Detection of SARS-CoV-2 variants in hospital wastewater in Peru, 2022

Pool Marcos-Carbajal; José Yareta-Yareta; Miguel Otiniano-Trujillo; Marco Galarza- Pérez; Abraham Espinoza-Culupu; Jorge L. Ramirez-Melgar; Mario Chambi-Quispe; Néstor Alejandro Luque-Chipana; Rosmery Gutiérrez Ajalcriña; Víctor Sucñer Cruz; Segundo Nicolas López Chegne; Diana Santillán Ruiz; Luis Felipe Segura Chavez; Cinthia Esther Sias Garay; Alberto Salazar Granara; Pablo Tsukayama Cisneros; Silvana Teresa Tapia Paniagua; Carmen María González-Domenech

doi:10.17843/rpmesp.2024.412.13484

Authors

Pool Marcos-Carbajal Universidad Peruana Unión, Escuela Profesional Medicina, Laboratorio de Investigación en Biología Molecular. Lima, Perú. https://orcid.org/0000-0002-7741-0337
José Yareta-Yareta Universidad Peruana Unión, Escuela Profesional Medicina, Laboratorio de Investigación en Biología Molecular. Lima, Perú. https://orcid.org/0000-0002-8909-1724
Miguel Otiniano-Trujillo Universidad Peruana Unión, Escuela Profesional Medicina, Laboratorio de Investigación en Biología Molecular. Lima, Perú https://orcid.org/0000-0002-8989-6637
Marco Galarza- Pérez Instituto Nacional de Salud, Centro Nacional de Salud Pública, Laboratorio de Biotecnología y Biología molecular. Lima, Perú. https://orcid.org/0000-0002-6547-2354
Abraham Espinoza-Culupu Universidad Nacional Mayor de San Marcos, Facultad de Ciencias Biológicas. Lima, Perú https://orcid.org/0000-0002-5553-6385
Jorge L. Ramirez-Melgar Universidad Nacional Mayor de San Marcos, Facultad de Ciencias Biológicas. Lima, Perú https://orcid.org/0000-0001-8138-9203
Mario Chambi-Quispe Hospital Carlos Monge Medrano, Patología Clínica. Puno, Perú https://orcid.org/0000-0003-3303-2087
Néstor Alejandro Luque-Chipana Universidad Peruana Unión, Escuela Profesional Medicina, Laboratorio de Investigación en Biología Molecular. Lima, Perú. Hospital de Ate Vitarte, Unidad de Cuidados Intensivos. Lima, Perú. https://orcid.org/0000-0002-6192-4392
Rosmery Gutiérrez Ajalcriña Hospital de Huaycan, Área de Epidemiología. Lima, Perú https://orcid.org/0000-0001-8237-6092
Víctor Sucñer Cruz Hospital Regional del Cusco, Patología Clínica. Cusco, Perú. https://orcid.org/0009-0009-5302-8502
Segundo Nicolas López Chegne Hospital Regional de Cajamarca, Patología Clínica. Cajamarca, Perú. https://orcid.org/0000-0001-6480-1235
Diana Santillán Ruiz Hospital de Tarapoto, Departamento de Anatomía Patológica y Patología Clínica. Tarapoto, Perú. https://orcid.org/0009-0009-8982-9539
Luis Felipe Segura Chavez Universidad Peruana Unión, Escuela Profesional Medicina, Laboratorio de Investigación en Biología Molecular. Lima, Perú https://orcid.org/0000-0002-1665-4733
Cinthia Esther Sias Garay Universidad Peruana Unión, Escuela Profesional Medicina, Laboratorio de Investigación en Biología Molecular. Lima, Perú https://orcid.org/0009-0006-1099-1620
Alberto Salazar Granara Universidad San Martin de Porres, Centro de Investigación en Medicina Tradicional y Farmacología. Lima, Perú. https://orcid.org/0000-0003-1996-3176
Pablo Tsukayama Cisneros Universidad Peruana Cayetano Heredia, Laboratorio de Genómica Microbiana. Lima, Perú. https://orcid.org/0000-0002-1669-2553
Silvana Teresa Tapia Paniagua Universidad de Málaga, Departamento de Microbiología, Facultad de Ciencias. Málaga, España. https://orcid.org/0000-0002-3656-5009
Carmen María González-Domenech Universidad de Málaga, Departamento de Microbiología, Facultad de Ciencias. Málaga, España. https://orcid.org/0000-0001-8248-3904

DOI:

https://doi.org/10.17843/rpmesp.2024.412.13484

Keywords:

Genomics, SARS-CoV-2, Wastewater, Sequencing, Wastewater-Based Epidemiological Monitoring

Abstract

Objetive. To identify the presence of the SARS-CoV-2 virus in wastewater from hospitals in Peru. Materials and methods. Water samples were collected from the effluents of nine hospitals in Peru during March and September 2022. SARS-CoV-2 was identified by using Illumina sequencing. Variant, lineage and clade assignments were carried out using the Illumina and Nextclado tools. We verified whether the SARS-CoV-2 variants obtained from wastewater were similar to those reported by the National Institute of Health of Peru from patients during the same period and region. Results. Eighteen of the 20 hospital wastewater samples (90%) provided sequences of sufficient quality to be classified as the Omicron variant according to the WHO classification. Among them, six (30%) were assigned by Nextclade to clades 21K lineage BA.1.1 (n=1), 21L lineage BA.2 (n=2), and 22B lineages BA.5.1 (n=2) and BA .5.5 (n=1). Conclusions. SARS-CoV-2 variants were found in hospital wastewater samples and were similar to those reported by the surveillance system in patients during the same weeks and geographic areas. Wastewater monitoring could provide information on the environmental and temporal variation of viruses such as SARS-CoV-2.

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