmed, isolation measures were recommended for the recovery and avoidance as much as 48 possible more contagiousness and more cases [10] . 49 The aim of this study was to analyze the presence of SARS-CoV-2 RNA in surface waters 50 contaminated with wastewater from a low-income settlement and to analyze its relationship 51 with the prevalence of COVID-19 disease at the population level as part of the surveillance 52 strategy. 53 Raw surface water samples were collected between June 5 th and September 7 th at Villa Itatí 55 neighborhood, Municipality of Quilmes, Buenos Aires, Argentina. It is estimated that Villa Itatí 56 has a population of 16,478 people, in an area of 55 hectares delimited by Montevideo, Levalle, 57 Ayacucho and Southeast access streets [11] . It is a neighborhood that has an average of 1.03 58 households per dwelling with on average 3.55 people [12] . Of the 4,261 homes in Villa Itatí, 59 3,966 (93.1%) have potable water from the network and 1,044 (24.5%) are connected to the 60 public sewer network [12] . 61 This community is characterized by being located around an endorheic urban basin formed by 62 an anthropogenic digging flooded by the groundwater table and the discharges of pluvial and 63 domestic waters [13] . Most households serve their sewage into the waterlogged digging 64 is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted October 25, 2020. ; https://doi.org/10.1101/2020.10.21.20215434 doi: medRxiv preprint cesspools. In order to avoid the overflowing of the lagoon, its content is daily discharged to the 66 urban rainwater network through a pumping system [13] . Water samples were taken from the 67 unique pumping station of the neighborhood. 68 Composite samples representing 6-hour period (from 8 a.m. to 2 p.m.) were collected in 69 sterilized 500 ml glass bottles and kept at 4 °C until analysis, the RNA purification and viral 70 detection were performed the same day as the sample was collected. Before processing, 71 samples were subjected to a 90 minutes treatment at 60 °C to ensure biological safety. Viral Time PCR System (Applied Biosystems). In our conditions, we obtained a standard curve for N1 82 primer set with an R 2 of 0.99 with efficiency of 85% (slope=-3.747; y intercept = 46.076). The 83 N2 primer set generated a standard curve with an R 2 of 0.98 with an efficiency of 92.3% 84 (slope=-3.508; y intercept=42.014). All determinations were made at least in duplicate. 85 We collected raw water samples eleven times from June to September at Villa Itatí pumping 87 station. Sampling was performed weekly with some exceptions mainly due to impediments 88 caused by heavy rains. 89 We optimized an RNA isolation procedure consisting in a PEG 8000 based precipitation step in 90 order to achieve viral concentration from the raw water samples. Then, a Trizol (chaotropic 91 agents/organic solvents) extraction followed by a silica-gel based RNA purification step were 92 carried out in order to recover the viral RNA free from interfering substances. 93 Real time RT-qPCR was performed using the same CDC N1 and N2 probe/primers sets which 94 are utilized for COVID-19 diagnostic [15] . We detected SARS-CoV-2 RNA in all the samples, and 95 also, we were able to quantify the relative SARS-CoV-2 RNA concentration in these samples 96 . CC-BY-NC-ND 4.0 International license It is made available under a perpetuity. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted October 25, 2020. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted October 25, 2020. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted October 25, 2020. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted October 25, 2020. ; https://doi.org/10.1101/2020.10.21.20215434 doi: medRxiv preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted October 25, 2020. ; https://doi.org/10.1101/2020.10.21.20215434 doi: medRxiv preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted October 25, 2020. ; https://doi.org/10.1101/2020.10.21.20215434 doi: medRxiv preprint Future perspectives of wastewater-based epidemiology: 171 Monitoring infectious disease spread and resistance to the community level Wastewater-Based Epidemiology for Early Detection of Viral 174 First confirmed detection of SARS-CoV-2 in untreated 177 wastewater in Australia: A proof of concept for the wastewater surveillance of COVID-19 in the 178 community SARS-CoV-2 Titers in Wastewater Are Higher than Expected 180 from Clinically Confirmed Cases. mSystems Presence of SARS-Coronavirus-2 183 RNA in Sewage and Correlation with Reported COVID-19 Prevalence in the Early Stage of the 184 Epidemic in The Netherlands CoV-2 RNA concentrations in primary municipal sewage sludge as a leading indicator of COVID-188 19 outbreak dynamics Timeline: WHO's COVID-19 response La OMS caracteriza a COVID-19 como 193 una pandemia Acciones del Municipio de Quilmes COVID-19. Quilmes Gobierno Community approach for the COVID19 pandemic in Quilmes: a case 199 study of Villa Itati Gobierno de la Provincia de Buenos Proyecto de Transformación Urbana del Área Metropolitana de Buenos Aires (AMBA) 203 "Mejora del Hábitat en Barrios Vulnerables del GBA" Financiamiento Adicional/Fase II Proyecto de Integración Social y Urbana Villa Itatí y Villa Azul EVALUACIÓN SOCIAL 2019 Informe Censo Villa Itati -Villa Azul Estudio ecohidrológico de la cuenca urbana de La Cava de Villa 208 Pepper mild mottle virus as 211 an indicator of fecal pollution Coronavirus disease 2019 (COVID-19) Persistent viral shedding of SARS-CoV-217 2 in faeces -a rapid review Shedding of SARS-CoV-2 in feces and urine and its 219 potential role in person-to-person transmission and the environment-based spread of COVID-220 19 Status of environmental surveillance for 223 SARS-CoV-2-virus Measurement of 227 SARS-CoV-2 RNA in wastewater tracks community infection dynamics Virological assessment of hospitalized 230 patients with COVID-2019 Gastrointestinal manifestations of SARS-CoV-2 233 infection and virus load in fecal samples from a Hong Kong cohort: Systematic review and 234 meta-analysis