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First Detection of SARS-CoV-2 Omicron Variant Using Nanopore Sequencing in Wastewater of Foz Do Iguassu-Brazil

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 Binational. SARS-CoV-2 wastewater monitoring is an important tool that has been helping health authorities to deal and plan the fight against 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. Samples from January/2022 were sequenced using Nanopore Technology and MinION device. All viable samples resulted in the presence of Omicron variant. The samples presented three unique mutations (T13195C ORF1ab, G14966- ORF1ab and A27259C ORF6) that are not defining mutations from any of the Variants of Concern (VOCs). One of these mutations (T13195C ORF1ab) is described as a signature mutation found in Omicron sequences from patients of two hospitals in Washington, United States. Since Foz do Iguassu receives thousands of visitors from all around the world, we suggest that the current Omicron variant circulating in the city could be originated from 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.