Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2025
Genomic surveillance of SARS-CoV-2 variants in Guangzhou, China, from April 2023 to March 2024.
СтатьяПоддержка исследования: вне правительства СШАНазвание и аннотация: Перевод в очереди
Обработка статьи · этапы, ошибки и управление
Загрузка состояния…
Ошибки и ограничения
История · было → стало
Состояние обновляется каждые 5 секунд, пока блок открыт. Процент показывается только там, где известен объём работы. Пауза останавливает продолжение этапа; текущий запрос к источнику может завершиться.
Li Zhuoyun, Li Liya, Min Yuyi, Lin Yaqing, Wen Yingfen, He Ruiying, Li Jiaojiao, Gao Quanyang, Hu Fengyu, Li Feng, Lan Yun
Аннотация
BACKGROUND: After the relaxation of stringent control measures, nationwide large-scale SARS-CoV-2 surveillance was gradually phased out post-2023, transitioning to focused monitoring of Influenza-like Illness (ILI) through sentinel hospitals and laboratory networks. Nationally, surveillance of respiratory pathogens was performed via random sampling, resulting in a lack of microbial monitoring results in Guangzhou China. A crucial area of scientific inquiry is whether the current cases are attributable to the emergence of a novel SARS-CoV-2 variant.
METHODS: Throat swab samples were obtained from 1478 outpatients and 337 hospitalized patients with fever (temperature ≥ 38 °C) and cough or sore throat to detect SARS-CoV-2. The positive samples were subjected to viral whole-genome sequencing and phylogenetic analysis. Respiratory pathogen multiplex PCR tests were performed on stratified random samples.
RESULTS: SARS-CoV-2 was detected in 517 (28.48 %) patients. There were higher rates of SARS-CoV-2 infection among women, older patients and those who were hospitalized. A total of 299 high-quality SARS-CoV-2 sequences were obtained, including 12 clades and 71 pango lineages. The advantageous clades evolved over three peak periods of infection, from BA.5 (April 2023) to XBB (June to July 2023) and then to JN.1 (February 2024). A total of 590 distinct amino acid mutations were identified across the sequences. The highest prevalence of mutations was observed for spike protein mutations, with more than 50 % of the three epidemic peaks detected. Epidemiological profiles of interactions between SARS-CoV-2 and other respiratory pathogens exhibit considerable variation across different seasons, with a tendency toward suppression within each.
CONCLUSION: Surveillance by Guangzhou Eighth People's Hospital provides a snapshot of the epidemic in Guangzhou, which is consistent with the national epidemic and offers important data for understanding the spread of SARS-CoV-2 in southern China.
METHODS: Throat swab samples were obtained from 1478 outpatients and 337 hospitalized patients with fever (temperature ≥ 38 °C) and cough or sore throat to detect SARS-CoV-2. The positive samples were subjected to viral whole-genome sequencing and phylogenetic analysis. Respiratory pathogen multiplex PCR tests were performed on stratified random samples.
RESULTS: SARS-CoV-2 was detected in 517 (28.48 %) patients. There were higher rates of SARS-CoV-2 infection among women, older patients and those who were hospitalized. A total of 299 high-quality SARS-CoV-2 sequences were obtained, including 12 clades and 71 pango lineages. The advantageous clades evolved over three peak periods of infection, from BA.5 (April 2023) to XBB (June to July 2023) and then to JN.1 (February 2024). A total of 590 distinct amino acid mutations were identified across the sequences. The highest prevalence of mutations was observed for spike protein mutations, with more than 50 % of the three epidemic peaks detected. Epidemiological profiles of interactions between SARS-CoV-2 and other respiratory pathogens exhibit considerable variation across different seasons, with a tendency toward suppression within each.
CONCLUSION: Surveillance by Guangzhou Eighth People's Hospital provides a snapshot of the epidemic in Guangzhou, which is consistent with the national epidemic and offers important data for understanding the spread of SARS-CoV-2 in southern China.