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

Abstract

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).

Wastewater-Based Epidemiology for Community Monitoring of SARS-CoV-2: Progress and Challenges

“…These ten studies have reported positive SARS-CoV-2 RNA signals in a portion of untreated wastewater samples. Positive detection of SARS-CoV-2 RNA in some treated wastewater samples was also reported, 32 , 69 indicating incomplete removal of SARS-CoV-2 RNA during wastewater treatment. Of these 10 studies, only two studies included both the supernatant and solid fractions of wastewater in their analysis.…”

“… 27 Several WBE studies have reported the occurrence of local community transmission of SARS-CoV-2 before the first notified clinical SARS-CoV-2 case. 28 − 32 D’Aoust et al observed increases of >400% of SARS-CoV-2 RNA in wastewater 48 h before the reported >300% increases in SARS-CoV-2 cases. 33 Two studies in the United States reported that WBE for SARS-CoV-2 foreshadowed new clinical case reports by 2–8 days, 21 , 34 and another study reported that viral titer trends in wastewater appeared 4–10 days earlier in wastewater than in clinical data.…”

Timing the SARS-CoV-2 index case in Hubei province

“…The reports of cases in December 2019 and January 2020 in France and California that did not establish sustained transmission fit this pattern ( 31 33 ). However, our results suggest that polymerase chain reaction evidence of SARS-CoV-2 in wastewater outside of China before November 2019 is unlikely to be valid ( 34 ), and the suggestion of international spread in mid-November or early December 2019 should be viewed with skepticism ( 35 37 ), given that our results suggest that fewer than 20 people were infected with SARS-CoV-2 at this time (table S4 and fig. S11).…”

Wastewater-Based Epidemiology as an Early Warning System for the Spreading of SARS-CoV-2 and Its Mutations in the Population

“…The authors pointed out on the early detection in wastewater (stools) compared to reported cases. Overall, the results of wastewater monitoring in Spain, Brazil, and Italy show that SARS-CoV-2 was circulating in the country since end of the November 2019, much earlier than the first reported cases in these countries [ 33 , 34 , 35 ].…”