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Evolutionary dynamics of the Severe acute respiratory syndrome coronavirus 2 genomes

Medical Review 2022年第1期2卷 3-22页

作者： Zhaohui Qian Pei Li Xiaolu Tang Jian Lu Institute of Pathogen Biology Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100176China NHC Key Laboratory of Systems Biology of Pathogens Institute of Pathogen BiologyChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100871China State Key Laboratory of Protein and Plant Gene Research Center for BioinformaticsSchool of Life SciencesPeking UniversityBeijing100176China State Key Laboratory of Protein and Plant Gene Research Center for BioinformaticsSchool of Life SciencesPeking UniversityBeijing100871China

The coronavirus disease 2019(COVID-19)pandemic has caused immense losses in human lives and the global economy and posed significant challenges for global public health.As severe acute respiratory syndrome coronavirus... 详细信息

The coronavirus disease 2019(COVID-19)pandemic has caused immense losses in human lives and the global economy and posed significant challenges for global public health.As Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),the causative agent of COVID-19,has evolved,thousands of single nucleotide variants(SNVs)have been identified across the viral genome.The roles of individual SNVs in the zoonotic origin,evolution,and transmission of SARS-CoV-2 have become the focus of many studies.This review summarizes recent comparative genomic analyses of SARS-CoV-2 and related coronaviruses(SC2r-CoVs)found in non-human animals,including delineation of SARS-CoV-2 lineages based on characteristic SNVs.We also discuss the current understanding of receptor-binding domain(RBD)evolution and characteristic mutations in variants of concern(VOCs)of SARS-CoV-2,as well as possible co-evolution between RBD and its receptor,angiotensin-converting enzyme 2(ACE2).We propose that the interplay between SARS-CoV-2 and host RNA editing mechanisms might have partially resulted in the bias in nucleotide changes during SARS-CoV-2 evolution.Finally,we outline some current challenges,including difficulty in deciphering the complicated relationship between viral pathogenicity and infectivity of different variants,and monitoring transmission of SARS-CoV-2 between humans and animals as the pandemic progresses.

关键词： molecular evolution population genetics Severe acute respiratory syndrome coronavirus 2 variant virus.

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Pushing past the tipping points in containment trajectories of Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)epidemics:A simple arithmetic rationale for crushing the curve instead of merely flattening it

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Infectious Disease Modelling 2020年第1期5卷 362-365页

作者： Gerry F.Killeen School of Biological Earth&Environmental Sciencesand Environmental Research InstituteUniversity College CorkIreland

Countries with ambitious national strategies to crush the curve of their Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)epidemic trajectories include China,Korea,Japan,Taiwan,New Zealand and Australia.However,the United States and many hard-hit European countries,like Ireland,Italy,Spain,France and the United Kingdom,currently appear content to merely flatten the curve of their epidemic trajectories so that transmission persists at rates their critical care services can cope with.Here I present a simple set of arithmetic modelling analyses that are accessible to non-specialists and explain why preferable crush the curve strategies,to eliminate transmission within months,would require only a modest amount of additional containment effort relative to the tipping point targeted by flatten the curve strategies,which allow epidemics to persist at supposedly steady,manageable levels for years,decades or even indefinitely.

关键词： coronavirus COVID SARS2 Severe acute respiratory syndrome coronavirus 2 SARS-CoV-2 Model Epidemiology Outbreak Zoonosis Emerging infection

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Fear can be more harmful than the Severe acute respiratory syndrome coronavirus 2 in controlling the corona virus disease 2019 epidemic

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World Journal of Clinical Cases 2020年第4期8卷 652-657页

作者： Shi-Yan Ren Rong-Ding Gao Ye-Lin Chen Vascular Surgery Department of General SurgeryAviation General HospitalChina Medical UniversityBeijing 100012China College of Robotics Beijing Union UniversityBeijing 100101China

The current corona virus disease 2019 outbreak caused by Severe acute respiratory syndrome coronavirus 2 started in Wuhan,China in December 2019 and has put the world on alert.To safeguard Chinese citizens and to strengthen global health security,China has made great efforts to control the epidemic.Many in the global community have joined China to limit the epidemic.However,discrimination and prejudice driven by fear or misinformation have been flowing globally,superseding evidence and jeopardizing the anti-Severe acute respiratory syndrome coronavirus 2 efforts.We analyze this phenomenon and its underlying causes and suggest practical solutions.

关键词： coronavirus severe acute respiratory syndrome Severe acute respiratory syndrome coronavirus 2 coronavirus disease 2019 Outbreak Fear Discrimination Prejudice

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Long, thin transmission chains of Severe acute respiratory syndrome coronavirus 2 may go undetected for several weeks at low to moderate reproduction numbers: Implications for containment and elimination strategy

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Infectious Disease Modelling 2021年第1期6卷 474-489页

作者： Gerry F.Killeen Patricia M.Kearney Ivan J.Perry Niall Conroy School of Biological Earth&Environmental SciencesUniversity College CorkCorkIreland Environmental Research Institute University College CorkCorkIreland School of Public Health University College CorkCorkIreland Wide Bay Public Health Unit QueenslandAustralia Faculty of Medicine University of QueenslandBrisbaneQueenslandAustralia

severe acute respiratory syndrome coronavirus 1(SARS-CoV-1)infections almost always caused overt symptoms,so effective case and contact management enabled its effective eradication within months.However,Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)usually causes only mild symptoms,so transmission chains may grow to include several individuals before at least one index case becomes ill enough to self-report for diagnosis and care.Here,simple mathematical models were developed to evaluate the implications of delayed index case detection for retrospective contact tracing and management responses.Specifically,these simulations illustrate how:(1)Contact tracing and management may effectively contain most but not all large SARS-CoV-2 clusters arising at foci with high reproduction numbers because rapidly expanding transmission chains ensure at least one overtly symptomatic index case occurs within two viral generations a week or less apart.(2)However,lower reproduction numbers give rise to thinner transmission chains extending through longer sequences of non-reporting asymptomatic and paucisymptomatic individuals,often spanning three or more viral generations(2 weeks of transmission)before an overtly symptomatic index case occurs.(3)Consequently,it is not always possible to fully trace and contain such long,thin transmission chains,so the community transmission they give rise to is underrepresented in surveillance data.(4)Wherever surveillance systems are weak and/or transmission proceeds within population groups with lower rates of overt clinical symptoms and/or self-reporting,case and contact management effectiveness may be more severely limited,even at the higher reproduction numbers associated with larger outbreaks.(5)Because passive surveillance platforms may be especially slow to detect the thinner transmission chains that occur at low reproduction numbers,establishing satisfactory confidence of elimination may require that no confirmed cases are detected for two full months,throughout which presump

关键词： coronavirus COVID SARS2 Severe acute respiratory syndrome coronavirus 2 SARS-CoV-2 Model Epidemiology Outbreak Case and contact management

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Severe acute respiratory syndrome coronavirus 2 Virus-Like Particle and Its Application in Chinese Medical Research

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World Journal of Traditional Chinese Medicine 2021年第2期7卷 258-264页

作者： Ruo-Dan Xu Ming-Fei Shi Jing Li Ning Li Institute of Basic Theory for Chinese Medicine China Academy of Chinese Medical Sciences Department of Nephroendocrine Dongzhimen HospitalBeijing University of Chinese MedicineBeijingChina

Background:The global outbreak of coronavirus disease 2019(COVID-19)has brought disastrous consequences to public health and medical systems,whereas no approved medications are currently available.Benefits of traditional Chinese medicine(TCM)against COVID-19 have been observed,however,the underlying mechanistic actions remain unclarified.Due to high pathogenicity and infectivity of the new coronavirus(Severe acute respiratory syndrome coronavirus 2[SARS-CoV-2]),the lack of access to SARS-CoV-2 and biosafety level 3(P3)facilities has impeded scientific investigations of TCM against COVID-19.Though low-pathogenic coronavirus and pseudoviral systems have been applied to substitute SARS-CoV-2 in fundamental studies,both models cannot imitate virological and clinical features associated with SARS-CoV-2.The virus-like particle(VLP)is a virological model that is safe and could be performed without biosafety protections.Aims and Objectives:To construct VLP of SARS-CoV-2 containing structural proteins of authentic viruses and resembling the morphology,partial life cycle,and immunoreactions of natural virions,and to introduce VLP into Chinese medical research.Materials and Methods:Using mammalian expression system,we have currently constructed SARS-CoV-2 VLP containing four essential structural proteins.Results:Based on this model,we propose six aspects of research that could be carried out for TCM formulas in the fight against COVID-19.Conclusion:Application of the VLP model provides a safe methodology to strengthen the response systems of Chinese medicine in preventing and controlling newly identified infectious diseases and offers collaborative opportunities for interdisciplinary deciphering of molecular and biological basis of anti-viral TCM formulas.

关键词： Chinese medical research coronavirus disease 2019 Severe acute respiratory syndrome coronavirus 2 virus-like particles

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Expert Recommendation for Novel Severe acute respiratory syndrome coronavirus 2 Vaccination in HIV-Infected Adults

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Infectious Diseases & Immunity 2021年第3期1卷 133-136页

作者： AIDS and Hepatitis C Professional Group,Chinese Society of Infectious Diseases Taisheng Li Hongzhou Lu 不详 Department of Infectious Diseases Peking Union Medical College HospitalChinese Academy of Medical Sciences Department of Infection and Immunology Shanghai Public Health Clinical Center

The outbreak of coronavirus disease 2019(COVID-19)caused by the novel Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)has become a pandemic.SARS-CoV-2 vaccination is currently being actively promoted worldwide as a promising measure to combat the pandemic.However,human immunodeficiency virus(HIV)-infected individuals who manifest varying degrees of immunodeficiency and chronic inflammation may require special consideration with regards to vaccine types and the timing of immunization depending on specific clinical situations.The present recommendation provides a reference for SARS-CoV-2 vaccination in HIV-infected patients.

关键词： HIV infections Severe acute respiratory syndrome coronavirus 2 Vaccines

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Severe acute respiratory syndrome coronavirus 2 may cause liver injury via Na^(+)/H^(+) exchanger

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World Journal of Virology 2023年第1期12卷 12-21页

作者： Medine Cumhur Cure Erkan Cure Department of Biochemistry Private Tanfer HospitalIstanbul 34394Turkey Department of Internal Medicine Bagcilar Medilife HospitalIstanbul 34200Turkey

The liver has many significant functions,such as detoxification,the urea cycle,gluconeogenesis,and protein synthesis.Systemic diseases,hypoxia,infections,drugs,and toxins can easily affect the liver,which is extremely sensitive to injury.Systemic infection of Severe acute respiratory syndrome coronavirus 2 can cause liver damage.The primary regulator of intracellular pH in the liver is the Na+/H+exchanger(NHE).Physiologically,NHE protects hepatocytes from apoptosis by making the intracellular pH alkaline.Severe acute respiratory syndrome coronavirus 2 increases local angiotensin II levels by binding to angiotensinconverting enzyme 2.In severe cases of coronavirus disease 2019,high angiotensin II levels may cause NHE overstimulation and lipid accumulation in the liver.NHE overstimulation can lead to hepatocyte death.NHE overstimulation may trigger a cytokine storm by increasing proinflammatory cytokines in the liver.Since the release of proinflammatory cytokines such as interleukin-6 increases with NHE activation,the virus may indirectly cause an increase in fibrinogen and D-dimer levels.NHE overstimulation may cause thrombotic events and systemic damage by increasing fibrinogen levels and cytokine release.Also,NHE overstimulation causes an increase in the urea cycle while inhibiting vitamin D synthesis and gluconeogenesis in the liver.Increasing NHE3 activity leads to Na+loading,which impairs the containment and fluidity of bile acid.NHE overstimulation can change the gut microbiota composition by disrupting the structure and fluidity of bile acid,thus triggering systemic damage.Unlike other tissues,tumor necrosis factor-alpha and angiotensin II decrease NHE3 activity in the intestine.Thus,increased luminal Na+leads to diarrhea and cytokine release.Severe acute respiratory syndrome coronavirus 2-induced local and systemic damage can be improved by preventing virus-induced NHE overstimulation in the liver.

关键词： Liver Hepatocyte Severe acute respiratory syndrome coronavirus 2 COVID-19 Na+/H+exchanger Sodium-proton pump

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Severe acute respiratory syndrome coronavirus 2 Infection as A Risk Factor for Thromboembolic and acute Ischemic Stroke:A Case Report

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Journal of Cerebrovascular Disease 2023年第4期6卷 26-30页

作者： Zhe-Chung Tan Department of Emergency Medicine The First Affiliated HospitalZhejiang University School of MedicineHangzhou 310003China

Increasing evidence reports a greater incidence of stroke in patients with coronavirus disease 2019(COVID-19)than in the non-COVID-19 population and suggests that Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)infection represents a risk factor for thromboembolic and acute ischemic stroke.Elderly people have higher risk factors for acute ischemic stroke or embolic vascular events,and advanced age is strongly associated with severe COVID-19 and death.We reported,instead,a case of an ischemic stroke in a young woman during her hospitalization for COVID-19-related pneumonia.A 29-year-old woman presented to the emergency department of the First Affiliated Hospital,Zhejiang University School of Medicine with progressive respiratory distress associated with a 2-day history of fever,nausea,and vomiting.The patient was transferred to the intensive care unit(ICU),where she underwent tracheostomy for mechanical ventilation due to her severe clinical condition and very low arterial partial pressure of oxygen.The nasopharyngeal swab test confirmed SARS-CoV-2 infection.Laboratory tests revealed neutrophilic leukocytosis,prolonged prothrombin time,and elevated D-dimer and fibrinogen levels.Left hemiplegia was reported 18 days later during her stay in the ICU after discontinuation of the sedative medications.Central facial palsy on the left side,dysarthria,and facial droop were present,with complete paralysis of the ipsilateral upper and lower limbs.Computed tomography(CT)of the head and magnetic resonance imaging of the brain confirmed the presence of lesions in the right hemisphere affecting the territories of the anterior and middle cerebral arteries,consistent with ischemic stroke.Pulmonary and splenic infarcts were also found after CT of the chest.The age of the patient and the absence of serious concomitant cardiovascular diseases place the emphasis on the capacity of SARS-CoV-2 infection to be an independent cerebrovascular risk factor.Increased levels of D-dimer and positivity forβ2-glycoprotein antibody cou

关键词： coronavirus disease 2019 Severe acute respiratory syndrome coronavirus 2 acute ischemic stroke Computed tomography Risk factor

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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);P25-12 days);P2-4 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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Effects of mild/asymptomatic COVID-19 on semen parameters and sex-related hormone levels in men:a systematic review and meta-analysis

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Asian Journal of Andrology 2023年第3期25卷 382-388页

作者： Bang-Wei Che Pan Chen Ying Yu Wei Li Tao Huang Wen-Jun Zhang Sheng-Han Xu Jun He Miao Liu Kai-Fa Tang Department of Urology The Affiliated Hospital of Guizhou Medical UniversityGuiyang 550004China

coronavirus disease 2019(COVID-19)has yet to be proven to alter male reproductive function,particularly in the majority of mild/asymptomatic patients.The purpose of this study was to explore whether mild/asymptomatic COVID-19 affects semen quality and sex-related hormone levels.To find suitable comparative studies,a systematic review and meta-analysis was done up to January 22,2022,by using multiple databases(Web of Science,PubMed,and Embase).Preferred Reporting Items for Systematic Reviews and Meta-Analyses(PRISMA)guidelines were used to identify and choose the studies.Meta-analysis was used to examine the semen parameters and sex-related hormones of mild/asymptomatic COVID-19 patients before and after infection.The effects of semen collection time,fever,and intensity of verification on semen following infection were also investigated.A total of 13 studies(n=770)were included in the analysis,including three case-control studies,six pre-post studies,and four single-arm studies.A meta-analysis of five pre-post studies showed that after infection with COVID-19,sperm concentration(I^(2)=0;P=0.003),total sperm count(I^(2)=46.3%;P=0.043),progressive motility(I^(2)=50.0%;P2)=76.1%;P=0.047),and normal sperm morphology(I^(2)=0;P=0.001)decreased.Simultaneously,a systematic review of 13 studies found a significant relationship between semen collection time after infection,inflammation severity,and semen parameter values,with fever having only bearing on semen concentration.Furthermore,there was no significant difference in sex-related hormone levels before and after infection in mild/asymptomatic patients.Mild/asymptomatic COVID-19 infection had a significant effect on semen quality in the short term.It is recommended to avoid initiating a pregnancy during this period of time.

关键词： coronavirus disease 2019 male infertility meta-analysis semen quality Severe acute respiratory syndrome coronavirus 2

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