Territorywide Study of Early Coronavirus Disease Outbreak, Hong Kong, China.

Initial cases of coronavirus disease in Hong Kong were imported from mainland China. A dramatic increase in case numbers was seen in February 2020. Most case-patients had no recent travel history, suggesting the presence of transmission chains in the local community. We collected demographic, clinical, and epidemiologic data from 50 patients, who accounted for 53.8% of total reported case-patients as of February 28, 2020. We performed whole-genome sequencing to determine phylogenetic relationship and transmission dynamics of severe acute respiratory syndrome coronavirus 2 infections. By using phylogenetic analysis, we attributed the community outbreak to 2 lineages; 1 harbored a common mutation, Orf3a-G251V, and accounted for 88.0% of the cases in our study. The estimated time to the most recent common ancestor of local coronavirus disease outbreak was December 24, 2019, with an evolutionary rate of 3.04 × 10-3 substitutions/site/year. The reproduction number was 1.84, indicating ongoing community spread.

Detection of SARS-CoV-2 in conjunctival secretions from patients without ocular symptoms.

PURPOSE: To evaluate the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in conjunctival secretions from patients without ocular symptoms. METHODS: Conjunctival swabs were prospectively collected from laboratory-confirmed Coronavirus disease 2019 (COVID-19) patients without ocular symptoms for reverse transcription-polymerase chain reaction (RT-PCR) and viral culture. RESULTS: A total of 158 conjunctival swabs were obtained from 49 laboratory-confirmed COVID-19 patients. The median duration of illness when the first conjunctival swab was obtained was 10 days (range 2-27 days). Four conjunctival swabs from four different patients (4/49, 8.2%) were positive for SARS-CoV-2 RNA by RT-PCR. The Ct values ranged from 32.7 to 37.7 (mean 35.4). Viral cultures were negative for all four RT-PCR-positive conjunctival swabs. CONCLUSION: Conjunctival secretions of a minority of COVID-19 patients without ocular symptoms may contain relatively low levels of SARS-CoV-2 RNA, but their infectiousness remains undetermined. Appropriate infection control measures should be implemented during ophthalmological assessment of COVID-19 patients to prevent potential nosocomial transmission of SARS-CoV-2.

Improved detection of Zika virus RNA in human and animal specimens by a novel, highly sensitive and specific real-time RT-PCR assay targeting the 5'-untranslated region of Zika virus.

OBJECTIVE AND METHOD: We developed and evaluated five novel real-time RT-PCR assays targeting conserved regions in the 5'-untranslated region (5'-UTR), envelope (E'), non-structural protein 2A (NS2A), NS5 and 3'-UTR of the ZIKV genome. RESULTS: The ZIKV-5'-UTR assay exhibited the lowest in vitro limit of detection (5-10 RNA copies/reaction and 3.0 × 10-1 plaque-forming units/ml). Compared to the modified version of a widely adopted RT-PCR assay targeting the ZIKV-E gene, the ZIKV-5'-UTR assay showed better sensitivity in human clinical specimens, and representative mouse specimens, including many organs which are known to be involved in human ZIKV infection but difficult to obtain in clinical settings. The ZIKV-5'-UTR assay detected ZIKV RNA in 84/84 (100.0%) ZIKV-E'-positive and an additional 30/296 (10.1%, P < 0.01) ZIKV-E'-negative mouse specimens. The higher sensitivity of the ZIKV-5'-UTR assay was most significant in kidney and testis/epididymis specimens (P < 0.01). No in vitro or in vivo cross-reactivity was found between the ZIKV-5'-UTR assay and dengue virus, yellow fever virus, Japanese encephalitis virus, West Nile virus, hepatitis C virus and Chikungunya virus. CONCLUSIONS: The highly sensitive and specific ZIKV-5'-UTR assay may help to improve the laboratory diagnosis of ZIKV infection.

An outbreak of Burkholderia cepacia complex exit site infection among peritoneal dialysis patients caused by contaminated spray dressing.

Background: Wound dressing is intended to provide a physical barrier from microorganisms. Spray dressing is convenient and can be applied to wounds of various contours. In July 2020, a cluster of four Burkholderia cepacia complex (BCC) exit site infections was identified among peritoneal dialysis patients in a regional hospital in Hong Kong. In response, our hospital infection control team conducted an epidemiologic investigation. Methods: We conducted a retrospective cohort study of peritoneal dialysis patients with culture-confirmed BCC exit site infections from January 2011 to July 2020. Outbreak investigations, including case finding, molecular typing and post-outbreak surveillance, were performed. Discussion: A substantial increase in BCC exit site infections has been observed since 2013, rising from 0.23 in 2012 to 1.09 episodes per 100 patient-year in 2015, with the number of cases in the first half of 2020 already surpassing the total from 2019. The potential source had been traced to a spray dressing introduced to exit site care in December 2012. Burkholderia cepacia complex was isolated from both the unopened and in-use sprays from the same lot. Multilocus sequence typing analysis confirmed their genetic relatedness. The spray dressing was subsequently removed from exit site care. Post-outbreak surveillance over two years showed a marked and sustained decrease in BCC exit site infection. Conclusion: Water-based spray dressing can be a source of BCC causing wound infections. The use of contaminated spray dressing, especially in chronic wounds with proximity to indwelling catheters, may pose an inherent risk to patients.

Bacterial co-infections and antibiotic prescribing practice in adults with COVID-19: experience from a single hospital cluster.

BACKGROUND: Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has affected millions of individuals since December 2019, resulting in significant morbidity and mortality globally. During the 1918 Influenza Pandemic, it was observed that influenza was associated with bacterial co-infections. However, empirical or prophylactic antibiotic use during viral pandemics should be balanced against the associated adverse drug events. METHODS: In this retrospective cohort study, we investigated bacterial co-infections in adults with COVID-19 in Hong Kong. Notably, at the time of writing this report, patients with varying disease severities were isolated in hospitals until confirmatory evidence of virological clearance or immunity was available. The study included adults with laboratory-confirmed COVID-19 admitted to a single hospital cluster between 8 January 2020 and 1 May 2020. We obtained data regarding patient demographics, clinical presentations, blood test results, treatment, and outcomes. Bacteriological profiles and risk factors for co-infections were investigated. Antibiotic prescription practices were also reviewed. RESULTS: Of the 147 patients recruited, clinical disease was suspected in 42% (n = 62) of patients who underwent testing for other respiratory infections. Notably, 35% (n = 52) of the patients were prescribed empirical antibiotics, predominantly penicillins or cephalosporins. Of these, 35% (n = 18) received more than one class of antibiotics and 37% (n = 19) received empirical antibiotics for over 1 week. Overall, 8.2% (n = 12) of patients developed bacterial co-infections since the detection of COVID-19 until discharge. Methicillin-susceptible Staphylococcus aureus was the most common causative pathogen identified. Although 8.2% (n = 12) of patients developed hypoxia and required oxygen therapy, no mortality was observed. Multivariate analysis showed that pneumonic changes on chest radiography at the time of admission predicted bacterial co-infections. CONCLUSION: These findings emphasise the importance of judicious administration of antibiotics throughout the disease course of COVID-19 and highlight the role of antimicrobial stewardship during a pandemic.

Evaluation of the commercially available LightMix® Modular E-gene kit using clinical and proficiency testing specimens for SARS-CoV-2 detection.

BACKGROUND: Rapid and sensitive diagnostic assays for SARS-CoV-2 detection are required for prompt patient management and infection control. The analytical and clinical performances of LightMix® Modular SARS and Wuhan CoV E-gene kit, a widely used commercial assay for SARS-CoV-2 detection, have not been well studied. OBJECTIVE: To evaluate the performance characteristics of the LightMix® E-gene kit in comparison with well-validated in-house developed COVID-19 RT-PCR assays. STUDY DESIGN: Serial dilutions of SARS-CoV-2 culture isolate extracts were used for analytical sensitivity evaluation. A total of 289 clinical specimens from 186 patients with suspected COVID-19 and 8 proficiency testing (PT) samples were used to evaluate the diagnostic performance of the LightMix® E-gene kit against in-house developed COVID-19-RdRp/Hel and COVID-19-N RT-PCR assays. RESULTS: The LightMix® E-gene kit had a limit of detection of 1.8 × 10-1 TCID50/mL, which was one log10 lower than those of the two in-house RT-PCR assays. The LightMix® E-gene kit (149/289 [51.6%]) had similar sensitivity as the in-house assays (144/289 [49.8%] for RdRp/Hel and 146/289 [50.5%] for N). All three assays gave correct results for all the PT samples. Cycle threshold (Cp) values of the LightMix® E-gene kit and in-house assays showed excellent correlation. Reproducibility of the Cp values was satisfactory with intra- and inter-assay coefficient of variation values <5%. Importantly, the LightMix® E-gene kit, when used as a stand-alone assay, was equally sensitive as testing algorithms using multiple COVID-19 RT-PCR assays. CONCLUSIONS: The LightMix® E-gene kit is a rapid and sensitive assay for SARS-CoV-2 detection. It has fewer verification requirements compared to laboratory-developed tests.