Epidemiological News Bulletin

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1 PUBLICATION OF THE COMMITTEE ON EPIDEMIC DISEASES Epidemiological News Bulletin SEPTEMBER 2003 VOL. 29 NO. 9 ISSN A laboratory-acquired case of severe acute respiratory syndrome A probable case of severe acute respiratory syndrome (SARS) was diagnosed by Singapore General Hospital (SGH) on 8 Sep 03. The patient had fever and dry cough but no chest x-ray changes. SARScoronavirus (CoV) was detected in his stool and sputum. WHO was notified. According to the new WHO guideline on case definition for SARS in the postoutbreak period, the patient did not fulfil the case definition. Ministry of Health (MOH) s assessment was that this case was of low public health risk as the patient was picked up and isolated early. Chronology of events The patient is a 27-year-old Chinese Singaporean man in his third year of a doctoral programme in microbiology at the National University of Singapore (NUS). He was working on the West Nile virus at a microbiology laboratory at NUS. He also did some work at the Environmental Health Institute (EHI) laboratory of the National Environment Agency. He last visited the EHI laboratory on 23 Aug 03. He had no history of travel to previously SARS-affected areas and no known contact with SARS patients. On 26 Aug 03, he went to work at the NUS laboratory and was well, but he developed a fever around midnight. On 27 Aug 03, he consulted a general practitioner (GP) and was given a course of antibiotics. The fever persisted and he sought treatment at SGH Accident & Emergency Dept (A&ED) on 29 Aug 03. His chest x-ray was normal. He was diagnosed to have a viral fever and discharged from the A&ED. As he did not feel better, he consulted a traditional Chinese medicine (TCM) physician on 1 Sep 03. Two days later, on 3 Sep 03, he sought treatment again at the SGH A&ED for persistent fever and was admitted. CONTENTS A laboratory-acquired case of severe acute respiratory syndrome... P. 57 Cases of specified notifiable diseases... P. 62

2 58 From the time he became unwell on midnight of 26 Aug 03 till his admission to SGH on 3 Sep 03, he remained at home apart from his two visits to SGH A&ED, the GP and TCM physician. When he was admitted to SGH, he complained of fever, muscle aches and joint pains, but did not have any significant respiratory symptoms. He developed a dry cough after admission, but his fever resolved two days later. Three serial chest x-rays done at SGH were all normal. Four clinical specimens (sputum, stool, conjunctiva swab and blood) were sent to SGH for testing of SARS-CoV by reverse transcriptase polymerase chain reaction (RT-PCR). On 8 Sep 03, his stool and sputum specimens were tested positive. Three serial serological tests done on 3 Sep, 4 Sep and 8 Sep showed a rising titre of SARS-CoV antibodies. He was immediately transferred to the Communicable Disease Centre for further management. A repeat of his PCR tests done in two other laboratories in Singapore on 9 Sep 03 was confirmed positive. Blood samples were also tested positive for antibodies to SARS-CoV in another laboratory in Singapore. The results from the Centers for Disease Control (CDC), Atlanta, corroborated with Singapore s PCR and serology results. Subsequent investigations of the chest by CT on 13 Sep showed that he had evidence of pneumonic changes in his left lung. Tests for a whole range of other pathogens, including two human coronaviruses (OC43, 229E) were negative. The patient was discharged on 16 Sep and placed on a 14-day home quarantine order (HQO). Contact tracing and home quarantine Among the community and hospital contacts of the case, only one (a health attendant) reported unwell and was admitted to hospital on 10 Sep. She was diagnosed to have an upper respiratory infection and her PCR for SARS-CoV was negative. No staff member of the laboratories at NUS and EHI had fever or felt unwell. One of the contacts at EHI left Singapore for vacation in China on 5 Sep before the new probable case was detected. She was contacted and found to develop flu-like symptoms on 7 Sep. The Chinese health authorities were immediately alerted. The contact was tested negative for SARS-CoV. All the other staff of the two laboratories were also tested negative. A total of 25 HQOs were served on close contacts of the case: family members (8), TCM physician (2), SGH A&ED outpatients (8), visitors (3) and discharged patients (4). Another 58 exposed persons were put under voluntary home quarantine and telephone surveillance. In addition 610 other contacts were identified and kept under surveillance. Precautionary measures taken Pending investigation into the source of infection, the two laboratories suspended all research ac-

3 59 tivities. The staff members were also asked to stay at home until the all-clear was given. Although the patient was isolated throughout his stay in SGH and the staff who had contact with him wore protective gear, the hospital did not take any chances and ramped up its precautionary measures to the Orange Alert Level. These included no admission to the affected wards, N95 masks for all staff in clinical areas, restrictions to visitation of the affected wards and more intensive temperature surveillance of staff. Source of infection A 11-member Review Panel, comprising local and international experts (including two from US CDC and 2 from WHO) was tasked by MOH to: review epidemiological data of the SARS case; review biosafety requirements and practices at the laboratories in the following areas: standard microbiological practices; safety equipment; laboratory facilities; training in biological safety; and other special practices; c) recommend changes to address biosafety issues, improve practices and structural design of the laboratories; and d) recommend the approaches to the adoption of national standards, audit and accreditation for biological safety. The panel interviewed the patient as well as his family and work colleagues. The timeline of events is depicted in Fig. 1. Inspection at EHI revealed several structural problems within the BSL-3 laboratory. The training of the laboratory workers was insufficient and depended on formal training in other institutions. The panel developed three transmission hypotheses and the evidences for and against are given in Table 1. Figure 1 Timeline of events in Singapore, August and September 2003 Case seonegative Case PCR positive (stool, sputum) Work colleague ill Case worked in BSL3 laboratory Case illness onset Case seropositive Work colleague seronegative August September

4 60 Table 1 Transmission hypotheses of a case of SARS 1) Patient acquired infection a while ago and carried it latently Evidence against: Patient had recent documentation of seroconversion that coincided with clinical infection (Fig. 1). Patient denied contact with any known SARS case or travel to previously SARS- affected areas. 2) Patient recently acquired infection from someone Evidence against: One work contact had recent illness, but clinical picture was not consistent with SARS (nausea and vomiting; no fever). This person did not work with live SARS-CoV. Serum taken from this person 27 days after illness onset was negative for antibodies to the SARS-CoV. Patient denied contact with any other ill person. Interviews with family and work colleagues supported this assertion. 3) Patient acquired infection through laboratory contamination Evidence for: Patient worked in the BSL-3 laboratory 3.5 days before his illness onset. This is consistent with the expected incubation period for SARS. Although the patient reported only working on West Nile virus, the laboratory was doing live SARS work around the time. Poor record keeping made it difficult to ascertain if there was live SARS-CoV in the BSL-3 laboratory on the day of his visit, but it was there 2 days before. Procedures for laboratory safety differed widely between laboratory personnel at EHI and were not always appropriate. Testing of the frozen specimen that patient worked with on August 23 was positive by RT-PCR for the SARS-CoV and West Nile virus, suggesting contamination. The laboratory only worked on one strain of the SARS-CoV, so the laboratory strain and patient strain were sequenced for comparison. Approximately 91% of the genome was sequenced from the patient strain and found to be most closely related to the sequence of the laboratory strain. Minor differences observed are likely the results of the natural mutation rate for the virus.

5 61 Conclusion and recommendations From the results of the epidemiological investigation surrounding the SARS case, the panel concluded that it appears that inappropriate laboratory standards and an accidental cross-contamination of West Nile virus samples with SARS-CoV in the EHI laboratory led to the infection of the doctoral student. No evidence could be found of any other source of the infection. West Nile virus and SARS-CoV were detected in the virus samples handled in the laboratory. There was no evidence of secondary transmission and this was an isolated case of SARS. The following recommendations pertaining to EHI BSL-3 laboratory were made by the panel: ( The laboratory should only be allowed to reopen once it has be re-audited and issues related to the structure, the use of the BSL-3 laboratory, training of staff, and a risk assessment of work have been carried out to a level acceptable by a safety committee. The laboratory should be pressure tested before reopening. The stocks of virus passages done in the BSL-3 laboratory during the time when SARS-CoV was present in the laboratory should be destroyed. ( After a complete disinfection (fumigation) of the laboratory, structural changes should be done to the laboratory to reach the BSL-3 standards: the air supply unit for BSL-3 laboratory should be separated; particulates air filter (97% efficiency) should be installed; pressure gauges indicating negative pressure level of change room and the laboratory must be installed in a convenient place with adequate alarms; doors should have cardkey access and biohazards signs must be displayed on them; autoclave should be moved inside the laboratory or better, a double-door autoclave should be installed; a low-temperature freezer should be moved inside the laboratory to keep the BSL-3 virus stocks; and CO 2 bottles should be installed outside of the main laboratory. An eye wash station should be installed in the change room, and if possible, a personal shower. (c) A daily checklist should be put in place to record date, time, name and laboratory pressure; standardized and computerized inventory of the virus stock in the freezers must be implemented and enforced. (d) The Institute develops or offers appropriate training (including refresher course) in biological safety and this training should be competency based. Training in the operation at BSL-3 laboratory could be mandatory if work is to be done under these conditions. Training records should be kept. Appropriate standard operating procedures (SOP) should be available and enforced. (e) The biosecurity aspects have to be considered. Access to the BSL-2 and BSL-3 laboratories should not be free and cardkeys system should be introduced.

6 Cases of specified notifiable diseases, Republic of Singapore, August 2003 Month ending Cumulative, first 35 weeks Diseases Median Median 30 Aug Aug Cholera Plague Yellow fever Chickenpox Dengue Dengue fever Dengue haemorrhagic fever Diphtheria Enteric fevers Typhoid fever Paratyphoid fever Leprosy Malaria Poliomyelitis Venereal diseases Chancroid Gonorrhoea c) Non-specific urethritis d) Syphilis i) Infectiou s ii) Non-infectious AIDS Tuberculosis Viral hepatitis Hepatitis A Hepatitis B c) Others Viral encephalitis Measles Mumps Rubella Hand, foot and mouth disease Legionellosis Nipah virus infection Severe acute respiratory syndrome* # - - * notifiable as from 17 March # additional probable SARS cases due to retrospective reclassification. The data in this Bulletin are provisional, based on reports to the Epidemiology & Disease Control Division, Ministry of Health and the Department of Clinical Epidemiology, Tan Tock Seng Hospital. Any comments or questions should be addressed to: The Editor Epidemiological News Bulletin Epidemiology & Disease Control Division College of Medicine Building, 16 College Road, Singapore169854

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