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. 2022 Sep 30;10(10):1954.
doi: 10.3390/microorganisms10101954.

Emergence of New SARS-CoV2 Omicron Variants after the Change of Surveillance and Control Strategy

José María González Alba  1   2 , Zulema Pérez-Martínez  1   2 , José A Boga  1   2 , Susana Rojo-Alba  1   2 , Juan Gómez de Oña  2   3 , Marta E Alvarez-Argüelles  1   2 , Garbriel Martín Rodríguez  1   2 , Isabel Costales Gonzalez  1   2 , Ismael Huerta González  4 , Eliecer Coto  2   3 , Santiago Melón García  1   2
Affiliations

Emergence of New SARS-CoV2 Omicron Variants after the Change of Surveillance and Control Strategy

José María González Alba et al. Microorganisms. .

Abstract

In January 2022, there was a global and rapid surge of the Omicron variant of SARS-CoV-2 related to more transmission. This coincided with an increase in the incidence in Asturias, a region where rapid diagnosis and containment measures had limited the circulation of variants.

Methods: From January to June 2022, 34,591 variants were determined by the SNP method. From them, 445 were characterized by the WGS method and classified following pangolin program and phylogenic analysis.

Results: The Omicron variant went from being detected in 2438 (78%) samples in the first week of January 2021 to 4074 (98%) in the third week, according to the SNP method. Using the WGS method, 159 BA.1 (35.7%), 256 BA.2 (57.6%), 1 BA.4 (0.2%) and 10 BA.5 (2.2%) Omicron variants were found. Phylogenetic analysis detected that three new sub-clades, BA.2,3.5, BA.2.56 and BF1, were circulating.

Conclusions: The increase in the incidence of SARS-CoV2 caused the circulation of new emerging variants. Viral evolution calls for continuous genomic surveillance.

Keywords: Omicron; new variants; phylogenetic analysis; surveillance.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Weekly distribution of each variant in Asurias according Spike mutations.
Figure 2
Figure 2
(A) Dated phylogeny of the 2022 GISAID Asturian sequences. Delta in green, BA.1 in blue, BA.2 in red, BA.4 in black and BA.5 in violet. (B) Dated phylogeny of BA.1 containing a monophyletic subclade of the BA.1.17 group found only in Asturias indicated in gray. (C) Dated phylogeny of BA.2 containing two monophyletic subclades found in Asturias and later defined as new groups, BA.2.56 in gold and BA.2.3.5 in spring green; and a monophyletic subclade that circulates in Asturias but has not evolved enough to be considered a new group in pink. (D) Dated phylogeny of BA.5 containing a monophyletic subclade found in Asturias later defined as a new group BF.1 in orange.
Figure 3
Figure 3
Phylogeographic analysis of the sequences deposited in GISAID belonging to the new Omicron lineages found in Asturias. The estimated country of origin with posterior probability > 90% is indicated in the nodes. AS is Asturias. (A) Lineage BA.2.3.5 with the Asturian sequences in spring green, (B) Lineage BA.2.56 with the Asturian sequences in gold and (C) Lineage BF.1 with the Asturian sequences in orange.
See this image and copyright information in PMC

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