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Genomic Surveillance for SARS-CoV-2 Variants: Dominance of XBB Replacement — China, January–June 2023

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China CDC weekly 2024年第15期6卷 324-331页

作者： Yenan Feng Qiudong Su Lili Li Xiaozhou He Peihua Niu Xiaojuan Guo Xiang Zhao Jing Tang Zhiyuan Jia Ji Wang Changcheng Wu Baicheng Xia Zhixiao Chen Yuchao Wu Jing Yang Songqi Chen Cao Chen Shiwen Wang Xiaoping Dong national Key Laboratory of Intelligent Tracking and Forecasting for Infectious diseases National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina NHC Key Laboratory of Medical Virology and viral diseases National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina

Introduction:In the first half of 2023,a global shift was observed towards the predominance of XBB *** faced a significant epidemic between late 2022 and early 2023 due to Omicron subvariants BA.5.2 and *** study aims to depict the evolving variant distribution among provincial-level administrative divisions(PLADs)in China and explore the factors driving the predominance of XBB ***:Sequences from local and imported coronavirus disease 2019(COVID-19)cases recorded between January 1 and June 30,2023,were *** study analyzed the changing distribution of viral variants and assessed how the prior dominance of specific variants,XBB subvariants,and imported cases influenced the prevalence of the XBB replacement ***:A total of 56,486 sequences were obtained from local cases,and 8,669 sequences were from imported *** in April,there was a shift in the prevalence of XBB from imported to local cases,with varying dominance among *** PLADs previously high in BF.7,the rise of XBB was delayed.A positive correlation was found between XBB proportions in imported cases from January to March and local cases in *** distribution pattern of XBB subvariants differed between local and imported cases within the same *** significant differences were noted in the replacement rates of XBB ***:The timing of XBB dominance differed among various PLADs in China in the first half of 2023,correlating closely with the prevalence of XBB variants among imported cases.

关键词： dominance imported distribution

Thirty Years of Experience of Acute Flaccid Paralysis Surveillance for Polio — China, 1993–2022

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China CDC weekly 2024年第16期6卷 344-349页

作者： Hong Yang Ning Wen Chunxiang Fan Fuzhen Wang Yong Zhang Lei Cao Shuangli Zhu Lixin Hao Dongmei Yan Lei Wang Quanwei Song Miao Wang Yifan Song Chao Ma Zhijie An Lance ERodewald Huaqing Wang Zundong Yin national Key Laboratory of Intelligent Tracking and Forecasting for Infectious diseases(NITFID) BeijingChina national Immunization Program Chinese Center for Disease Control and PreventionBeijingChina Institute for viral disease control and prevention Chinese Center for Disease Control and PreventionBeijingChina

Introduction:Detecting poliovirus infections proves to be highly challenging due to their asymptomatic nature and infectious potential,highlighting the crucial importance of effective detection methods in the context of polio eradication *** many countries,including China,the primary approach for identifying polio outbreaks has been through acute flaccid paralysis(AFP)*** this study,we conducted an evaluation spanning three decades(1993–2022)to assess the effectiveness of AFP surveillance in ***:Data on all AFP cases identified since 1993 and national-level AFP surveillance system quality indicators aligned with the World Health Organization(WHO)standards were collected for *** quality indicators assess surveillance sensitivity,completeness,timeliness of detection notification,case investigation,and laboratory *** sensitivity is determined by the non-polio AFP(NPAFP)detection rate among children under 15 years of ***:Between 1993 and 2022,a total of 150,779 AFP cases were identified and *** this pool,surveillance identified 95 cases of wild poliovirus(WPV)and 24 cases due to vaccinederived *** 1995 onwards,the detection rate of NPAFP cases consistently adhered to the WHO and national standards of≥1 case per 100,000,falling between 1.38 and *** in 1997,all timeliness indicators consistently achieved the criteria of 80%,apart from the consistency in meeting standards set for the rate of positive specimens sent to the national ***:AFP surveillance has been instrumental in China’s accomplishment of maintaining a polio-free *** ongoing adherence to key performance indicators,ensuring sensitivity and prompt specimen collection,demonstrates that AFP surveillance is proficient in detecting poliovirus in *** we move into the post-eradication phase,AFP surveillance remains crucial for the sustained absence of polioviruses in the long term.

关键词： sustained prompt surveillance

The Epidemiological Characteristics of Mpox Cases-China,2023

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China CDC weekly 2024年第26期6卷 619-623页

作者： Ruiqi Ren Chao Li Wenqing Bai Yali Wang Dan Li Fan Ding Niu Yan Qi Wang Nijuan Xiang Lianmei Jin Lei Zhou Wenling Wang Fan Lyu Peilong Li Dapeng Zhang Yan Li Quanyi Wang Qun Li Guoqing Shi national Key Laboratory of Intelligent Tracking and Forecasting for Infectious diseases Chinese Center for Disease Control and PreventionBeijingChina Chinese Center for disease control and prevention BeijingChina national Institute for viral disease control and prevention Chinese Center for Disease Control and PreventionBeijingChina national Center for AIDS/STD control and prevention Chinese Center for Disease Control and PreventionBeijingChina Guangdong Provincial Center for disease control and prevention Guangzhou CityGuangdong ProvinceChina Beijing Municipal Center for disease prevention and control BeijingChina

Summary What is already known about this topic?Since May 2022,a global outbreak of mpox has emerged in more than 100 non-endemic *** of December 2023,over 90,000 cases had been *** outbreak has predominantly affected men who have sex with men(MSM),with sexual contact identified as the principal mode of *** is added by this report?Since June 2023,China has faced an occurrence of mpox,predominantly affecting the MSM *** 90%of those affected reported engaging in homosexual behavior within 21 days prior to symptom onset,a trend that aligns with the global outbreak *** prompt identification of cases,diligent tracing of close contacts,and the implementation of appropriate management strategies have successfully mitigated the spread of mpox virus in *** are the implications for public health practice?We propose that mpox is transmitted locally within *** from our experiences in controlling the virus spread,it is crucial to investigate and formulate effective surveillance and educational ***,we must encourage high-risk populations to promptly seek medical care upon the onset of symptoms.

关键词： prompt Drawing spread

Comparative Study on the Immunogenicity and Efficacy of Different Post-exposure Intramuscular Rabies Vaccination Regimens in China

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Biomedical and Environmental Sciences 2024年第2期37卷 178-186页

作者： SONG Yun HE Ying LU Xue Xin ZHANG Xiao Mei JIANG XIAO Lin SONG Qing HUANG Xue Yong MA Hong Xia YU Peng Cheng ZHU Wu Yang Henan Provincial Center for disease control and prevention Infectious Disease Prevention and Control InstituteHenan Provincial Key Laboratory of Infectious Disease PathogensZhengzhou 450000HenanChina national Institute for viral disease control and prevention China CDCKey Laboratory of BiosafetyNational Health CommissionBeijing 102206China Shandong Provincial Center for disease control and prevention Jinan 250014ShandongChina Qingdao Chengyang District Center for disease control and prevention Qingdao 266108ShandongChina

Objective This study aimed to compare the current Essen rabies post-exposure immunization schedule(0-3-7-14-28)in China and the simple 4-dose schedule(0-3-7-14)newly recommended by the World Health Organization in terms of their safety,efficacy,and *** Mice were vaccinated according to different immunization schedules,and blood was collected for detection of rabies virus neutralizing antibodies(RVNAs)on days 14,21,28,35,and 120after the first ***,different groups of mice were injected with lethal doses of the CVS-11 virus on day 0,subjected to different rabies immunization schedules,and assessed for morbidity and death *** a clinical trial,185 rabies-exposed individuals were selected for post-exposure vaccination according to the Essen schedule,and blood was collected for RVNAs detection on days 28and 42 after the first *** A statistically significant difference in RVNAs between mice in the Essen and 0-3-7-14 schedule groups was observed on the 35th day(P0.05)in RVNAs levels at any time *** post-exposure immune protective test showed that the survival rate of mice in the control group was 20%,whereas that in the immunization groups was 40%.In the clinical trial,the RVNAs positive conversion rates on days 28(14 days after 4 doses)and 42(14 days after 5 doses)were both 100%,and no significant difference in RVNAs levels was observed(P>0.05).Conclusion The simple 4-dose schedule can produce sufficient RVNAs levels,with no significant effect of a delayed fourth vaccine dose(14–28 d)on the immunization potential.

关键词： Rabies Post-exposure immunization Essen regimen RVNAs

Serological Investigation into the Infected Genotypes of Patients with Japanese Encephalitis in the Coastal Provinces of China

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Biomedical and Environmental Sciences 2024年第7期37卷 716-725页

作者： Weijia Zhang Jierong Zhao Qikai Yin Shenghui Liu Ruichen Wang Shihong Fu Fan Li Ying He Kai Nie Guodong Liang Songtao Xu Guang Yang Huanyu Wang national Key Laboratory of Intelligent Tracking and Forecasting for Infectious diseases National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijing 102206China School of Basic Medicine and Public Health Jinan UniversityGuangzhou 510000GuangdongChina

Objective Genotypes(G)1,3,and 5 of the Japanese encephalitis virus(JEV)have been isolated in China,but the dominant genotype circulating in Chinese coastal areas remains *** searched for G5 JEV-infected cases and attempted to elucidate which JEV genotype was most closely related to human Japanese encephalitis(JE)in the coastal provinces of *** In this study,we collected serum specimens from patients with JE in three coastal provinces of China(Guangdong,Zhejiang,and Shandong)from 2018 to 2020 and conducted JEV cross-neutralization tests against G1,G3,and *** Acute serum specimens from clinically reported JE cases were obtained for laboratory confirmation from hospitals in Shandong(92 patients),Zhejiang(192 patients),and Guangdong(77 patients),China,from 2018 to *** of the 361 serum specimens were laboratory-confirmed to be infected with *** cases were confirmed to be infected with G1 JEV,32 with G3 JEV,and two with G5 *** G3 was the primary infection genotype among JE cases with a definite infection genotype,and the infection caused by G5 JEV was confirmed serologically in China.

关键词： Japanese encephalitis virus Serological investigation Plaque reduction neutralization test Cross-neutralization test Genotype

Development of a High-throughput Sequencing Platform for Detection of viral Encephalitis Pathogens Based on Amplicon Sequencing

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Biomedical and Environmental Sciences 2024年第3期37卷 294-302页

作者： ZHANG Ya Li SU Wen Zhe WANG Rui Chen LI Yan ZHANG Jun Feng LIU Sheng Hui HU Dan He XU Chong Xiao YIN Jia Yu YIN Qi Kai HE Ying LI Fan FU Shi Hong NIE Kai LIANG Guo Dong TAO Yong XU Song Tao MA Chao Feng WANG Huan Yu Shaanxi University of Chinese Medicine Xianyang 712000ShaanxiChina national Key Laboratory of Intelligent Tracking and Forecasting for Infectious diseases National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijing 102206China Guangzhou Center for disease control and prevention Guangzhou 510000GuangdongChina Shandong Center for disease control and prevention Jinan 250000ShandongChina Department of Ophthalmology Beijing Chaoyang HospitalCapital Medical UniversityBeijing 100020China Xi'an Center for disease control and prevention Xi’an 710054ShaanxiChina

Objective viral encephalitis is an infectious disease severely affecting human *** is caused by a wide variety of viral pathogens,including herpes viruses,flaviviruses,enteroviruses,and other *** laboratory diagnosis of viral encephalitis is a worldwide ***,high-throughput sequencing technology has provided new tools for diagnosing central nervous system ***,In this study,we established a multipathogen detection platform for viral encephalitis based on amplicon *** We designed nine pairs of specific polymerase chain reaction(PCR)primers for the 12 viruses by reviewing the relevant *** detection ability of the primers was verified by software simulation and the detection of known positive *** sequencing was used to validate the samples,and consistency was compared with Sanger *** The results showed that the target sequences of various pathogens were obtained at a coverage depth level greater than 20×,and the sequence lengths were consistent with the sizes of the predicted *** sequences were verified using the national Center for Biotechnology Information BLAST,and all results were consistent with the results of Sanger *** Amplicon-based high-throughput sequencing technology is feasible as a supplementary method for the pathogenic detection of viral *** is also a useful tool for the high-volume screening of clinical samples.

关键词： viral encephalitis Amplicon sequencing High-throughput sequencing Multipathogen detection

Seasonal and Genetic Characteristics of Human Metapneumovirus Circulating—Henan Province,China,2017-2023

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China CDC weekly 2024年第20期6卷 450-456,I0001页

作者： Zhibo Xie Zhen Zhu Jin Xu Naiying Mao Aili Cui Wenhui Wang Yage Wang Zhibo Zhang Baicheng Xia Haoran Wang Zhen Sun Yan Zhang national Key Laboratory of Intelligent Tracking and Forecasting for Infectious diseases NHC Key Laboratory of Medical Virology and Viral DiseaseNational Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina Henan Provincial Center for disease control and prevention Luohe CityHenan ProvinceChina Luohe Center for disease control and prevention Luohe CityHenan ProvinceChina Luohe Central Hospital Luohe CityHenan ProvinceChina

Introduction:This study examines the seasonal and genetic characteristics of human metapneumovirus(HMPV)in Henan from 2017 to ***:Samples from patients with acute respiratory infection(ARI)testing positive for HMPV were subjected to real-time reverse transcription polymerase chain reaction The G gene was amplified and sequenced from these samples for epidemiological and phylogenetic ***:We enrolled 2,707 ARI patients from October 2017 to March 2023,finding an HMPV positivity rate of 6.17%(167/2,707).Children under five exhibited the highest infection rate at 7.78%(138/1,774).The 2018 and 2019 HMPV outbreaks predominantly occurred in spring(March to May),with peak positivity rates of 31.11%in May 2018 and 19.57%in May 2019.A notable increase occurred in November 2020,when positivity reached a historic high of 42.11%,continuing until January *** February 2021 through March 2023,no significant seasonal peaks were observed,with rates ranging from 0%to 8.70%.Out of 81 G gene sequences analyzed,46.91%(38/81)were identified as subtype A(A2c:45.67%,37/81;A2b:1.23%,1/81)and 53.09%(43/81)as subtype B(B1:9.88%,8/81;B2:43.21%,35/81).Notably,an AAABBA switch pattern was observed in HMPV *** dominant strains were A2c111nt-dup in subtype A and B2 in subtype ***:Six years of surveillance in Henan Province has detailed the seasonal and genetic dynamics of HMPV,contributing valuable insights for the control and prevention of HMPV infections in *** findings support the development of targeted HMPV vaccines and immunization strategies.

关键词： prevention finding seasonal

Establishment of the benchmarking tool for evaluating the operation of biorepositories for pathogenic resource using a modified Delphi method

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生物安全与健康(英文) 2024年第4期06卷 199-205页

作者： Hong Geng Liu Dongxin Zhao Yuanyuan Zhai Yalin Zhao Fengzekuan Wang Yanhai Jiang Mengnan Wei Qiang national Pathogen Resource Center Chinese Center for Disease Control and Prevention Beijing China China Center for Food and Drug International Exchange Beijing China Henan Puruixin Data Technology Co. Ltd Henan China Tonglu Center for disease control and prevention Zhejiang China national Institute for viral disease control and prevention Chinese Center for Disease Control and Prevention Beijing China

In recent years, as the infectious diseases caused by pathogens such as novel coronavirus and mpox (formerly called monkeypox) spread globally, the significance of identification, preservation, and sharing of pathogenic resources become prominent. Along with the rapid development of biorepositories, it is imperative to evaluate their operation in a scientific manner. By using the literature review and modified Delphi method, this study develops a benchmarking tool for the comprehensive evaluation of the operation of biorepositories for pathogenic resources. The effective response rates of both rounds of expert surveys were 100 %. The authority coefficients (Cr) were 0.82 and 0.85, respectively, manifesting the reliability of consultation results. In the second-round survey, the Kendall’s coefficient of concordance (Kendall’s W) of all indicators ranged from 0.09 to 0.31 (P < 0.001), the comprehensive score ranged from 4.02 to 4.94, the standard deviation ranged from 0.21 to 0.77, and the coefficient of variation (CV) ranged from 0.04 to 0.22, indicating that the expert opinions reached consensus. The final benchmarking tool was composed of 4 primary indicators, 12 secondary indicators, and 65 tertiary indicators. The weights of the four primary indicators allocated through the ranksum ratio method, namely organizational structure, management requirements, biobanking capacity, and sharing capacity, were 30.50 %, 30.08 %, 25.45 %, and 13.97 %, respectively. The benchmarking tool established in this study provides references for the comprehensive evaluation of the operation and puts forward advice for the sustainable development of biorepositories for pathogenic resources.

关键词： Biorepository Pathogenic resource Evaluation Benchmarking tool Modified Delphi method

Application of wastewater-based epidemiological monitoring of COVID-19 for disease surveillance in the city

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Frontiers of Environmental Science & Engineering 2024年第8期18卷 81-87页

作者： Heng Chen Zhenhua Chen Liwen Hu Fengzhu Tang Dan Kuang Jiayi Han Yao Wang Xiao Zhang Yue Cheng Jiantong Meng Rong Lu Lan Zhang Chengdu Workstation for Emerging Infectious disease control and prevention Chinese Academy of Medical SciencesChengdu 610047China Chengdu Center for disease control and prevention Chengdu 610047China national Key Laboratory of Intelligent Tracking and Forecasting for Infectious diseases Beijing 100050China national Institute of Environmental Health Chinese Center for Disease Control and PreventionBeijing 100050China

Wastewater-based surveillance serves as a supplementary approach to clinical surveillance of COVID-19 during the *** study aimed to track the prevalence of the disease and the viral genetic variability through wastewater-based surveillance in the post-epidemic *** January to December 2023,samples were collected from the influent lines of two wastewater treatment plants(WWTPs),concentrated using PEG8000,and subjected to detection of the target genes ORF 1ab and N of SARS-CoV-2 via reverse transcriptional quantitative PCR(RT-qPCR).For next-generation sequencing(NGS),high-quality samples from both wastewater and clinical patients were *** analysis were performed using R software to evaluate the correlation between the SARSCoV-2 RNA concentrations in wastewater and positive rate of reported cases,indicating a positive *** diversity patterns of SARS-CoV-2 in wastewater resembled those in the patient source based on Principal Coordinates Analysis(PCoA)with three clusters for different *** rise of RNA concentration in wastewater indicates the growth of cases and the emergence of new variants,serving as an early warning of potential viral mutations,disease outbreaks even possible ***,the genomic surveillance of wastewater could help identify new variants that may not be captured through population monitoring,especially when sample sizes are ***,surveillance of SARS-CoV-2 in municipal wastewater has emerged as a reliable,earlywarning monitoring system for COVID-19 in the post-epidemic era.

关键词： Wastewater-based epidemiology Monitoring COVID-19 Post-epidemic era