tetano
Editor, Senior Moderator
Virol J
. 2024 Jan 8;21(1):13.
doi: 10.1186/s12985-023-02279-6. A regional genomic surveillance program is implemented to monitor the occurrence and emergence of SARS-CoV-2 variants in Yubei District, China
Fangyuan Liu[SUP] #[/SUP][SUP] 1 [/SUP], Peng Deng[SUP] #[/SUP][SUP] 1 [/SUP], Jiuhong He[SUP] 1 [/SUP], Xiaofeng Chen[SUP] 1 [/SUP], Xinyu Jiang[SUP] 1 [/SUP], Qi Yan[SUP] 1 [/SUP], Jing Xu[SUP] 1 [/SUP], Sihan Hu[SUP] 1 [/SUP], Jin Yan[SUP] 2 [/SUP]
Affiliations
Background: In December 2022, Chongqing experienced a significant surge in coronavirus disease 2019 (COVID-19) epidemic after adjusting control measures in China. Given the widespread immunization of the population with the BA.5 variant, it is crucial to actively monitor severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant evolution in Chongqing's Yubei district.
Methods: In this retrospective study based on whole genome sequencing, we collected oropharyngeal and nasal swab of native COVID-19 cases from Yubei district between January to May 2023, along with imported cases from January 2022 to January 2023. Through second-generation sequencing, we generated a total of 578 genomes.
Results: Phylogenetic analyses revealed these genomes belong to 47 SARS-CoV-2 Pango lineages. BA.5.2.48 was dominant from January to April 2023, rapidly replaced by XBB* variants from April to May 2023. Bayesian Skyline Plot reconstructions indicated a higher evolutionary rate (6.973 × 10[SUP]-4[/SUP] subs/site/year) for the XBB.1.5* lineage compared to others. The mean time to the most recent common ancestor (tMRCA) of BA.5.2.48* closely matched BA.2.75* (May 27, 2022). Using multinomial logistic regression, we estimated growth advantages, with XBB.1.9.1 showing the highest growth advantage (1.2, 95% HPI:1.1-1.2), followed by lineage FR.1 (1.1, 95% HPI:1.1-1.2).
Conclusions: Our monitoring reveals the rapid replacement of the previously prevalent BA.5.2.48 variant by XBB and its sub-variants, underscoring the ineffectiveness of herd immunity and breakthrough BA.5 infections against XBB variants. Given the ongoing evolutionary pressure, sustaining a SARS-CoV-2 genomic surveillance program is imperative.
Keywords: Bayesian analysis; Epidemiology; Genomic surveillance; Phylogenetics; SARS-CoV-2; Whole genome amplicon sequencing; YuBei.
. 2024 Jan 8;21(1):13.
doi: 10.1186/s12985-023-02279-6. A regional genomic surveillance program is implemented to monitor the occurrence and emergence of SARS-CoV-2 variants in Yubei District, China
Fangyuan Liu[SUP] #[/SUP][SUP] 1 [/SUP], Peng Deng[SUP] #[/SUP][SUP] 1 [/SUP], Jiuhong He[SUP] 1 [/SUP], Xiaofeng Chen[SUP] 1 [/SUP], Xinyu Jiang[SUP] 1 [/SUP], Qi Yan[SUP] 1 [/SUP], Jing Xu[SUP] 1 [/SUP], Sihan Hu[SUP] 1 [/SUP], Jin Yan[SUP] 2 [/SUP]
Affiliations
- PMID: 38191416
- DOI: 10.1186/s12985-023-02279-6
Background: In December 2022, Chongqing experienced a significant surge in coronavirus disease 2019 (COVID-19) epidemic after adjusting control measures in China. Given the widespread immunization of the population with the BA.5 variant, it is crucial to actively monitor severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant evolution in Chongqing's Yubei district.
Methods: In this retrospective study based on whole genome sequencing, we collected oropharyngeal and nasal swab of native COVID-19 cases from Yubei district between January to May 2023, along with imported cases from January 2022 to January 2023. Through second-generation sequencing, we generated a total of 578 genomes.
Results: Phylogenetic analyses revealed these genomes belong to 47 SARS-CoV-2 Pango lineages. BA.5.2.48 was dominant from January to April 2023, rapidly replaced by XBB* variants from April to May 2023. Bayesian Skyline Plot reconstructions indicated a higher evolutionary rate (6.973 × 10[SUP]-4[/SUP] subs/site/year) for the XBB.1.5* lineage compared to others. The mean time to the most recent common ancestor (tMRCA) of BA.5.2.48* closely matched BA.2.75* (May 27, 2022). Using multinomial logistic regression, we estimated growth advantages, with XBB.1.9.1 showing the highest growth advantage (1.2, 95% HPI:1.1-1.2), followed by lineage FR.1 (1.1, 95% HPI:1.1-1.2).
Conclusions: Our monitoring reveals the rapid replacement of the previously prevalent BA.5.2.48 variant by XBB and its sub-variants, underscoring the ineffectiveness of herd immunity and breakthrough BA.5 infections against XBB variants. Given the ongoing evolutionary pressure, sustaining a SARS-CoV-2 genomic surveillance program is imperative.
Keywords: Bayesian analysis; Epidemiology; Genomic surveillance; Phylogenetics; SARS-CoV-2; Whole genome amplicon sequencing; YuBei.