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COMPARATIVE EPIDEMIC EXPANSION OF SARS-COV-2 VARIANTS DELTA AND OMICRON IN AMAZONAS, A BRAZILIAN SETTING WITH HIGH LEVELS OF HYBRID IMMUNITY
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Abstract
The SARS-CoV-2 variants of concern (VOCs) Delta and Omicron have globally spread since mid and late 2021, respectively, with variable impact according to the immune population landscape. In this study, we compare the dissemination dynamics of these VOCs in the Amazonas state, one of Brazil's most heavily affected regions. We sequenced the virus genome from 4,128 patients collected in Amazonas between 1st July 2021 and 31st January 2022 and used a phylodynamic approach to investigate the lineage replacement dynamics. The VOCs Delta and Omicron displayed similar patterns of phylogeographic spread but significantly different epidemic dynamics. The Delta and Omicron epidemics were fueled by multiple introduction events, followed by the successful establishment of a few local transmission lineages of considerable size that mainly arose in the capital city of Manaus. The VOC Omicron spread and became dominant much faster than the VOC Delta. We estimate that under the same epidemiological conditions, the average Re of Omicron was ~3.3 times higher than that of Delta and the average Re of the Delta was ~1.3 times higher than that of Gamma. Furthermore, the gradual replacement of Gamma by Delta occurred without a new upsurge of SARS-CoV-2 cases, while the rise of Omicron fueled a sharp increase in the number of SARS-CoV-2 cases. The Omicron wave displayed a shorter duration and a clear decoupling between the number of SARS-CoV-2 cases and deaths compared with previous (B.1.* and Gamma) waves in the Amazonas state. These findings suggest that the high level of hybrid immunity (infection plus vaccination) acquired by the Amazonian population by mid-2021 was able to limit the spread of the VOC Delta and was also probably crucial to curb the number of severe cases, although not the number of infections, by the VOC Omicron.
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