Spatiotemporal dynamics and epidemiological impact of SARS-CoV-2 XBB lineages dissemination in Brazil in 2023
Author:
Arantes IghorORCID, Gomes MarceloORCID, Ito Kimihito, Sarafim Sharbilla, Miyajima Fábio, Khouri Ricardo, Gräf Tiago, Siqueira Marilda Mendonça, Resende Paola CristinaORCID, Naveca Felipe GomesORCID, Bello GonzaloORCID,
Abstract
ABSTRACTThe SARS-CoV-2 XBB is a group of highly immune-evasive lineages of the Omicron VOC that emerged by recombining BA.2-descendent lineages and spread worldwide during 2023. In this study, we combine SARS-CoV-2 genomic data (n =11,065 sequences) with epidemiological data of Severe Acute Respiratory Infection (SARI) cases collected in Brazil between October 2022 and July 2023 to reconstruct the space-time dynamics and epidemiologic impact of XBB dissemination in the country. Our analyses revealed that the introduction and local emergence of lineages carrying convergent mutations within the Spike protein, especially F486P, F456L, and L455F, propelled the spread of XBB* lineages in Brazil. The average relative instantaneous reproduction numbers of XBB*+F486P, XBB*+F486P+F456L, and XBB*+F486P+ F456L+L455F lineages in Brazil were estimated to be 1.24, 1.33, and 1.48 higher than that of other co-circulating lineages (mainly BQ.1*/BE*), respectively. Despite such a growth advantage, the dissemination of these XBB* lineages had a reduced impact on Brazil’s epidemiological scenario concerning previous Omicron subvariants. The peak number of SARI cases from SARS-CoV-2 during the XBB wave was approximately 90%, 80%, and 70% lower than that observed during the previous BA.1*, BA.5*, and BQ.1* waves, respectively. These findings revealed the emergence of multiple XBB lineages with progressively increasing growth advantage, yet with relatively limited epidemiological impact in Brazil throughout 2023. The XBB*+F486P+F456L+L455F lineages stand out for their heightened transmissibility, warranting close monitoring in the months ahead.
Publisher
Cold Spring Harbor Laboratory
Reference74 articles.
1. Convergent evolution in sars-cov-2 spike creates a variant soup from which new COVID-19 waves emerge;International Journal of Molecular Sciences,2023 2. Emergence and geographic dominance of Omicron subvariants XBB/XBB.1.5 and BF.7 – the public health challenges;International Journal of Infectious Diseases,2023 3. Does the COVID-19 XBB Omicron subvariant signal the beginning of the end of the pandemic?;Singapore Medical Journal,2023 4. Characteristics of the omicron XBB subvariant wave in Singapore;The Lancet,2023 5. Tamura T , Ito J , Uriu K , Zahradnik J , Kida I , Anraku Y , Nasser H , Shofa M , Oda Y , Lytras S , Nao N , Itakura Y , Deguchi S , Suzuki R , Wang L , Begum MM , Kita S , Yajima H , Sasaki J , Sasaki-Tabata K , Shimizu R , Tsuda M , Kosugi Y , Fujita S , Pan L , Sauter D , Yoshimatsu K , Suzuki S , Asakura H , Nagashima M , Sadamasu K , Yoshimura K , Yamamoto Y , Nagamoto T , Schreiber G , Maenaka K , Ito H , Misawa N , Kimura I , Suganami M , Chiba M , Yoshimura R , Yasuda K , Iida K , Ohsumi N , Strange AP , Takahashi O , Ichihara K , Shibatani Y , Nishiuchi T , Kato M , Ferdous Z , Mouri H , Shishido K , Sawa H , Hashimoto R , Watanabe Y , Sakamoto A , Yasuhara N , Suzuki T , Kimura K , Nakajima Y , Nakagawa S , Wu J , Shirakawa K , Takaori-Kondo A , Nagata K , Kazuma Y , Nomura R , Horisawa Y , Tashiro Y , Kawai Y , Irie T , Kawabata R , Motozono C , Toyoda M , Ueno T , Hashiguchi T , Ikeda T , Fukuhara T , Saito A , Tanaka S , Matsuno K , Takayama K , Sato K . 2023. Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants. Nature Communications 14.
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