临床应用重组SARS病毒双抗原夹心诊断试剂盒的检测效果评价

严重急性呼吸综合征(severe acute respiralory syndrome,SARS)的临床表现为非典型性肺炎.继加拿大首次完成SARS病毒株Tor2的全基因组测序后[1],世界卫生组织(WTO)宣布一种新型的冠状病毒(coronavirus)是引发SARS的病原体[2,3].由于SARS具有极强的传染性和较高的病死率(5%～15%),且早期疾病体征较难与某些非SARS病毒引起的非典型肺炎相区分[4],由此导致大量疑似病例无法确诊,以及因误诊引起的交叉感染给人们造成巨大的心理压力和社会恐慌.所以,建立快速、准确的早期诊断方法显得尤为重要.目前的实验室诊断方法中,主要有基于病毒抗体检测的免疫荧光法和酶联免疫吸附试验(ELISA),以及基于基因检测的多聚酶链式反应(PCR)和基因芯片法.其中ELISA主要是使用病毒裂解抗原,检测病毒IgG及IgM抗体的间接ELISA.由于病毒裂解抗原的复杂性,以及间接ELISA中二抗带来的假阳性结果,间接ELISA试剂在正常人群中有1.5%～2%的阳性结果.     

Epidemiology, transmission dynamics and control of SARS: the 2002-2003 epidemic

This paper reviews current understanding of the epidemiology, transmission dynamics and control of the aetiological agent of severe acute respiratory syndrome (SARS). We present analyses of data on key parameters and distributions and discuss the processes of data capture, analysis and public health policy formulation during the SARS epidemic are discussed. The low transmissibility of the virus, combined with the onset of peak infectiousness following the onset of clinical symptoms of disease, transpired to make simple public health measures, such as isolating patients and quarantining their contacts, very effective in the control of the SARS epidemic. We conclude that we were lucky this time round, but may not be so with the next epidemic outbreak of a novel aetiological agent. We present analyses that help to further understanding of what intervention measures are likely to work best with infectious agents of defined biological and epidemiological properties. These lessons learnt from the SARS experience are presented in an epidemiological and public health context.     

国外防治重症急性呼吸综合征的措施概况

目前重症急性呼吸综合征(SARS)的疫情仍处于不稳定状态,并且呈现蔓延之势,引起了全球的重视。为了有效地控制其流行,打赢与SARS的战争,包括中国在内的许多国家和地区纷纷采取了强有力的预防和治疗措施,竭尽全力将疫情控制在最小的范围之内。本通过介绍世界各国针对SARS所采取的行之有效的反应措施,了解一些相关情况及经验,以开阔我们的眼界,同时冀望对建立和完善我国在突发性传染病、环境灾难以及生化恐怖袭击等公共危机突发事件的应急反应机制上提供借鉴意义。     

Bayesian modelling of an epidemic of severe acute respiratory syndrome

This paper analyses data arising from a SARS epidemic in Shanxi province of China involving a total of 354 people infected with SARS-CoV between late February and late May 2003. Using Bayesian inference, we have estimated critical epidemiological determinants. The estimated mean incubation period was 5.3 days (95% CI 4.2–6.8 days), mean time to hospitalisation was 3.5 days (95% CI 2.8–3.6 days), mean time from symptom onset to recovery was 26 days (95% CI 25–27 days) and mean time from symptom onset to death was 21 days (95% CI 16–26 days). The reproduction ratio was estimated to be 4.8 (95% CI 2.2–8.8) in the early part of the epidemic (February and March 2003) reducing to 0.75 (95% CI 0.65–0.85) in the later part of the epidemic (April and May 2003). The infectivity of symptomatic SARS cases in hospital and in the community was estimated. Community SARS cases caused transmission to others at an estimated rate of 0.4 per infective per day during the early part of the epidemic, reducing to 0.2 in the later part of the epidemic. For hospitalised patients, the daily infectivity was approximately 0.15 early in the epidemic, but fell to 0.0006 in the later part of the epidemic. Despite the lower daily infectivity level for hospitalised patients, the long duration of the hospitalisation led to a greater number of transmissions within hospitals compared with the community in the early part of the epidemic, as estimated by this study. This study investigated the individual infectivity profile during the symptomatic period, with an estimated peak infectivity on the ninth symptomatic day.     

用数学模型分析非典型肺炎预防和隔离措施的有效性

利用时滞常微分方程建立数学模型,研究在无任何预防和隔离措施的假想情况下非典型肺炎传染和发展的终极状态．通过对模型的讨论发现,在无任何预防和隔离措施的情况下,当非典疫情自生自灭以后,感染非典型肺炎的总人数占总人口的比例z主要取决于基本传染数R,即每个“非典”患者在其整个病程中的平均传染人数．根据有关报道[3,4],非典型肺炎的基本传染数R在2．2至3．6之间．根据我们的模型分析,当R=2．2时,z值可达85％左右,而当R=3．6时,z值可达97％左右．而事实上由于采取了预防和隔离措施,以北京市为例,感染非典型肺炎的总人数只有几千人,不到其总人口的千分之一．这充分说明了有关非典的预防和隔离措施的有效性．     

Molecular biology of severe acute respiratory syndrome coronavirus

The worldwide epidemic of severe acute respiratory syndrome (SARS) in 2003 was caused by a novel coronavirus called SARS-CoV. Coronaviruses and their closest relatives possess extremely large plus-strand RNA genomes and employ unique mechanisms and enzymes in RNA synthesis that separate them from all other RNA viruses. The SARS epidemic prompted a variety of studies on multiple aspects of the coronavirus replication cycle, yielding both rapid identification of the entry mechanisms of SARS-CoV into host cells and valuable structural and functional information on SARS-CoV proteins. These recent advances in coronavirus research have important implications for the development of anti-SARS drugs and vaccines.     

Bayesian analysis of severe acute respiratory syndrome: the 2003 Hong Kong epidemic

This paper analyzes data arising from a Severe Acute Respiratory Syndrome (SARS) epidemic in Hong Kong in 2003 involving 1755 cases. A discrete time stochastic model that uses a back-projection approach is proposed. Markov Chain Monte Carlo (MCMC) methods are developed for estimation of model parameters. The algorithm is further extended to integrate numerically over unobserved variables of the model. Applying the method to SARS data from Hong Kong, a value of 3.88 with a posterior standard deviation of 0.09 was estimated for the basic reproduction number. An estimate of the transmission parameter at the beginning of the epidemic was also obtained as 0.149 with a posterior standard deviation of 0.003. A reduction in the transmission parameter during the course of the epidemic forced the effective reproduction number to cross the threshold value of one, seven days after control interventions were introduced. At the end of the epidemic, the effective reproduction number was as low as 0.001 suggesting that the epidemic was brought under control by the intervention measures introduced.     

SARS冠状病毒病毒样颗粒疫苗的研究进展

2003年严重急性呼吸综合征(SARS)大流行之后,研究人员为防控SARS冠状病毒(SARS-CoV)的传播研制了多种不同形式的候选疫苗,大多是利用SARS-CoV表面的一种或多种结构蛋白制备的。SARS-CoV病毒样颗粒是具有较好的应用前景的一种候选疫苗,现将其制备方法及免疫原性做简要综述。     

Preparing the biochemistry laboratory for the next outbreak: lessons from SARS in Singapore

Severe acute respiratory syndrome (SARS) is an emerging disease characterised by fever and atypical pneumonia and caused by a novel coronavirus. Singapore was affected by the global pandemic in early 2003, with 238 cases and 33 deaths. Samples sent to the biochemistry laboratory made up the majority (69%) of all SARS samples, yet remained a minority (29%) of total biochemistry workload. This paper describes the problems encountered and solutions adopted by the biochemistry laboratory at the designated SARS hospital in coping with this epidemic. It provides practical advice for laboratories planning for the handling of samples from future outbreaks.     

Evolution of genomes, host shifts and the geographic spread of SARS-CoV and related coronaviruses

Severe acute respiratory syndrome (SARS) is a novel human illness caused by a previously unrecognized coronavirus (CoV) termed SARS‐CoV. There are conflicting reports on the animal reservoir of SARS‐CoV. Many of the groups that argue carnivores are the original reservoir of SARS‐CoV use a phylogeny to support their argument. However, the phylogenies in these studies often lack outgroup and rooting criteria necessary to determine the origins of SARS‐CoV. Recently, SARS‐CoV has been isolated from various species of Chiroptera from China (e.g., Rhinolophus sinicus) thus leading to reconsideration of the original reservoir of SARS‐CoV. We evaluated the hypothesis that SARS‐CoV isolated from Chiroptera are the original zoonotic source for SARS‐CoV by sampling SARS‐CoV and non‐SARS‐CoV from diverse hosts including Chiroptera, as well as carnivores, artiodactyls, rodents, birds and humans. Regardless of alignment parameters, optimality criteria, or isolate sampling, the resulting phylogenies clearly show that the SARS‐CoV was transmitted to small carnivores well after the epidemic of SARS in humans that began in late 2002. The SARS‐CoV isolates from small carnivores in Shenzhen markets form a terminal clade that emerged recently from within the radiation of human SARS‐CoV. There is evidence of subsequent exchange of SARS‐CoV between humans and carnivores. In addition SARS‐CoV was transmitted independently from humans to farmed pigs (Sus scrofa). The position of SARS‐CoV isolates from Chiroptera are basal to the SARS‐CoV clade isolated from humans and carnivores. Although sequence data indicate that Chiroptera are a good candidate for the original reservoir of SARS‐CoV, the structural biology of the spike protein of SARS‐CoV isolated from Chiroptera suggests that these viruses are not able to interact with the human variant of the receptor of SARS‐CoV, angiotensin‐converting enzyme 2 (ACE2). In SARS‐CoV we study, both visually and statistically, labile genomic fragments and, putative key mutations of the spike protein that may be associated with host shifts. We display host shifts and candidate mutations on trees projected in virtual globes depicting the spread of SARS‐CoV. These results suggest that more sampling of coronaviruses from diverse hosts, especially Chiroptera, carnivores and primates, will be required to understand the genomic and biochemical evolution of coronaviruses, including SARS‐CoV. © The Willi Hennig Society 2008.     

The 3a accessory protein of SARS coronavirus specifically interacts with the 5'UTR of its genomic RNA, Using a unique 75 amino acid interaction domain

More than four years have passed since the outbreak of the severe acute respiratory syndrome (SARS) epidemic, and still very little is known about the molecular biology and pathogenesis of this deadly virus. Among the accessory proteins of the SARS coronavirus (SARS-CoV), the 3a protein has been shown to interact with the spike, envelope, and membrane glycoprotein and has recently been established to be a structural component of capsid. Recent studies suggest that the 3a protein may function as an ion channel and may promote virus release. In order to further characterize the functional properties of this protein, we initiated studies to check its RNA binding activity. Using the yeast three-hybrid system, electrophoretic mobility shift assay (EMSA), and ultraviolet (UV) cross-linking techniques, we have shown that the 3a protein is capable of binding specifically to the 5' untranslated region (5'UTR) of the SARS virus genomic RNA. Further, we have mapped the interaction domain of the 3a protein responsible for this RNA-protein interaction using a series of deletion mutants and defined it to the central 75 amino acid region. This RNA binding motif of 3a does not share homology with any other known RNA binding protein and may have an important role in viral capsid assembly and pathogenesis.     

Curtailing transmission of severe acute respiratory syndrome within a community and its hospital

Severe acute respiratory syndrome (SARS) has been transmitted extensively within hospitals, and healthcare workers (HCWs) have comprised a large proportion of SARS cases worldwide. We present a stochastic model of a SARS outbreak in a community and its hospital. For a range of basic reproductive numbers (R(0)) corresponding to conditions in different cities (but with emphasis on R(0) approximately 3 as reported for Hong Kong and Singapore), we evaluate contact precautions and case management (quarantine and isolation) as containment measures. Hospital-based contact precautions emerge as the most potent measures, with hospital-wide measures being particularly important if screening of HCWs is inadequate. For R(0) = 3, case isolation alone can control a SARS outbreak only if isolation reduces transmission by at least a factor of four and the mean symptom-onset-to-isolation time is less than 3 days. Delays of a few days in contact tracing and case identification severely degrade the utility of quarantine and isolation, particularly in high-transmission settings. Still more detrimental are delays between the onset of an outbreak and the implementation of control measures; for given control scenarios, our model identifies windows of opportunity beyond which the efficacy of containment efforts is reduced greatly. By considering pathways of transmission in our system, we show that if hospital-based transmission is not halted, measures that reduce community-HCW contact are vital to preventing a widespread epidemic. The implications of our results for future emerging pathogens are discussed.     

Mathematical modeling of severe acute respiratory syndrome nosocomial transmission in Japan: the dynamics of incident cases and prevalent cases

An outbreak of Severe Acute Respiratory Syndrome (SARS) occurred in Hong Kong in late February 2003, resulting in 8,096 cumulative cases with 774 deaths. The outbreak was amplified by nosocomial transmission in many hospitals. Using mathematical modeling, we simulated the number of new incident and prevalent cases of SARS after one infected person was admitted to a hospital (index case). The simulation was tested stochastically using the SEIR model based on previously reported Gamma distributions. We estimated the duration time until 10 beds in negative pressure rooms in Chiyoda-ku, one of the 23 wards in Tokyo, were fully occupied with SARS-infected patients. We determined the impact of an increasing number of days on the number of prevalent cases until the index case was isolated. The prevalent cases increase exponentially along with the increase of the non-isolation period of the index case, and all the beds were fully occupied if the index case was not isolated until more than 6 days. However even 2 days non-isolation period of the index case could fill up all the beds when 16% of secondary infections are transmitted outside the hospital. There is a possibility that an epidemic will occur with the isolation of the index case even at early days if the infection is transmitted outside the hospital. The simulation results revealed that it was important to recognize and isolate SARS patients as early as possible and also to prevent the transmission spreading outside the hospital to control an epidemic.     

Synthetic reconstruction of zoonotic and early human severe acute respiratory syndrome coronavirus isolates that produce fatal disease in aged mice

The severe acute respiratory syndrome (SARS) epidemic was characterized by high mortality rates in the elderly. The molecular mechanisms that govern enhanced susceptibility of elderly populations are not known, and robust animal models are needed that recapitulate the increased pathogenic phenotype noted with increasing age. Using synthetic biology and reverse genetics, we describe the construction of a panel of isogenic SARS coronavirus (SARS-CoV) strains bearing variant spike glycoproteins that are representative of zoonotic strains found in palm civets and raccoon dogs, as well as isolates spanning the early, middle, and late phases of the SARS-CoV epidemic. The recombinant viruses replicated efficiently in cell culture and demonstrated variable sensitivities to neutralization with antibodies. The human but not the zoonotic variants replicated efficiently in human airway epithelial cultures, supporting earlier hypotheses that zoonotic isolates are less pathogenic in humans but can evolve into highly pathogenic strains. All viruses replicated efficiently, but none produced clinical disease or death in young animals. In contrast, severe clinical disease, diffuse alveolar damage, hyaline membrane formation, alveolitis, and death were noted in 12-month-old mice inoculated with the palm civet HC/SZ/61/03 strain or early-human-phase GZ02 variants but not with related middle- and late-phase epidemic or raccoon dog strains. This panel of SARS-CoV recombinants bearing zoonotic and human epidemic spike glycoproteins will provide heterologous challenge models for testing vaccine efficacy against zoonotic reintroductions as well as provide the appropriate model system for elucidating the complex virus-host interactions that contribute to more-severe and fatal SARS-CoV disease and acute respiratory distress in the elderly.     

Estimating Temporal Transmission Parameters from Infectious Disease Household Data, with Application to Taiwan SARS Data

Taking households having at least one infective as standard units and considering both a within-household infection rate and a global infection rate, we propose a Bayesian two level mixing S-I-R (susceptible-infective-removed) counting process model in which the transmission parameters may change over time and the parameters of interest are the within-household infection rate and the removal rate. Customized Markov chain Monte Carlo methods are developed for generating samples from the posterior distribution for inference purpose, based only on the removal times. The numerical performance of this method is examined in a simulation study. Applying this method to 2003 Taiwan SARS data, we find that the within-household infection rate decreases, the removal rate increases and their ratio is less than one and decreases significantly during the epidemic. This method allows the estimation of these parameters during the epidemic. For a rapidly transmitted disease, it provides a method to nearly real-time tracking of infection measures.     

New infections: myths and reality

New contemporary data about new infectious diseases of XXI century are presented. Data on morbidity and mortality from severe acute respiratory syndrome (SARS, atypical pneumonia) and avian influenza are analyzed and compared with World Health Organization data on human influenza. Biologic characteristics of avian influenza virus A/H5N1 are discussed as well as possibility of its human-to-human transmission. Principles of SARS and avian influenza infections transmission as zoonoses are described as well as mechanisms of transmission impeding their ability to infect humans. It has been argued that SARS should be regarded as contagious infection, whereas avian influenza - as non-contagious. Features of all stages of epidemic process of these infections are analyzed.     

SARS冠状病毒的Spike蛋白以及病毒的细胞侵入机制

严重急性呼吸系统综合征（SARS）是由SARS冠状病毒（SARS—CoV）引起的一种新型人类疾病,具有高致病性、高传染性、高死亡率的特点。Spike蛋白是冠状捅毒膜表面的糖蛋白突出,构成病毒的包膜子粒,在病毒与其受体结合、通过膜融合进入宿主细胞以及诱导机体产生中和性抗体的过程中发挥着重要的作用：目前利用Spike蛋白开发出的一些防治SARS的药物和疫苗在动物和体外实验中有良好的抗病毒作用。本文阐述了SARS—CoV Spike蛋白的结构与功能,为抗SARS药物及疫苗的研发提供一定的理论基础.     

SARS相关冠状病毒及其基因组

正在全球部分地区流行的严重急性呼吸综合征(SARS),由于其传染性强、危害性大而引起了广泛关注。各国实验室密切协作,在数月时间内分离出了SARS冠状病毒(SARSCoV),测定了病毒基因组序列,并在猴体内初步再现出SARSCoV所致肺部疾病与人相似,这些工作为遏制SARS的蔓延发挥了重要作用。现就SARSCoV的鉴定、基因组及其产物的结构与功能做一综述。     

Association of HLA classⅠand classⅡgenes with severe acute respiratory syndrome in the northern Chinese population

Severe acute respiratory syndrome (SARS) was a major epidemic at the beginning of the 21^st century. This highly infectious disease is caused by a novel coronavirus (SARS-CoV), whose immune reaction is still not completely understood. This study described the genetic patterns of HLA-A, -B, and -DRB1 loci in patients from Beijing who survived SARS, and examined whether an association between HLA genes and susceptibility/resistance to SARS exists. A total of 148 Chinese Han SARS survivors were recruited to donate convalescent plasma in 2003. HLA low-resolution genotyping was carried out using PCR-SSP. Allele frequencies were compared with published frequencies of HLA alleles from 11 755 unrelated northern Chinese Han bone marrow donors by Fisher's exact test. In this cohort, 13, 25 and 13 alleles were observed at HLA-A, -B, and -DRB1 loci respectively. Fisher's exact tests revealed four alleles (A*26, DRB1*04, DRB1*09, and DRB1*16) that showed a nominal association significance with the SARS virus (P<0.05), yet none of these associations remained significant after correction. Our study suggests that HLA polymorphisms were unlikely to have contributed significantly to either the susceptibility or resistance to the SARS-Cov infection in patients who survived SARS in the Northern Chinese population, thus leaving an open question for future studies into a possible association HLA class Ⅰ and class Ⅱ genes with SARS in patients who were unable to survive the infection.     

The Kermack-McKendrick epidemic model revisited

The Kermack-McKendrick epidemic model of 1927 is an age of infection model, that is, a model in which the infectivity of an individual depends on the time since the individual became infective. A special case, which is formulated as a two-dimensional system of ordinary differential ordinary differential equations, has often been called the Kermack-McKendrick model. One of the products of the SARS epidemic of 2002-2003 was a variety of epidemic models including general contact rates, quarantine, and isolation. These models can be viewed as age of infection epidemic models and analyzed using the approach of the full Kermack-McKendrick model. All these models share the basic properties that there is a threshold between disappearance of the disease and an epidemic outbreak, and that an epidemic will die out without infecting the entire population.