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Efficacyand Safetyof Huashi Baidu Granules in Treating Patients with SARS-CoV-2omicron variant: A Single-Center Retrospective Cohort Study

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Chinese Journal of Integrative Medicine 2024年第2期30卷 107-114页

作者： CHEN Cai-yu ZHANG Wen XU Xiang-ru PU Yu-ting TU Ya-dan PENG Wei YAO Xuan ZHOU Shuang FANG Bang-jiang Department of Emergency Longhua HospitalShanghai University of Traditional Chinese MedicineShanghai(200032)China Department of Classical Traditional Chinese Medicine Chongqing Hospital of Traditional Chinese MedicineChongqing(400021)China Acupuncture and Massage College Shanghai University of Traditional Chinese MedicineShanghai(201203)China Institute of Emergency and Critical Care Medicine Shanghai University of Traditional Chinese MedicineShanghai(200032)China

Objective:To evaluate the efficacy and safety of Huashi Baidu Granules(HSBD)in treating patients with severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)omicron variant.Methods:A single-center retrospective cohort study was conducted during COVID-19 omicron epidemic in the Mobile Cabin Hospital of Shanghai New International Expo Center from April 1st to May 23rd,2022.All COVID-19 patients with asymptomatic or mild infection were assigned to the treatment group(HSBD users)and the control group(non-HSBD users).After propensity score matching in a 1:1 ratio,496 HSBD users of treatment group were matched by propensity score to 496 non-HSBD users.Patients in the treatment group were administrated HSBD(5 g/bag)orally for 1 bag twice a day for 7 consecutive days.Patients in the control group received standard care and routine treatment.The primary outcomes were the negative conversion time of nucleic acid and negative conversion rate at day 7.Secondary outcomes included the hospitalized days,the time of the first nucleic acid negative conversion,and new-onset symptoms in asymptomatic patients.Adverse events(AEs)that occurred during the study were recorded.Further subgroup analysis was conducted in vaccinated(378 HSBD users and 390 non-HSBD users)and unvaccinated patients(118 HSBD users and 106 non-HSBD users).Results:The median negative conversion time of nucleic acid in the treatment group was significantly shortened than the control group[3 days(IQR:2-5 days)vs.5 days(IQR:4-6 days);P<0.01].The negative conversion rate of nucleic acid in the treatment group were significantly higher than those in the control group at day 7(91.73%vs.86.90%,P=0.014).Compared with the control group,the hospitalized days in the treatment group were significantly reduced[10 days(IQR:8-11 days)vs.11 days(IQR:10.25-12 days);P<0.01].The time of the first nucleic acid negative conversion had significant differences between the treatment and control groups[3 days(IQR:2-4 days)vs.5 days(IQR:4-6 days);P<0.01].The incidence of new-onset sym

关键词： Huashi Baidu Granule severe acute respiratory syndrome coronavirus 2 omicron variant retrospective cohort trial Chinese medicine

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Symptomatic COVID-19 in University Students: A School-Wide Web-Based Questionnaire Survey during the omicron variant Outbreak

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Advances in Infectious Diseases 2024年第1期14卷 133-146页

作者： Mai Kitahara Hisami Sameshima Rie Tanuma Kumi Setoyama Yuka Yamaguchi Akiyo Kamachi Satoko Nakamura Mayuko Sakuma Yoichi Kawaike Tamotsu Furuya Shinji Ijichi Health Service Center Kagoshima University Kagoshima Japan Center for Management of Information Technologies Kagoshima University Kagoshima Japan

Aim: To detect risk and preventive factors associated with the omicron variant infection in university students, a combination of a web-based survey and multivariate logistic regression analysis was introduced as the front-line initiatives by the school health practitioners. Design: Questionnaire survey. Methods: The school-wide web-based questionnaire survey was conducted among our university students as a part of the annual health check-up in April, 2023. The positive outcome was confined to the first symptomatic COVID-19 onset during the omicron variant outbreak. Results: In this self-administered survey, risk or protective associations were merely estimated statistically in university students (n = 5406). In measured factors, karaoke and club/group activities could maintain the statistical significance in adjusted odds ratios (ORs) as relative risk factors, and science course, measles/ rubella (MR) vaccination, and COVID-19 vaccination remained as relative protective factors in adjusted OR analyses. Club/group activities with member gathering and karaoke sing-along sessions in university students may frequently have WHO’s three Cs. These risk factors are still important topics for the infection control of COVID-19 in university students. Together with some recent reports from other researchers, the significant protective role of MR vaccine in our survey warrants further clinical investigation. If the breakthrough infection continuously constitutes the majority of infection, real data in test-negative case-control or web-based questionnaire design continue to be important for statistical analysis to determine the minimal requirement of our strategies which may be equivalent to or replace COVID-19 vaccines.

关键词： Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Coronavirus Disease 2019 (COVID-19) omicron variant Risk Behaviors Protective Factors

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A CRISPR/Cas12a-empowered surface plasmon resonance platform for rapid and specific diagnosis of the omicron variant of SARS-CoV-2

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National Science Review 2022年第8期9卷 100-109页

作者： Zhi Chen Jingfeng Li Tianzhong Li Taojian Fan Changle Meng Chaozhou Li Jianlong Kang Luxiao Chai Yabin Hao Yuxuan Tang Omar A.Al-Hartomy Swelm Wageh Abdullah G.Al-Sehemi Zhiguang Luo Jiangtian Yu Yonghong Shao Defa Li Shuai Feng William J.Liu Yaqing He Xiaopeng Ma Zhongjian Xie Han Zhang Department of Physics Faculty of Science King Abdulaziz University Research Center for Advanced Materials Science (RCAMS) King Khalid University Department of Chemistry College of Science King Khalid University Zhongmin (Shenzhen) Intelligent Ecology Co.Ltd Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province College of Physics and Optoelectronic Engineering Shenzhen University Department of Laboratory Medicine Shenzhen Children’s Hospital Optoelectronics Research Center School of Science Minzu University of China NHC Key Laboratory of Biosafety National Institute for Viral Disease Control and Prevention Chinese Center for Disease Control and Prevention Research Unit of Adaptive Evolution and Control of Emerging Viruses Chinese Academy of Medical Sciences Institute of Pathogenic Organism Shenzhen Center for Disease Control and Prevention Shenzhen Engineering Laboratory of Phosphorene and Optoelectronics Respiratory Department Shenzhen Children’s Hospital Institute of Pediatrics Shenzhen Children’s Hospital International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education 3. Shenzhen Institute of Translational Medicine 4. Department of Otolaryngology Shenzhen Second People’s Hospital 5. the First Affiliated Hospital 6. Institute of Microscale Optoelectronics Shenzhen University 7. Shenzhen International Institute for Biomedical Research 8. Shenzhen Han’s Tech Limited Company 9. Shenzhen Metasensing Tech Limited Company

The outbreak of the COVID-19 pandemic was partially due to the challenge of identifying asymptomatic and presymptomatic carriers of the virus, and thus highlights a strong motivation for diagnostics with high sensitivity that can be rapidly deployed. On the other hand, several concerning SARS-Co V-2 variants,including omicron, are required to be identified as soon as the samples are identified as ‘positive’.Unfortunately, a traditional PCR test does not allow their specific identification. Herein, for the first time,we have developed MOPCS(Methodologies of Photonic CRISPR Sensing), which combines an optical sensing technology-surface plasmon resonance(SPR) with the ‘gene scissors’ clustered regularly interspaced short palindromic repeat(CRISPR) technique to achieve both high sensitivity and specificity when it comes to measurement of viral variants. MOPCS is a low-cost, CRISPR/Cas12a-systemempowered SPR gene-detecting platform that can analyze viral RNA, without the need for amplification,within 38 min from sample input to results output, and achieve a limit of detection of 15 fM. MOPCS achieves a highly sensitive analysis of SARS-Co V-2, and mutations appear in variants B.1.617.2(Delta),B.1.1.529(omicron) and BA.1(a subtype of omicron). This platform was also used to analyze some recently collected patient samples from a local outbreak in China, identified by the Centers for Disease Control and Prevention. This innovative CRISPR-empowered SPR platform will further contribute to the fast, sensitive and accurate detection of target nucleic acid sequences with single-base mutations.

关键词： surface plasmon resonance CRISPR SARS-CoV-2 omicron variant

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Clinical practice of rapid antigen tests for SARS-CoV-2 omicron variant:A single-center study in China

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Virologica Sinica 2022年第6期37卷 842-849页

作者： Mengyuan Chen Jiaqin Xu Lingjun Ying Miaoguo Cai Tao-Hsin Tung Kai Zhou Yufen Zheng Xiaojie Bi Jing Wang Xi Tu Bo Shen Dongqing Lv Department of Laboratory Medicine Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical UniversityTaizhou317000China Hepatology and Infectious Diseases Center Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical UniversityTaizhou317000China Department of Radiation Oncology Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical UniversityTaizhou317000China Evidence-based Medicine Center Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical UniversityTaizhou317000China Department of Respiratory and Critical Diseases Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical UniversityTaizhou317000China

Responding to the fast-spreading SARS-CoV-2 omicron variant, to improve screening efficiency, rapid antigen tests(RATs) were first added as a supplementary detection method in China in mid-March, 2022. What and how big a role RATs should play need to be supported by clinical data. Here, RAT performance and relevant factors in comparison with nucleic acid amplification tests(NAATs) were assessed in omicron-infected inpatients. From the NAAT results, nasopharyngeal swabs(NPs) performed better than oropharyngeal swabs(OPs). RATs tested on NAAT positive NPs performed better than those with OP-positive samples. The RAT positivity rate was strongly associated with high levels of N and OFR1ab genes, especially in NPs where patients also had significantly longer hospital stays and shorter days from symptom onset to RAT testing. Self-performed RATs had a detection accuracy that was comparable to professionally performed RATs when the subjects were well guided. The antigen negative rate of the studied patients was 100% at discharge. These findings suggest that, in addition to a supplementary detection role, RATs can be an important strategy for evaluating the disease progression of omicron-infected inpatients. This study provides important clinical data to support better rules regarding RATs under China’s COVID-19 prevention and control policy.

关键词： SARS-CoV-2 omicron variant Rapid antigen tests(RATs) Dynamic zero-COVID policy COVID-19 progression evaluation

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Clinical characteristics of pediatric cases infected with the SARS-CoV-2 omicron variant in a tertiary children's medical center in Shanghai,China

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World Journal of Pediatrics 2023年第1期19卷 87-95页

作者： Nan Shen Yu-Fen Wu Yi-Wei Chen Xiao-Yan Fang Min Zhou Wen-Yu Wang Ming-Yu Tang Qiu-Hui Pan Ji Ma Hao Zhang Qing Cao Department of Infectious Disease Shanghai Children's Medical CenterNational Children's Medical CenterSchool of MedicineShanghai Jiao Tong UniversityDongfang Rd.1678Shanghai 200127China Department of Outpatient and Emergency Shanghai Children's Medical CenterNational Children's Medical CenterSchool of MedicineShanghai Jiao Tong UniversityShanghai 200127China Department of Cardiology Shanghai Children's Medical CenterNational Children's Medical CenterSchool of MedicineShanghai Jiao Tong UniversityShanghai 200127China Department of Psychosomatic Medicine and Psychotherapy Klinikum Rechts Der IsarTechnische Universitat Munchen81675 MunichGermany Medical Department Shanghai Children's Medical CenterNational Children's Medical CenterSchool of MedicineShanghai Jiao Tong UniversityShanghai 200127China Department of Gastroenterology Shanghai Children's Medical CenterNational Children's Medical CenterSchool of MedicineShanghai Jiao Tong UniversityShanghai 200127China Department of Respiratory Medicine Shanghai Children's Medical CenterNational Children's Medical CenterSchool of MedicineShanghai Jiao Tong UniversityShanghai 200127China Department of Laboratory Medicine Shanghai Children's Medical CenterNational Children's Medical CenterSchool of MedicineShanghai Jiao Tong UniversityShanghai 200127China Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics Shanghai 200127China Heart Center and Shanghai Institute of Pediatric Congenital Heart Disease Shanghai Children's Medical CenterNational Children's Medical CenterSchool of MedicineShanghai Jiao Tong UniversityDongfang Rd.1678Shanghai 200127China

Background The number of pediatric cases of infection with the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)omicron variant has increased.Here,we describe the clinical characteristics of children in a tertiary children's medical center in Shanghai.Methods A total of 676 pediatric coronavirus disease 2019(COVID-19)cases caused by the omicron variant who were admitted to the Shanghai Children's Medical Center from March 28 to April 30,2022 were enrolled in this single-center,prospective,observational real-world study.Patient demographics and clinical characteristics,especially COVID-19 vaccine status,were assessed.Results Children of all ages appeared susceptible to the SARS-CoV-2 omicron variant,with no significant difference between sexes.A high SARS-CoV-2 viral load upon admission was associated with leukocytopenia,neutropenia,and thrombocytopenia(P=0.003,P=0.021,and P=0.017,respectively)but not with physical symptoms or radiographic chest abnormalities.Univariable linear regression models indicated that comorbidities(P=0.001)were associated with a longer time until viral clearance,and increasing age(Pomicron variant of SARS-CoV-2 and calls for additional studies to evaluate the effectiveness and safety of vaccination against COVID-19 in children.

关键词： COVID-19vaccine omicron variant Pediatric COVID-19 SARS-CoV-2

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Mathematical modeling for Delta and omicron variant of SARS-CoV-2 transmission dynamics in Greece

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Infectious Disease Modelling 2023年第3期8卷 794-805页

作者： Sofia Liossi E.Tsiambas S.Maipas E.Papageorgiou A.Lazaris N.Kavantzas 1st Department of Pathology School of MedicineNational and Kapodistrian University of AthensAthens General Hospital“Laikon”AthensGreece Department of Cytopathology 417 Army Equity Fund Hospital(NIMTS)AthensGreece Master Program“Environment and Health.Management of Environmental Health Effects” School of MedicineNational and Kapodistrian University of AthensAthensGreece Department of Biomedical Sciences School of Health&Welfare SciencesUniversity of West AtticaEgaleoGreece

A compartmental,epidemiological,mathematical model was developed in order to analyze the transmission dynamics of Delta and omicron variant,of SARS-CoV-2,in Greece.The model was parameterized twice during the 4th and 5th wave of the pandemic.The 4th wave refers to the period during which the Delta variant was dominant(approximately July to December of 2021)and the 5th wave to the period during which the omicron variant was dominant(approximately January to May of 2022),in accordance with the official data from the National Public Health Organization(NPHO).Fitting methods were applied to evaluate important parameters in connection with the transmission of the variants,as well as the social behavior of population during these periods of interest.Mathematical models revealed higher numbers of contagiousness and cases of asymptomatic disease during the omicron variant period,but a decreased rate of hospitalization compared to the Delta period.Also,parameters related to the behavior of the population in Greece were also assessed.More specifically,the use of protective masks and the abidance of social distancing measures.Simulations revealed that over 5,000 deaths could have been avoided,if mask usage and social distancing were 20%more efficient,during the short period of the Delta and omicron outbreak.Furthermore,the spread of the variants was assessed using viral load data.The data were recorded from PCR tests at 417 Army Equity Fund Hospital(NIMTS),in Athens and the Ct values from 746 patients with COVID-19 were processed,to explain transmission phenomena and disease severity in patients.The period when the Delta variant prevailed in the country,the average Ct value was calculated as 25.19(range:12.32e39.29),whereas during the period when the omicron variant prevailed,the average Ct value was calculated as 28(range:14.41e39.36).In conclusion,our experimental study showed that the higher viral load,which is related to the Delta variant,may interpret the severity of the disease.However,no correlation was confirmed reg

关键词： Delta variant omicron variant Mathematical modeling Transmission dynamics Ct value Data fitting

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Importation of SARS-CoV-2 omicron variant in Beijing,China

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Biosafety and Health 2022年第3期4卷 150-153页

作者： Fu Li Zhichao Liang Shujuan Cui Bing Lv Zhaomin Feng Hui Xu Lei Jia Peng Yang Quanyi Wang Yang Pan Daitao Zhang Beijing Center for Disease Prevention and Control Beijing 100013China

omicron(B.1.1.529),the fifth variant of concern(VOC)of severe acute respiratory syndrome coronavirus 2(SARS‐CoV‐2),was firstly identified in November 2021 in South Africa.omicron contains far more genome mutations than any other VOCs ever found,raising significant concerns about its increased transmissibility and immune evasion.Here,we report the importation of the omicron variant into Beijing,China,in December 2021.Full‐length genome sequences of five imported strains were obtained,with their genetic features characterized.Each strain contained 57 to 61 nucleotide substitutions,39 deletions,and 9 insertions in the genome.Thirty to thirty‐two amino acid changes were found in the spike proteins of the five strains.The phylogenetic tree constructed by the maximum likelihood method showed that all five imported genomes belonged to omicron(BA.1)(alias of B.1.1.529.1),which is leading to the current surge of coronavirus disease 2019(COVID‐19)cases worldwide.The globally increased COVID‐19 cases driven by the omicron variant pose a significant challenge to disease prevention and control in China.Continuous viral genetic surveillance and increased testing among international travellers are required to contain this highly contagious variant.

关键词： COVID‐19 SARS‐CoV‐2 omicron variant Genomic characteristics

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Origin and evolutionary analysis of the SARS-CoV-2 omicron variant

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Journal of Biosafety and Biosecurity 2022年第1期4卷 33-37页

作者： Yamin Sun Wenchao Lin Wei Dong Jianguo Xu Research Institute of Public Health Nankai UniversityTianjinPR China State Key Laboratory for Infectious Disease Prevention and Control National Institute for Communicable Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingPR China Engineering and Research Center for Microbial Functional Genomics and Detection Technology Ministry of EducationNankai University

The severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)has evolved rapidly into new variants throughout the pandemic.The omicron variant has more than 50 mutations when compared with the original wild-type strain and has been identified globally in numerous countries.In this report,we analyzed the mutational profiles of several variants,including the per-site mutation rate,to determine evolutionary relationships.The omicron variant was found to have a unique mutation profile when compared with that of other SARS-CoV-2 variants,containing mutations that are rare in clinical samples.Moreover,the presence of five mouse-adapted mutation sites suggests that omicron may have evolved in a mouse host.Mutations in the omicron receptor-binding domain(RBD)region,in particular,have potential implications for the ongoing pandemic.

关键词： SARS-CoV-2 omicron variant Mouse-adapted mutation Reverse zoonosis

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Genomic surveillance of emerging SARS-CoV-2 omicron variations in Tianjin Municipality, China 2022

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Biosafety and Health 2024年第2期6卷 61-69页

作者： Xin Gao Ming Zou Yue Lei Zhaolin Tan Zhichao Zhuang Baolu Zheng Aiping Yu Yanzhen Han Xiaohui Lu Xiaochang Liu Ying Wang Yuan Wang Liru Guo Guangwen Liu Wen Li Yang Liu Likun Lv Peiyong Ning Xiaoyan Li Tianjin Centers for Disease Control and Prevention Tianjin 300011China Tianjin Key Laboratory of Pathogenic Microbiologyof Infectious Disease Tianjn Centers for Disease Controland PreventionTianjin 300011China

The coronavirus disease 2019(COvID-19)pandemic caused by severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)has severely impacted public health.In 2022,the omicron variant of SARS-CoV-2 rapidly became the dominant circulating variant in the local COVID-19 outbreaks in Tianjin Municipality,China.To gain a deeper understanding of the genetic variations of the omicron variant in Tianjin,specimens from indi-viduals who tested positive for SARS-CoV-2 between December 2021 and November 2022 were used for virus whole genome sequencing and phylogenetic analysis.A total of 1,674 high-quality omicron sequences were obtained,consisting of 1,339 sequences from local cases belonging to 20 Phylogenetic Assignment of Named Global Outbreak(PANGO)lineages and 335 sequences from imported cases belonging to 70 lineages.Tianjin experienced five waves of local outbreaks,accompanied by multiple substitutions among subvariants,ranging from the initial BA.1.1 lineage to the subsequent BA.2,BF.7,and BA.5.2 lineages.The evolutionary rate of local strains,estimated to be 28.999 substitutions per year,and the evolutionary rate of imported strains,estimated to be 24.946 substitutions per year,were lower than that of the strains circulating globally.The addi-tional substitutions and deletions of local strains have been used to identify and disrupt the virus transmission chains.The subvariants such as BA.5.2.48,BA.5.2.49,BF.7.14,and XBB.1 circulating in the fifth epidemic wave presented criterial immune escape mutations including S:R346T,S:L452R and S:F486V.It is essential to implement genomic surveillance strategies to investigate further the development of genomic mutation char-acteristics in the SARS-CoV-2 variant.This ongoing monitoring will contribute to a better understanding of the virus's genetic changes and aid in effective control measures.

关键词： Severeacute respiratory syndrome coronavirus 2(SARS-CoV-2) Coronavirusdisease2019(COVID-19) omicron variant Wholegenome sequencing(WGS)

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Development and validation of a nomogram to predict failure of 14-day negative nucleic acid conversion in adults with non-severe COVID-19 during the omicron surge: a retrospective multicenter study

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Infectious Diseases of Poverty 2023年第1期12卷 36-46页

作者： Honglian Gui Zhenglan Zhang Bin Chen Yaoxing Chen Yue Wang Zhuo Long Chuanwu Zhu Yinling Wang Zhujun Cao Qing Xie Department of Infectious Diseases Ruijin HospitalShanghai Jiao Tong University School of MedicineShanghaiChina Department of Infectious Diseases Shanghai Pudong HospitalFudan University Pudong Medical CenterShanghaiChina Department of Hepatology Wuwei People’s HospitalGansuChina Department of Infectious Diseases The Affiliated Infectious Diseases Hospital of Soochow UniversitySuzhouChina Department of Endocrine and Metabolic Diseases Fengcheng Hospital of Fengxian DistrictShanghaiChina

Background With the variability in emerging data,guidance on the isolation duration for patients with coronavirus disease 2019(COVID-19)due to the omicron variant is controversial.This study aimed to determine the predictors of prolonged viral RNA shedding in patients with non-severe COVID-19 and construct a nomogram to predict patients at risk of 14-day PCR conversion failure.Methods Adult patients with non-severe COVID-19 were enrolled from three hospitals of eastern China in Spring 2022.Viral shedding time(VST)was defined as either the day of the first positive test or the day of symptom onset,whichever was earlier,to the date of the first of two consecutively negative PCR tests.Patients from one hospital(Cohort I,n=2033)were randomly grouped into training and internal validation sets.Predictors of 14-day PCR conversion failure were identified and a nomogram was developed by multivariable logistic regression using the training dataset.Two hospitals(Cohort II,n=1596)were used as an external validation set to measure the performance of this nomogram.Results Of the 2033 patients from Cohort I,the median VST was 13.0(interquartile range:10.0-16.0)days;716(35.2%)lasted>14 days.In the training set,increased age[per 10 years,odds ratio(OR)=1.29,95%confidence interval(CI):1.15-1.45,P14 days,whereas full or boosted vaccination(OR=0.63,95%CI:0.42-0.95,P=0.028)and antiviral therapy(OR=0.56,95%CI:0.31-0.96,P=0.040)were protective factors.These predictors were used to develop a nomogram to predict VST>14 days,with an area under the ROC curve(AUC)of 0.73 in the training set(AUC,0.74 in internal validation set;0.76 in external validation set).Conclusions Older age,increasing comorbidities,incomplete vaccinations,and lack of antiviral therapy are risk factors for persistent infection with omicron variant for>14 days.A nomogram based on these predictors could be used as a prediction tool to guide treatment and isola

关键词： Nomogram Viral shedding time Prediction omicron variant COVID-19

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