Detection of SARS-CoV-2 and Omicron variant RNA in wastewater samples from Manila, Philippines

• Published in: The Science of the total environment 2024-04, Vol.919, p.170921-170921, Article 170921
• Main Authors: Inson, Jessamine Gail M., Malla, Bikash, Amalin, Divina M., Carvajal, Thaddeus M., Enriquez, Ma. Luisa D., Hirai, Soichiro, Raya, Sunayana, Rahmani, Aulia Fajar, Angga, Made Sandhyana, Sthapit, Niva, Shrestha, Sadhana, Ruti, Annisa Andarini, Takeda, Tomoko, Kitajima, Masaaki, Alam, Zeba F., Haramoto, Eiji
• Format: Article
• Language: English
• Subjects: COVID-19; COVID-19 infection; environment; Omicron variant; Pepper mild mottle virus; Philippines; polymerase chain reaction; RNA; SARS-CoV-2; Severe acute respiratory syndrome coronavirus 2; sewage treatment; Sewage treatment plant; urbanization; wastewater; Wastewater-based epidemiology
• ISSN: 0048-9697; 1879-1026
• DOI: 10.1016/j.scitotenv.2024.170921

Manila, a highly urbanized city, is listed as one of the top cities with the highest recorded number of coronavirus disease 2019 (COVID-19) cases in the Philippines. This study aimed to detect and quantify the RNA of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the Omicron variant in 51 wastewater samples collected from three locations in Manila, namely Estero de Santa Clara, Estero de Pandacan, which are open drainages, and a sewage treatment plant (STP) at De La Salle University–Manila, between July 2022 and February 2023. Using one-step reverse transcription-quantitative polymerase chain reaction, SARS-CoV-2 and Omicron variant RNA were detected in 78 % (40/51; 4.9 ± 0.5 log10 copies/L) and 60 % (24/40; 4.4 ± 0.3 log10 copies/L) of wastewater samples collected from all sampling sites, respectively. SARS-CoV-2 RNA was detected frequently at Estero de Santa Clara (88 %, 15/17); its highest concentration was at the STP (6.3 log10 copies/L). The Omicron variant RNA was present in the samples collected (4.4 ± 0.3 log10 copies/L) from all sampling sites, with the highest concentration at the STP (4.9 log10 copies/L). Regardless of normalization, using concentrations of pepper mild mottle virus RNA, SARS-CoV-2 RNA concentrations exhibited the highest positive correlation with COVID-19 reported cases in Manila 5 days after the clinical report. These findings revealed that wastewater-based epidemiology may aid in identifying and monitoring of the presence of pathogens in open drainages and STPs in the Philippines. This paper provides the first documentation on SARS-CoV-2 and the Omicron variant in wastewater from Manila. [Display omitted] •SARS-CoV-2 and Omicron variant finding in wastewater was first reported in Manila.•SARS-CoV-2 and Omicron were detected in 78 % and 60 % of samples, respectively.•Omicron variant was detected at all sites mirroring the dominant COVID-19 strain.•Even when the city had only reported 5 COVID-19 cases, SARS-CoV-2 RNA was detected.