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First Detection of SARS-CoV-2 Omicron Variant Using Nanopore Sequencing in Wastewater of Foz Do Iguassu-Brazil
23 Pages Posted: 28 Feb 2022
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First Detection of SARS-CoV-2 Omicron Variant Using Nanopore Sequencing in Wastewater of Foz Do Iguassu-Brazil
First Detection of SARS-CoV-2 Omicron Variant Using Nanopore Sequencing in Wastewater of Foz Do Iguassu-Brazil
Abstract
Background: Foz do Iguassu is a famous Brazilian tourist site located on the Triple Frontier, where Brazil has borders with Argentina and Paraguay, and it is home of the world second largest hydroelectric power plant, named Itaipu Binacional. SARS-CoV-2 wastewater monitoring is an essential tool that has been helping health authorities to deal with and plan the fight against the COVID-19 ongoing pandemic. Since 2020, Foz do Iguassu has been weekly monitoring 20 points in the city and at the Itaipu Hydroelectric Power Plant.
Methods: Samples from January/2022 wastewater monitoring activities in the city were sequenced using Nanopore Technology and MinION device to investigate SARS-CoV-2 variants.
Findings: All viable samples resulted in the presence of the Omicron variant. The samples presented three unique mutations (T13195C ORF1ab, G14966del ORF1ab, and A27259C ORF6) that are not defining mutations from any of the Variants of Concern (VOCs). One of these mutations (T13195C ORF1ab) was described as a signature mutation found in Omicron sequences from patients of two hospitals in Washington, United States.
Interpretation: Since Foz do Iguassu receives thousands of visitors worldwide, we suggest that the current Omicron variant circulating in the city could be originated from the United States. We demonstrated that, despite inherent difficulties associated with sequencing environmental samples, sequencing SARS-CoV-2 using Nanopore technologies as a complement of the wastewater surveillance is feasible and can help health authorities to make improvements and determinations to act against the COVID-19 pandemic.
Funding Information: The authors would like to acknowledge the financial support from the following Brazilian institutions: Federal University of ABC (UFABC) No. 23006.002360/2020-43 and Brazilian National Council of Scientific and Technological Development (CNPq) in partnership with the Ministry of Science, Technology, Innovations, and Communications (MCTIC), and Ministry of Health (MS), Secretariat of Science, Technology, Innovation, and Strategic Inputs – Decit/SCTIE 07/2020 (Research to cope with COVID-19, its consequences and other severe acute respiratory syndromes – No. 402432/2020-7) and Itaipu Binational and Itaipu Technological Park for financial support [grant number 4500049462 / NIT.FP4.005 - Saneamento].
Declaration of Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
Keywords: wastewater-based epidemiology, SARS-CoV-2, wastewater variant monitoring
Suggested Citation: Suggested Citation