Molecular epidemiology and population immunity of SARS-CoV-2 in Guangdong (2022–2023) following a pivotal shift in the pandemic

Zhencui Li, Pei Hu, Lin Qu, Mingda Yang, Ming Qiu, Chunyan Xie, Haiyi Yang, Jiadian Cao, Lina Yi, Zhe Liu, Lirong Zou, Huimin Lian, Huiling Zeng, Shaojian Xu, Pengwei Hu, Jiufeng Sun, Jianfeng He, Liang Chen, Ying Yang, Baisheng Li (), Limei Sun () and Jing Lu ()
Additional contact information
Zhencui Li: Guangdong Provincial Center for Disease Control and Prevention
Pei Hu: Guangdong Provincial Center for Disease Control and Prevention
Lin Qu: Guangdong Provincial Center for Disease Control and Prevention
Mingda Yang: Guangdong Provincial Center for Disease Control and Prevention
Ming Qiu: Guangdong Provincial Center for Disease Control and Prevention
Chunyan Xie: Guangdong Provincial Center for Disease Control and Prevention
Haiyi Yang: Guangdong Provincial Center for Disease Control and Prevention
Jiadian Cao: Guangdong Provincial Center for Disease Control and Prevention
Lina Yi: Guangdong Provincial Center for Disease Control and Prevention
Zhe Liu: Guangdong Provincial Center for Disease Control and Prevention
Lirong Zou: Guangdong Provincial Center for Disease Control and Prevention
Huimin Lian: Guangdong Provincial Center for Disease Control and Prevention
Huiling Zeng: Guangdong Provincial Center for Disease Control and Prevention
Shaojian Xu: Longhua District Center for Disease Control and Prevention
Pengwei Hu: Nanshan District Center for Disease Control and Prevention
Jiufeng Sun: Guangdong Provincial Center for Disease Control and Prevention
Jianfeng He: Guangdong Provincial Center for Disease Control and Prevention
Liang Chen: Guangdong Provincial Center for Disease Control and Prevention
Ying Yang: Guangdong Provincial Center for Disease Control and Prevention
Baisheng Li: Guangdong Provincial Center for Disease Control and Prevention
Limei Sun: Guangdong Provincial Center for Disease Control and Prevention
Jing Lu: Guangdong Provincial Center for Disease Control and Prevention

Nature Communications, 2024, vol. 15, issue 1, 1-12

Abstract: Abstract The SARS-CoV-2 Omicron variant sparked the largest wave of infections worldwide. Mainland China eased its strict COVID-19 measures in late 2022 and experienced two nationwide Omicron waves in 2023. Here, we investigated lineage distribution and virus evolution in Guangdong, China, 2022-2023 by comparing 5813 local viral genomes with the datasets from other regions of China and worldwide. Additionally, we conducted three large-scale serological surveys involving 1696 participants to measure their immune response to the BA.5 and XBB.1.9 before and after the corresponding waves. Our findings revealed the Omicron variants, mainly the BA.5.2.48 lineage, causing infections in over 90% of individuals across different age groups within a month. This rapid spread led to the establishment of widespread immunity, limiting the virus’s ability to further adaptive mutation and dissemination. While similar immune responses to BA.5 were observed across all age groups after the initial wave, children aged 3 to 11 developed a stronger cross immune response to the XBB.1.9 strain, possibly explaining their lower infection rates in the following XBB.1 wave. Reinfection with Omicron XBB.1 variant triggered a more potent neutralizing immune response among older adults. These findings highlight the impact of age-specific immune responses on viral spread in potential future waves.

Date: 2024
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DOI: 10.1038/s41467-024-51141-y

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