Evaluation of measures to reduce international spread of SARS

Mathematical models are used to quantify the effect of border control measures in reducing the international spread of SARS. Border screening is shown to play a relatively minor role in reducing disease spread. Assuming detection rates similar to those reported for arrival screening in Australia, screening can detect up to 10% (95% CI 3-23) of infected travellers, and reduce the probability of a large outbreak by up to 7% (95% CI 2-17). Rapid reductions in the time to diagnosis and effective facilities for the isolation of cases are essential to ensure that there will not be a large outbreak, and each week of delay in responding to imported infection approximately doubles the total number of cases. While the control response is being developed in a currently uninfected region, border screening can provide up to one week's additional time in which to improve methods for early isolation of cases.

Screening and identification of severe acute respiratory syndrome-associated coronavirus-specific CTL epitopes

Severe acute respiratory syndrome (SARS) is a highly contagious and life-threatening disease that emerged in China in November 2002. A novel SARS-associated coronavirus was identified as its principal etiologic agent; however, the immunopathogenesis of SARS and the role of special CTLs in virus clearance are still largely uncharacterized. In this study, potential HLA-A*0201-restricted spike (S) and nucleocapsid protein-derived peptides were selected from an online database and screened for potential CTL epitopes by in vitro refolding and T2 cell-stabilization assays. The antigenicity of nine peptides which could refold with HLA-A*0201 molecules was assessed with an IFN-gamma ELISPOT assay to determine the capacity to stimulate CTLs from PBMCs of HLA-A2(+) SARS-recovered donors. A novel HLA-A*0201-restricted decameric epitope P15 (S411-420, KLPDDFMGCV) derived from the S protein was identified and found to localize within the angiotensin-converting enzyme 2 receptor-binding region of the S1 domain. P15 could significantly enhance the expression of HLA-A*0201 molecules on the T2 cell surface, stimulate IFN-gamma-producing CTLs from the PBMCs of former SARS patients, and induce specific CTLs from P15-immunized HLA-A2.1 transgenic mice in vivo. Furthermore, significant P15-specific CTLs were induced from HLA-A2.1-transgenic mice immunized by a DNA vaccine encoding the S protein; suggesting that P15 was a naturally processed epitope. Thus, P15 may be a novel SARS-associated coronavirus-specific CTL epitope and a potential target for characterization of virus control mechanisms and evaluation of candidate SARS vaccines.

Detection of severe acute respiratory syndrome coronavirus in stool specimens by commercially available real-time reverse transcriptase PCR assays

Three commercially available real-time reverse transcriptase PCR assays (the Artus RealArt HPA coronavirus LightCycler, the Artus RealArt HPA coronavirus Rotor-Gene, and the EraGen severe acute respiratory syndrome coronavirus POL assay) and three RNA extraction methodologies were evaluated for the detection of severe acute respiratory syndrome coronavirus RNA from 91 stool specimens. The assays' sensitivities were highest (58% to 75%) for specimens obtained 8 to 21 days after symptom onset. The assays were less sensitive when specimens were obtained less than 8 days or more than 21 days after the onset of symptoms. All assays were 100% specific.

Risk of ruling out severe acute respiratory syndrome by ruling in another diagnosis: variable incidence of atypical bacteria coinfection based on diagnostic assays

BACKGROUND

Severe acute respiratory syndrome (SARS) caused the first epidemic of the 21st century and continues to threaten the global community.

OBJECTIVE

To assess the incidence of coinfection in patients confirmed to have SARS-associated coronavirus (SARS-CoV) infection, and thus, to determine the risk of ruling out SARS by ruling in another diagnosis.

METHODS

The present report is a retrospective study evaluating the incidence and impact of laboratory-confirmed SARS-CoV and other pulmonary pathogens in 117 patients. These patients were evaluated in a Toronto, Ontario, community hospital identified as the epicentre for the second SARS outbreak.

RESULTS

Coinfection with other pulmonary pathogens occurred in patients with SARS. Seventy-three per cent of the patient population evaluated had laboratory-confirmed SARS-CoV infection. Serology showing acute or recent Chlamydophila pneumoniae or Mycoplasma pneumoniae infection revealed an incidence of 30% and 9%, respectively, in those with SARS. These rates are similar to previously published studies on coinfection in pneumonia. All nucleic acid diagnostic assays were negative for C pneumoniae and M pneumoniae in respiratory samples from patients with SARS having serological evidence for these atypical pathogens.

CONCLUSIONS

Diagnostic assays for well-recognized pulmonary pathogens have limitations, and ruling out SARS-CoV by ruling in another pulmonary pathogen carries significant risk. Despite positive serology for atypical pathogens, in a setting where clinical suspicion for SARS is high, specific tests for SARS should be performed to confirm or exclude a diagnosis.

The large 386-nt deletion in SARS-associated coronavirus: evidence for quasispecies?

The severe acute respiratory syndrome–associated coronavirus (SARS-CoV) is reported to have deletions of various sizes. Recently, the large 386-nucleotide deletion (L386del) comprising nucleotide positions 27719-28104 and spanning open reading frames 9–11 has been reported in the genomes of some human isolates from Hong Kong. In this study, archived specimens from 71 patients with SARS who were admitted to the New Territory East Cluster Hospitals in Hong Kong were analyzed to determine whether the L386del variant of SARS-CoV was present. There was no clear relationship between the presence of the L386del variant and SARS clinical severity as defined either by the need for intensive-care therapy and/or ventilation or by death. One patient had evidence of both the L386del variant and the wild-type variant in the same clinical specimen, supporting the idea that SARS-CoV exists as a quasispecies in some patients, although the clinical significance of these quasispecies remains unclear

Severe acute respiratory syndrome (SARS): development of diagnostics and antivirals

abstract: The previously unknown coronavirus that caused severe acute respiratory syndrome (SARS‐CoV) affected more than 8,000 persons worldwide and was responsible for more than 700 deaths during the first outbreak in 2002–2003. For reasons unknown, the SARS virus is less severe and the clinical progression a great deal milder in children younger than 12 years of age. In contrast, the mortality rate can exceed 50% for persons at or above the age of 60. As part of the Sino‐European Project on SARS Diagnostics and Antivirals (SEPSDA), an immune phage‐display library is being created from convalescent patients in a phagemid system for the selection of single‐chain fragment variables (scFv) antibodies recognizing the SARS‐CoV.

[An epidemiological investigation of bats carrying SARS-CoV in Guangzhou and its vicinity]

OBJECTIVE

To detect serve acute respiratory syndrome-associated coronavirus (SARS-CoV) and SARS-like-CoV in fruit bats captured in Guangzhou and its vicinity.

METHODS

Totally 927 bats of 9 species (Cynopterus sphinx, Rousettus leschenaulti, Miniopterus schreibersi, Hipposideros pratti, Rhinolophusasinicus, Scotophilusakuhlii, Hipposideros Pomona, Rhinolophus affinis, and Rhinolophus pusillus) captured in Guangzhou and its vicinity from September 2004 to November 2005 were available for this investigation, from which 3,043 samples (813 throat swasb, 524 sera, 853 lung tissues and 853 colorectal tissue specimens) were obtained. SARS-Cov and SARS-like-CoV were detected in these specimens using diagnostic kit for novel coronavirus N protein (ELISA), SARS-CoV Virus RNA detection kit, fluorescence PCR, Genchip, RT-PCR and cell isolation culture methods.

RESULTS AND CONCLUSION

No SARS-CoV and SARS-like-CoV were detected in the 3043 samples, indicating the current absence of SARS-CoV and SARS-like-CoV in the bats captured in Guangzhou and its vicinity.

Early diagnosis of SARS: lessons from the Toronto SARS outbreak

The clinical presentation of SARS is nonspecific and diagnostic tests do not provide accurate results early in the disease course. Initial diagnosis remains reliant on clinical assessment. To identify features of the clinical assessment that are useful in SARS diagnosis, the exposure status and the prevalence and timing of symptoms, signs, laboratory and radiographic findings were determined for all adult patients admitted with suspected SARS during the Toronto SARS outbreak. Findings were compared between patients with laboratory-confirmed SARS and those in whom SARS was excluded by laboratory or public health investigation. Of 364 cases, 273 (75%) had confirmed SARS, 30 (8%) were excluded, and 61 (17%) remained indeterminate. Among confirmed cases, exposure occurred in the healthcare environment (80%) or in the households of affected patients (17%); community or travel-related cases were rare (<3%). Fever occurred in 97% of patients by the time of admission. Respiratory findings including cough, dyspnea and pulmonary infiltrates evolved later and were present in only 59, 37 and 68% of patients, respectively, at admission. Direct exposure, fever on the first day of illness, and elevated temperature, pulmonary infiltrates, lymphopenia and thrombocytopenia at admission were associated with confirmed cases. Rhinorrhea, sore throat, and an elevated neutrophil count at admission were associated with excluded cases. In the absence of fever or significant exposure, SARS is unlikely. Other clinical, laboratory and radiographic findings further raise or lower the likelihood of SARS and provide a rational basis for estimating the likelihood of SARS and directing initial management.

Respiratory viral threats

PURPOSE OF REVIEW

To assess new information from peer-reviewed publications in 2005 regarding emerging respiratory viral threats.

RECENT FINDINGS

The expanding epizootic of avian A/H5N1 influenza and increasing number of human cases heighten concern regarding the threat of pandemic influenza. Studies of the 1918 pandemic virus have shown the potential for direct interspecies transmission from an avian host. In the absence of an effective vaccine, antiviral agents could provide an important response measure. Inadequate supplies and potential antiviral resistance are limiting factors. Seasonal influenza heavily affects infants and young children, who also serve to foster transmission at the community level, findings that indicate the need for broader immunization strategies in pediatric populations. Like avian influenza, the severe acute respiratory syndrome coronavirus was a zoonotic infection, perhaps derived from related coronaviruses in bats. Molecular diagnostic techniques have led to the recent identification of several new coronaviruses and a respiratory parvovirus. It has also helped to define the impact of previously described ones such as human metapneumovirus and rhinoviruses, which account for the majority of asthma exacerbations and frequent lower respiratory tract illnesses.

SUMMARY

Progress has been made in development of possible specific interventions for influenza and possibly severe acute respiratory syndrome coronavirus, but effective antivirals and vaccines for most other respiratory viruses are currently lacking.

Is there an ideal animal model for SARS?

The outbreak of severe acute respiratory syndrome (SARS) in 2003 was controlled by public health measures at a time when specific interventions such as antiviral drugs, vaccines and immunotherapy were not available. Since then, several animal models have been developed for the study of SARS and, although no model replicates the human disease in all aspects, the use of animal models for SARS has led to the establishment of several important principles for vaccine and immunotherapy. Consistency and reproducibility of findings in a given model must be demonstrated to establish the superiority of one model over others. Here, we suggest aspects of an ideal animal model for studies of SARS pathogenesis and vaccine development and present our assessment of the strengths and limitations of the current animal models for SARS.

Bats and human emerging diseases

Recently, two independent research teams reported evidence of infection with SARS-like coronaviruses in insectivorous horseshoe bats (genus Rhinolophus) in China [1, 2]. SARS emerged in China in 2002, and eventually infected over 8000 people around the world, killing about 10% of them. Early epidemiological studies suggested that the human disease may have originated in Chinese live-animal food markets, and the hunt for a source of the virus quickly identified apparently healthy Himalayan palm civets (Paguma larvata) as prime suspects [3]. Other studies, however, failed to find any evidence of widespread infection in civets [4] or a variety of other animals traditionally used as food in China. Rather, palm civets, like human beings, seem to be only accidental hosts of the virus, becoming infected, again like people, when mixed with other species in markets. More structured hunts for the reservoir continued, although not before thousands of palm civets had been slaughtered.

Severe Acute Respiratory Syndrome in a Naval Diver

Severe acute respiratory syndrome (SARS) is a highly infectious, rapidly progressive, emerging disease. Early diagnosis and preventive measures are key for treatment and minimization of secondary spread. In the context of the armed forces, aggressive containment measures are essential to prevent an outbreak. In this study, we present the first reported case, to our knowledge, of SARS in a naval diver. The special physical requirements for divers and the potential complications associated with deep sea diving necessitate extensive investigation before certification of fitness for diving after SARS. In the early recovery period, potential problems during diving are caused by inadequate lung ventilation in relation to exercise level and increased breathing resistance attributable to weak respiratory muscles, with corresponding risk of hypoxia and hypercapnia, as well as decreased ability to respond to nonrespiratory problems during diving. Problems in the late recovery period include increased risk of diving complications (such as pulmonary barotrauma) resulting from fibrosis and scarring within the lung parenchyma, which are known complications of SARS. From our experience, we suggest that computed tomographic scans of the thorax, lung function tests, and careful follow-up monitoring should play a vital role in the assessment of patients during the convalescent period, before certification of fitness to dive.

Waste water disinfection during SARS epidemic for microbiological and toxicological control

OBJECTIVE

To evaluate the disinfection of wastewater in China.

METHODS

During the SARS epidemic occurred in Beijing, a study of different disinfection methods used in the main local wastewater plants including means of chlorine, chlorine dioxide, ozone, and ultraviolet was carried out in our laboratory. The residual coliform, bacteria and trihalomethanes, haloacetic acids were determined after disinfection.

RESULTS

Chlorine had fairly better efficiency on microorganism inactivation than chlorine dioxide with the same dosage. Formation of THMs and HAAs does not exceed the drinking water standard. UV irradiation had good efficiency on microorganism inactivation and good future of application in China. Organic material and ammonia nitrogen was found to be significant on inactivation and DBPs formation.

CONCLUSION

Chlorine disinfection seems to be the best available technology for coliform and bacteria inactivation. And it is of fairly low toxicological hazard due to the transformation of monochloramine.

[Establishment of molecular differential diagnostic (MDD) technology for detection of common respiratory viruses]

BACKGROUND

To provide rapid laboratory evidence for diagnosis of respiratory infection and help diagnose accurately and reduce the spread of disease, so that the patients can be diagnosed and treated early.

METHODS

Thirteen kinds of respiratory viruses were detected by using Genaco's MDD technology.

RESULTS

All the specimens were detected, the total positive rate was 100%; the sensitivity of the method was 10e2 (pfu/ml).

CONCLUSION

The MDD system can distinguish the 13 respiratory viruses, which helps diagnosis of respiratory viral infection.

Molecular epidemiology of SARS-associated coronavirus, Beijing

Viral adaptation to the host may be occurring under selective immune pressure.

Single nucleotide variations (SNVs) at 5 loci (17564, 21721, 22222, 23823, and 27827) were used to define the molecular epidemiologic characteristics of severe acute respiratory syndrome–associated coronavirus (SARS-CoV) from Beijing patients. Five fragments targeted at the SNV loci were amplified directly from clinical samples by using reverse transcription–polymerase chain reaction (RT-PCR), before sequencing the amplified products. Analyses of 45 sequences obtained from 29 patients showed that the GGCTC motif dominated among samples collected from March to early April 2003; the TGTTT motif predominanted afterwards. The switch from GGCTC to TGTTT was observed among patients belonging to the same cluster, which ruled out the possibility of the coincidental superposition of 2 epidemics running in parallel in Beijing. The Beijing isolates underwent the same change pattern reported from Guangdong Province. The same series of mutations occurring in separate geographic locations and at different times suggests a dominant process of viral adaptation to the host.

A simple method for preparing synthetic controls for conventional and real-time PCR for the identification of endemic and exotic disease agents

Medical and veterinary diagnostic and public health laboratories world-wide are increasingly being called upon to introduce molecular diagnostic tests for both endemic and exotic diseases. This demand has accelerated following increasing terrorism fears. Ironically these same concerns have lead to tightening of both import and export controls preventing many laboratories, particularly those outside of the United States, from gaining access to positive control material. This in turn has prevented many laboratories from introducing much needed molecular diagnostic tests. We describe here a generic approach for preparing synthetic DNA or RNA control material for use in either TaqMan or conventional PCR assays. The production of synthetic controls using this approach does not require cloning or special equipment or facilities beyond that found in any laboratory performing molecular diagnostics. The approach significantly reduces the possibility of contamination or erroneously reporting false-positive reactions due to contamination from positive control material. Synthetic controls produced using this approach have been employed in all molecular diagnostic tests performed in our laboratory and are used irrespective of whether we possess the organism or not.

Laboratory containment of SARS virus

Following the severe acute respiratory syndrome (SARS) outbreak in 2003, a large number of clinical and environmental samples containing/potentially containing SARS coronavirus (SARSCoV) as well as SARS-CoV stocks were retained in clinical and research laboratories. The importance of laboratory biosafety was demonstrated by the occurrence of laboratory incidents in Singapore, Taiwan and Beijing. It is imperative that safe practice and techniques, safety equipment and appropriate facility design should be in place to reduce or eliminate exposure of laboratory workers, other persons and the outside environment to SARS-CoV containing materials. Discussion on laboratory containment of SARS-CoV was initiated in Hong Kong in August 2003. It was agreed that an inventory of all specimens with the potential presence of SARS-CoV collected for any diagnostic or research purposes from November 2002 to July 2003 should be established in each laboratory. They should be stored in a secure place at the appropriate biosafety level with access control. Un-needed samples collected during the period should be destroyed. These laboratories should be audited to ensure inventories are updated. The audit should include safety and security measures to detect irregularities. Any laboratory accidents involving materials suspected of containing SARS-CoV should be reported to the authorities and all personnel exposed closely followed medically. A contingency plan should be in place in the laboratory and a drill conducted regularly to test its efficacy. By January 2004, all clinical laboratories performing SARS-CoV testing in Hong Kong set up inventories to document location and types of SARS-CoV containing materials retained in their laboratory. Audits of these laboratories in 2004 showed that laboratory safety and containment requirements as recommended were generally met.

Epidemiologic study and containment of a nosocomial outbreak of severe acute respiratory syndrome in a medical center in Kaohsiung, Taiwan

OBJECTIVE

We conducted an epidemiologic investigation at the beginning of a nosocomial outbreak of severe acute respiratory syndrome (SARS) to clarify the dynamics of SARS transmission, the magnitude of the SARS outbreak, and the impact of the outbreak on the community.

METHODS

We identified all potential cases of nosocomially acquired SARS, linked them to the most likely infection source, and described the hospital containment measures.

SETTING

A 2,300-bed medical center in Kaohsiung, Taiwan.

RESULTS

A total of 55 cases of SARS were identified, and 227 hospital workers were quarantined. The index patient and neighboring patients were isolated. A chest physician team reviewed medical charts and chest radiographs and monitored the development of SARS in patients staying in the ward. The presence of underlying lung disease and immunocompromise in some patients made the diagnosis of SARS difficult. Some cases of SARS were diagnosed after the patients had died. Medical personnel were infected only if they cared for patients with unrecognized SARS, and caretakers played important roles in transmission of SARS to family members. As the number of cases of nosocomial SARS increased, the hospital closed the affected ward and expedited construction of negative-pressure rooms on other vacated floors for patient cohorting, and the last case in the hospital was identified 1 week later.

CONCLUSIONS

Timely recognition of SARS is extremely important. However, given the limitations of SARS testing, possible loss of epidemic links, and the nonspecific clinical presentations in hospitalized patients, it is very important to establish cohorts of persons with low, medium, and high likelihoods of SARS acquisition. Rapid closure of affected wards may minimize the impact on hospital operations. Establishment of hospitals dedicated to appropriate treatment of patients with SARS might minimize the impact of the disease in future epidemics.

Airborne severe acute respiratory syndrome coronavirus concentrations in a negative-pressure isolation room

This study used a sensitive polymerase chain reaction method coupled with filter sampling to detect the presence of airborne severe acute respiratory syndrome (SARS) coronavirus in an isolation patient room with a patient with severe acute respiratory syndrome receiving mechanical ventilatory support. Polymerase chain reaction results were negative for SARS coronavirus in room air both before and after patient extubation.

[Enhanced-real time PCR: a highly sensitive method for SARS-coronavirus detection]

An enhanced real-time polymerase chain reaction (ERT-PCR) assay to detect the coronavirus associated with severe acute respiratory syndrome (SARS-Cov) has been designed for detection of SARS-Cov with high sensitivity and easy-to-interpret results, in which a target gene pre-amplification step preceded TaqMan real-time fluorescent PCR. The limit of detection of the ERT-PCR method was 10(-2) higher than the standard real-time PCR assay and 10(-7) higher than conventional PCR methods. The increased sensitivity of the assay would have major benefits in screening suspected SARS patients rapidly and efficiently and may help control the spread of SARS and other infectious diseases during future outbreak.

[Variability analysis of S2 gene of SARS-CoV]

OBJECTIVE

To determine the sequence of S2 gene of SARS-associated coronavirus (SARS-CoV) GD322 and analyze the phyletic evolution of S2 gene.

METHOD

S2 gene fragment was amplified from SARS-CoV GD322 genome with RT-PCR and ligated to pGEM-T vector for sequence analysis after transformation of the plasmid into E. coli DH5a. The variability of S2 genes and S2 proteins from 12 strains isolated in the early, intermediate and advanced stages of the SARS outbreak were analyzed and the phylogenetic tree was constructed with Lasergene, Clustal X, DNAman and Treeview. T cell antigen epitopes of S2 protein were predicted on the basis of Internet database.

RESULT

With the epidemic spread of SARS-CoV, the S2 genes of the virus tended to become stable. Homology of S2 genes of SARS-CoV isolated in advanced stage of the outbreak reached 99.9%. Prediction of T cell antigen epitope showed that mutation at the 57th amino acid effected T cell antigen epitope.

CONCLUSION

S2 gene of GD322 SARS-CoV is relatively stable during the epidemic spread of the virus, and mutation at the 57th amino acids of S2 protein may affect the T cell antigen epitope.

[Serological analysis of SARS Coronavirus in children diagnosed clinically as severe acute respiratory syndrome cases during SARS epidemic in Beijing]

OBJECTIVE

To identify the etiologic agents from children who had been clinically diagnosed as severe acute respiratory syndrome (SARS) during the epidemic in Beijing and to characterize the transmissibility of SARS from those children to others.

METHODS

One hundred and seventy-seven serum specimens were collected during the period of June to August, 2003 from children and adults who had been clinically diagnosed as SARS and who closely contacted with those diagnosed as SARS during SARS epidemic in Beijing. Serum specimens were also collected from 49 children from Anhui province which was non-epidemic region and 93 healthy kindergarten children without history of contacting with SARS patients in Beijing during SARS epidemic. Serum specimens collected from 90 healthy kindergarten children in Beijing in September 2002 were included in the study. All the 409 serum specimens were tested for specific antibodies against SARS-associated coronavirus (SARS-CoV) by different methods including ELISA for specific IgM and IgG, whole antibodies against SARS-CoV, IFA for specific IgM and IgG against SARS-CoV, and Western-blot for IgG to expressed N protein from SARS-CoV.

RESULTS

The positive rates of specific IgG and whole antibodies against SARS-CoV ranged from 39.1% to 43.5% in the children who had been clinically diagnosed as SARS, zero in children and 6.0% to 9.0% in adults who had closely contacted with the clinically diagnosed SARS children. Among those clinically diagnosed SARS adult patients, the positive rates of specific IgG and whole antibodies against SARS-CoV were 57.1% to 71.4%. In children and adults who closely contacted with these clinically diagnosed SARS adult patients, the positive rates of specific IgG and whole antibodies against SARS-CoV were 0 to 9.7% and 4.4% to 7.1%, respectively. None of the serum specimens collected from healthy children before and during epidemic in Beijing and children from non-epidemic region was positive when IFA methods and ELISA with Beier kits were used for detection, but some were positive when ELISA with the diagnostic kit from other source was applied.

CONCLUSION

The positive rates of specific IgG and whole antibodies against SARS-CoV in children who had been clinically diagnosed as SARS were around 40%, which is much lower than the positive rate in clinically diagnosed adult SARS patients, indicating that a large proportion of those "SARS" children were infected with respiratory viruses other than SARS-CoV during SARS epidemic in Beijing. Some of the children who closely contacted with children and adults SARS patients showed positive SARS-CoV antibodies, suggesting that asymptomatic infections may occur. The value of some approved diagnostic kit at least in children for SARS etiological diagnosis needs to be analyzed further.

[The research and development of new diagnostic gene chips for SARS coronavirus]

The loci of cDNA sequences for valid diagnosis have been identified through the selection of the genome of SARS coronaries. The gene chips for diagnosing such virus have been developed, based on our own-developed technology for manufacturing and application of gene chips. The diagnoses given by such gene chips were consistent well with the reports of clinical laboratories (94.29%) and the sensitivity reached 10(-2)/ml virus molecules. This method is well suited for the clinical use in SARS coronaries diagnosis.

SARS-CoV infection in a restaurant from palm civet

Epidemiologic investigations showed that 2 of 4 patients with severe acute respiratory syndrome (SARS) identified in the winter of 2003-2004 were a waitresss at a restaurant in Guangzhou, China, that served palm civets as food and a customer who ate in the restaurant ashort distance from animal cages. All 6 palm civets at the restaurant were positive for SARS-associated coronavirus (SARS-CoV). Partial spike (S) gene sequences of SARS-CoV from the 2 patients were identical to 4 of 5 Sgene viral sequences from palm civets. Phylogenetic analysis showed that SARS-CoV from palm civets in the restaurant was most closely related to animal isolates. SARS cases at the restaurant were the result of recent interspecies transfer from the putative palm civet reservoir, and not the result of continued circulation of SARS-CoV in the human population.

Severe acute respiratory syndrome diagnostics using a coronavirus protein microarray

To monitor severe acute respiratory syndrome (SARS) infection, a coronavirus protein microarray that harbors proteins from SARS coronavirus (SARS-CoV) and five additional coronaviruses was constructed. These microarrays were used to screen approximately 400 Canadian sera from the SARS outbreak, including samples from confirmed SARS-CoV cases, respiratory illness patients, and healthcare professionals. A computer algorithm that uses multiple classifiers to predict samples from SARS patients was developed and used to predict 206 sera from Chinese fever patients. The test assigned patients into two distinct groups: those with antibodies to SARS-CoV and those without. The microarray also identified patients with sera reactive against other coronavirus proteins. Our results correlated well with an indirect immunofluorescence test and demonstrated that viral infection can be monitored for many months after infection. We show that protein microarrays can serve as a rapid, sensitive, and simple tool for large-scale identification of viral-specific antibodies in sera.