SARS-CoV-2 Genomic Surveillance in Nayarit, Mexico (Summer-Winter 2021-2022)

Abstract

Background: COVID-19, whose etiologic agent is SARS-CoV-2, an RNA virus, is characterized by a high mutation rate. Therefore, while more subjects are infected, greater probability that the virus will potentially undergo changes that confer evolutionary advantages (immune response evasion, increased virulence, and reduced vaccination efficacy). Efforts to acquire herd immunity through vaccination may be compromised in low- and middle-income countries, where the vaccination process is slow and inequitable. This may lead to new variant outbreaks with greater transmission capacity. Therefore, it is important to surveillance the circulating variants in the populations. Methods: In this sense, in Tepic, Nayarit, Mexico, 100 viral genomes of positive patients were sequenced during the beginning and end of the third (August 4th to September 3rd, 2021) and fourth (January 3rd, to February 2nd, 2022) COVID-19 waves. Results: Sequence analysis revealed the presence of several variants; alpha (B.1.1.7), gamma (P.1), local variant (B.1.1.519), mu (B.1.621), delta (B.1.617.2), and its subtypes (AY.3, AY.4, AY.10, AY.11, AY.20, and AY.23.1) during the third wave. Later, during the fourth wave, delta subtypes were still detected (AY.26 and AY.113), as well as omicron (B.1.1.529) and omicron subtypes (B.A.1 and BA.1.1). Conclusion: Obtained data revealed a progressive shift of the dominant variants, delta, and subtypes in the third wave and omicron and subtypes in the fourth wave.