The presence of SARS-CoV-2 RNA in human sewage in Santa Catarina, Brazil, November 2019

Human sewage from Florianopolis (Santa Catarina, Brazil) was analyzed for severe acute respiratory syndrome coronavirus-2 (SARS-CoV2) from October 2019 until March 2020. Twenty five ml of sewage samples were clarified and viruses concentrated using a glycine buffer method coupled with polyethylene glycol precipitation, and viral RNA extracted using a commercial kit. SARS-CoV-2 RNA was detected by RT-qPCR using oligonucleotides targeting N1, S and two RdRp regions. The results of all positive samples were further confirmed by a different RT-qPCR system in an independent laboratory. S and RdRp amplicons were sequenced to confirm identity with SARS-CoV-2. Genome sequencing was performed using two strategies; a sequence-independent single-primer amplification (SISPA) approach, and by direct metagenomics using Illumina's NGS. SARS-CoV-2 RNA was detected on 27th November 2019 (5.49 +/- 0.02 log(10) SARS-CoV-2 genome copies (GC) L-1), detection being confirmed by an independent laboratory and genome sequencing analysis. The samples in the subsequent three events were positive by all RT-qPCR assays; these positive results were also confirmed by an independent laboratory. The average load was 5.83 +/- 0.12 log(10) SARS-CoV-2 GC L-1, ranging from 5.49 +/- 0.02 log(10) GC L-1 (27th November 2019) to 6.68 +/- 0.02 log(10) GC L-1 (4th March 2020). Our findings demonstrate that SARS-CoV-2 was likely circulating undetected in the community in Brazil since November 2019, earlier than the first reported case in the Americas (21st January 2020). (C) 2021 Elsevier B.V. All rights reserved.

Automated summary

SARS-CoV-2 RNA was detected in human sewage samples from Florianopolis, Brazil from November 2019 to March 2020, earlier than the first reported case in the Americas. This suggests that the virus may have been circulating undetected in the community.