Rapid adaptation and continuous performance evaluation of SARS-CoV-2 envelope gene (E-gene) real-time RT-PCR assays to support the hospital surge in test demand.

We describe the timely adaption of both published WHO E-gene protocol and commercially available LightMix Modular E-gene assay to the test platform (ABI 7900 Fast real-time analyzer and TaqMan Fast One-step Virus Master Mix) available in an accredited tertiary hospital laboratory with an on-going evaluation to ensure the provision of quality service within the time constraint. The LightMix Modular E-gene was slightly more sensitive when compared to the WHO E-gene, both analytically and diagnostically. The assay was recommended for screening of SARS-CoV-2 infection. With the availability of technically competent staff through continuous training, the provision of round-the-clock service is feasible despite the test is of high complexity. The thermal cycling duration of the adapted LightMix E-gene and WHO E-gene is shortened by half and one hour respectively and allows the number of runs to double when 24-h round-the-clock service is provided. An increase in testing capacity could support surges in testing demand, which is essential to control the current SARS-CoV-2 pandemic, to prevent potential overwhelming of the healthcare system, and to optimize utilization of the isolation beds.

Comparison of CaptiaTM Measles IgG Assay with Vidas® Measles IgG Assay for determination of immune protection status against measles virus.

BACKGROUND: Correlation of the assay cut-off values for CaptiaTM Measles IgG and the Vidas® Measles IgG assays with the World Health Organization recommended immunoprotective level of ≥120 mIU/mL is not stated by the manufacturers. Lack of such information may affect interpretation of immune protection (IP) for measles. OBJECTIVE: The aim of this study was to compare the relative performance of the CaptiaTM Measles IgG assay and the Vidas® Measles IgG assay for determination of IP against measles virus. STUDY DESIGN: Correlation of the cut-off value of both assays with the immunoprotective level was determined with the 3rd WHO Measles IgG International Standard. One hundred clinical samples including frozen and fresh were tested with both assays. The positive percentage agreement (PPA) based on the manufacturers' interpretation and the WHO recommended immunoprotective level was compared. RESULTS: Samples tested positive by the CaptiaTM assay were at or above the immunoprotective level while those tested equivocal and positive by the Vidas® assay were immune protective. The overall PPA between both assays was 78.31 % (95 % CI = 67.91-86.61%). When Vidas® equivocal results were regarded as immunoprotective, the overall IP agreement was 96.39 % (95 % CI = 89.80-99.25 %). CONCLUSIONS: CaptiaTM assay was more sensitive than the Vidas® assay in determination of IP against measles virus. Testing of measles immunity with the Vidas® Measles IgG assay might underestimate the IP unless equivocal results were regarded as immunoprotective.

Performance evaluation of the re-standardized Abbott Architect anti-HBs assay.

BACKGROUND: As defined by World Health Organization (WHO), an antibody level of ≥ 10mIU/mL to hepatitis B virus confers protection. With the launching of Abbott anti-HBs assay re-standardized to the 2nd WHO International Reference Preparation, a positive bias in antibody level would be anticipated. Manufacturer provides limited data for samples around the immune cut-off which has potential implication on vaccine guidance. OBJECTIVES: To evaluate the performance of the re-standardized Abbott Architect anti-HBs assay and to determine the impact of the upward shift. STUDY DESIGN: A total of 52 samples, including 12 external quality assurance programme samples and 40 clinical samples were tested with both the Abbott 1st WHO standardized and the 2nd WHO re-standardized assay and results compared. The 2nd WHO anti-HBs standard and Acometrix anti-HBs control were also included for comparison. RESULTS: Verification of the re-standardized assay with the 2nd WHO anti-HBs standard revealed positive bias with mean closer to target value. Overall, the positive bias introduced by the new assay will only affect interpretation of samples with anti-HBs levels > 5.00 to < 10.00 mIU/mL previously tested on the Abbott 1st WHO standardized anti-HBs assay. CONCLUSIONS: Final interpretation of immune status to hepatitis B was not affected by the upward shift following introduction of the new Abbott anti-HBs assay except for previously negative samples with anti-HBs levels between >5.00 to <10.00 mIU/mL.

Higher Viral Load of Emerging Norovirus GII.P16-GII.2 than Pandemic GII.4 and Epidemic GII.17, Hong Kong, China.

We compared viral load of emerging recombinant norovirus GII.P16-GII.2 with those for pandemic GII.Pe-GII.4 and epidemic GII.P17-GII.17 genotypes among inpatients in Hong Kong. Viral load of GII.P16-GII.2 was higher than those for other genotypes in different age groups. GII.P16-GII.2 is as replication competent as the pandemic genotype, explaining its high transmissibility and widespread circulation.

Comparison of the Cepheid Xpert Xpress Flu/RSV Assay to in-house Flu/RSV triplex real-time RT-PCR for rapid molecular detection of Influenza A, Influenza B and Respiratory Syncytial Virus in respiratory specimens.

This study compared the performance of the commercially available Xpert Xpress Flu/RSV assay to an in-house FluAB/RSV triplex real-time RT-PCR assay for the detection of influenza A/B viruses and respiratory syncitial virus (RSV) from both nasopharyngeal aspirate (NPA) and nasopharyngeal flocked swab (NPS). A total of 20 external quality assurance (EQA) samples and 172 clinical respiratory samples were tested prospectively using both the Xpert Xpress Flu/RSV assay and the in-house FluAB/RSV triplex assay. For the EQA samples, concordance rate was 100 % when tested with both assays. For clinical samples, there was 100 % agreement between the two assays for detection of influenza A and influenza B, 96.7 % agreement for detection of RSV and 99.7 % agreement for negative results. With a shortened turnaround time and good diagnostic performance, application of the Xpert Xpress Flu/RSV assay can facilitate patient triage for prompt implementation of infection control measures and management of high-risk patients during influenza epidemics.

Bimodal Seasonality and Alternating Predominance of Norovirus GII.4 and Non-GII.4, Hong Kong, China, 2014-20171.

We report emerging subtropical bimodal seasonality and alternating predominance of norovirus GII.4 and non-GII.4 genotypes in Hong Kong. GII.4 predominated in summer and autumn months and affected young children, whereas emergent non-GII.4 genotypes predominated in winter months and affected all age groups. This highly dynamic epidemiology should inform vaccination strategies.

Surveillance of antibiotic resistance among common Clostridium difficile ribotypes in Hong Kong.

Incidence of Clostridium difficile infection (CDI) is rapidly increasing and it poses a major health burden globally. However, data regarding the epidemiology of CDI in Asia are limited. We aimed to characterize the antimicrobial susceptibility patterns of common ribotypes of toxigenic C. difficile in Hong Kong. Fifty-three PCR ribotypes were identified among 284 toxigenic C. difficile clinical isolates. The five most prevalent ribotypes were 002 (13%), 017 (12%), 014 (10%), 012 (9.2%), and 020 (9.5%). All tested C. difficile strains remained susceptible to metronidazole, vancomycin, meropenem and piperacillin/tazobactam, but highly resistant to cephalosporins. Of the fluoroquinolones, highest resistance to ciprofloxacin was observed (99%), followed by levofloxacin (43%) and moxifloxacin (23%). The two newly emerged PCR ribotypes, 017 and 002, demonstrated high levels of co-resistance towards clindamycin, tetracycline, erythromycin and moxifloxacin. PCR ribotypes 017 and 002 with multi-drug resistance are rapidly emerging and continuous surveillance is important to monitor the epidemiology of C. difficile to prevent outbreaks of CDI.

Increased Detection of Emergent Recombinant Norovirus GII.P16-GII.2 Strains in Young Adults, Hong Kong, China, 2016-2017.

A new recombinant norovirus GII.P16-GII.2 outnumbered pandemic GII.4 as the predominant GII genotype in the winter of 2016-2017 in Hong Kong, China. Half of hospitalized case-patients were older children and adults, including 13 young adults. This emergent norovirus targets a wider age population compared with circulating pandemic GII.4 strains.

Rapid emergence and predominance of a broadly recognizing and fast-evolving norovirus GII.17 variant in late 2014.

Norovirus genogroup II genotype 4 (GII.4) has been the predominant cause of viral gastroenteritis since 1996. Here we show that during the winter of 2014-2015, an emergent variant of a previously rare norovirus GII.17 genotype, Kawasaki 2014, predominated in Hong Kong and outcompeted contemporary GII.4 Sydney 2012 in hospitalized cases. GII.17 cases were significantly older than GII.4 cases. Root-to-tip and Bayesian BEAST analyses estimate GII.17 viral protein 1 (VP1) evolves one order of magnitude faster than GII.4 VP1. Residue substitutions and insertion occur in four of five inferred antigenic epitopes, suggesting immune evasion. Sequential GII.4-GII.17 infections are noted, implicating a lack of cross-protection. Virus bound to saliva of secretor histo-blood groups A, B and O, indicating broad susceptibility. This fast-evolving, broadly recognizing and probably immune-escaped emergent GII.17 variant causes severe gastroenteritis and hospitalization across all age groups, including populations who were previously less vulnerable to GII.4 variants; therefore, the global spread of GII.17 Kawasaki 2014 needs to be monitored.

Hospitalization Incidence, Mortality, and Seasonality of Common Respiratory Viruses Over a Period of 15 Years in a Developed Subtropical City.

Information on respiratory viruses in subtropical region is limited.Incidence, mortality, and seasonality of influenza (Flu) A/B, respiratory syncytial virus (RSV), adenovirus (ADV), and parainfluenza viruses (PIV) 1/2/3 in hospitalized patients were assessed over a 15-year period (1998-2012) in Hong Kong.Male predominance and laterally transversed J-shaped distribution in age-specific incidence was observed. Incidence of Flu A, RSV, and PIV decreased sharply from infants to toddlers; whereas Flu B and ADV increased slowly. RSV conferred higher fatality than Flu, and was the second killer among hospitalized elderly. ADV and PIV were uncommon, but had the highest fatality. RSV, PIV 2/3 admissions increased over the 15 years, whereas ADV had decreased significantly. A "high season," mainly contributed by Flu, was observed in late-winter/early-spring (February-March). The "medium season" in spring/summer (April-August) was due to Flu and RSV. The "low season" in late autumn/winter (October-December) was due to PIV and ADV. Seasonality varied between viruses, but predictable distinctive pattern for each virus existed, and temperature was the most important associating meteorological variable.Respiratory viruses exhibit strong sex- and age-predilection, and with predictable seasonality allowing strategic preparedness planning. Hospital-based surveillance is crucial for real-time assessment on severity of new variants.

High mortality in adults hospitalized for active tuberculosis in a low HIV prevalence setting.

BACKGROUND: This study aims to evaluate the outcomes of adults hospitalized for tuberculosis in a higher-income region with low HIV prevalence. METHODS: A retrospective cohort study was conducted on all adults hospitalized for pulmonary and/or extrapulmonary tuberculosis in an acute-care hospital in Hong Kong during a two-year period. Microscopy and solid-medium culture were routinely performed. The diagnosis of tuberculosis was made by: (1) positive culture of M. tuberculosis, (2) positive M. tuberculosis PCR result, (3) histology findings of tuberculosis infection, and/or (4) typical clinico-radiological manifestations of tuberculosis which resolved after anti-TB treatment, in the absence of alternative diagnoses. Time to treatment ('early', started during initial admission; 'late', subsequent periods), reasons for delay, and short- and long-term survival were analyzed. RESULTS: Altogether 349 patients were studied [median(IQR) age 62(48-77) years; non-HIV immunocompromised conditions 36.7%; HIV/AIDS 2.0%]. 57.9%, 16.3%, and 25.8% had pulmonary, extrapulmonary, and pulmonary-extrapulmonary tuberculosis respectively. 58.2% was smear-negative; 0.6% multidrug-resistant. 43.4% developed hypoxemia. Crude 90-day and 1-year all-cause mortality was 13.8% and 24.1% respectively. 57.6% and 35.8% received 'early' and 'late' treatment respectively, latter mostly culture-guided [median(IQR) intervals, 5(3-9) vs. 43(25-61) days]. Diagnosis was unknown before death in 6.6%. Smear-negativity, malignancy, chronic lung diseases, and prior exposure to fluoroquinolones (adjusted-OR 10.6, 95%CI 1.3-85.2) delayed diagnosis of tuberculosis. Failure to receive 'early' treatment independently predicted higher mortality (Cox-model, adjusted-HR 1.8, 95%CI 1.1-3.0). CONCLUSIONS: Mortality of hospitalized tuberculosis patients is high. Newer approaches incorporating methods for rapid diagnosis and initiation of anti-tuberculous treatment are urgently required to improve outcomes.

A "pre-seasonal" hospital outbreak of influenza pneumonia caused by the drift variant A/Victoria/361/2011-like H3N2 viruses, Hong Kong, 2011.

BACKGROUND: Beginning from late 2011 and early 2012, increasing circulation of antigenically drifted influenza A/Victoria/361/2011-like H3N2 viruses within genotype 3 of the A/Victoria/208/2009 clade have been reported in multiple European countries and elsewhere. Whether these emerging viruses are associated with increased disease severity is unclear. OBJECTIVES: To report the clinical and virological findings of a moderately severe hospital outbreak of A/Victoria/361/2011-like viruses that occurred in November 2011 in Hong Kong. STUDY DESIGN: Clinical and virological hospital outbreak investigation. RESULTS: The outbreak occurred in an adult psychiatric ward in November 2011, a time well before the usual local seasonal influenza winter peak. Altogether, 7 patients and 1 healthcare-worker were affected (mean age, 47 [range, 34-61] years). The attack rates among patients and healthcare-workers were 33% (7/21) and 7% (1/15), respectively. Pneumonia developed in 38% (3/8) of cases; none had underlying immunocompromised conditions. High nasopharyngeal viral loads were detected. All cases responded to antiviral treatment. Multiple amino acid mutations with reference to earlier A(H3N2) vaccine strains were mapped to key antigenic sites on hemagglutinin; however, no critical mutations on receptor binding sites were detected. Viral sequence variations jeopardized the performance of molecular diagnostic assays. CONCLUSIONS: Severe disease and pneumonia occurred in a substantial proportion of non-immunocompromised adults in a hospital outbreak attributed to the emerging antigenically drifted A/Victoria/361/2011-like H3N2 viruses. Close monitoring of the transmission of this drift variant is required. Further studies are also necessary to determine virus virulence.

Complications and outcomes of pandemic 2009 Influenza A (H1N1) virus infection in hospitalized adults: how do they differ from those in seasonal influenza?

BACKGROUND: It is unclear whether pandemic 2009 influenza A (pH1N1) infection caused more significant disease among hospitalized adults than seasonal influenza. METHODS: A prospective, observational study was conducted in adults hospitalized with polymerase chain reaction-confirmed pH1N1 infection in 2 acute-care general hospitals from June 2009 to May 2010 (n = 382). Complications and outcomes were described and compared with those in a seasonal influenza cohort (2007-2008, same hospitals; n = 754). RESULTS: Hospitalized patients with pH1N1 influenza were younger than those with seasonal influenza (mean age ± standard deviation, 47 ± 20 vs 70 ± 19 years) and fewer had comorbid conditions (48% vs 64%). The rate of positive immunofluorescence assay results was low (54% vs 84%), and antiviral use was frequent (96% vs 52%). Most patients in both cohorts developed complicated illnesses (67.8% vs 77.1%), but patients with pH1N1 influenza had higher rates of extrapulmonary complications (23% vs 16%; P = .004) and intensive care unit admission and/or death (patient age <35 years, 2.3% vs 0%; 35-65 years, 12.4% vs 3.2%; >65 years, 13.5% vs 8.5%; adjusted odds ratio [OR] 2.13; 95% confidence interval [CI], 1.25-3.62; P = .005). Patients who received antiviral treatment within 96 h after onset had better survival (log-rank test, P < .001). However, without timely treatment, the mortality risk was higher with pH1N1 infection (9.0% vs 5.8% for seasonal influenza; adjusted OR, 6.85; 95% CI, 1.64-28.65; P = .008]. Bacterial superinfection worsened outcomes. CONCLUSIONS: Adults hospitalized for pH1N1 influenza had significant complications and mortality despite being younger than patients with seasonal influenza. Antiviral treatment within 96 h may improve survival.

Possible role of aerosol transmission in a hospital outbreak of influenza.

BACKGROUND: We examined the role of aerosol transmission of influenza in an acute ward setting. METHODS: We investigated a seasonal influenza A outbreak that occurred in our general medical ward (with open bay ward layout) in 2008. Clinical and epidemiological information was collected in real time during the outbreak. Spatiotemporal analysis was performed to estimate the infection risk among patients. Airflow measurements were conducted, and concentrations of hypothetical virus-laden aerosols at different ward locations were estimated using computational fluid dynamics modeling. RESULTS: Nine inpatients were infected with an identical strain of influenza A/H3N2 virus. With reference to the index patient's location, the attack rate was 20.0% and 22.2% in the "same" and "adjacent" bays, respectively, but 0% in the "distant" bay (P = .04). Temporally, the risk of being infected was highest on the day when noninvasive ventilation was used in the index patient; multivariate logistic regression revealed an odds ratio of 14.9 (95% confidence interval, 1.7-131.3; P = .015). A simultaneous, directional indoor airflow blown from the "same" bay toward the "adjacent" bay was found; it was inadvertently created by an unopposed air jet from a separate air purifier placed next to the index patient's bed. Computational fluid dynamics modeling revealed that the dispersal pattern of aerosols originated from the index patient coincided with the bed locations of affected patients. CONCLUSIONS: Our findings suggest a possible role of aerosol transmission of influenza in an acute ward setting. Source and engineering controls, such as avoiding aerosol generation and improving ventilation design, may warrant consideration to prevent nosocomial outbreaks.

Viral loads and duration of viral shedding in adult patients hospitalized with influenza.

BACKGROUND: The goal of this study was to characterize viral loads and factors affecting viral clearance in persons with severe influenza. METHODS: This was a 1-year prospective, observational study involving consecutive adults hospitalized with influenza. Nasal and throat swabs were collected at presentation, then daily until 1 week after symptom onset. Real-time reverse-transcriptase polymerase chain reaction to determine viral RNA concentration and virus isolation were performed. Viral RNA concentration was analyzed using multiple linear or logistic regressions or mixed-effect models. RESULTS: One hundred forty-seven inpatients with influenza A (H3N2) infection were studied (mean age+/-standard deviation, 72+/-16 years). Viral RNA concentration at presentation positively correlated with symptom scores and was significantly higher than that among time-matched outpatients (control subjects). Patients with major comorbidities had high viral RNA concentration even when presenting>2 days after symptom onset (mean+/-standard deviation, 5.06+/-1.85 vs 3.62+/-2.13 log10 copies/mL; P=.005; beta, +0.86 [95% confidence interval, +0.03 to +1.68]). Viral RNA concentration demonstrated a nonlinear decrease with time; 26% of oseltamivir-treated and 57% of untreated patients had RNA detected at 1 week after symptom onset. Oseltamivir started on or before symptom day 4 was independently associated with an accelerated decrease in viral RNA concentration (mean beta [standard error], -1.19 [0.43] and -0.68 [0.33] log10 copies/mL for patients treated on day 1 and days 2-3, respectively; P<.05) and viral RNA clearance at 1 week (odds ratio, 0.10 [95% confidence interval, 0.03-0.35] and 0.30 [0.10-0.90] for patients treated on day 1-2 and day 3-4, respectively). Conversely, major comorbidities and systemic corticosteroid use for asthma or chronic obstructive pulmonary disease exacerbations were associated with slower viral clearance. Viral RNA clearance was associated with a shorter hospital stay (7.0 vs 13.5 days; P=.001). CONCLUSION: Patients hospitalized with severe influenza have more active and prolonged viral replication. Weakened host defenses slow viral clearance, whereas antivirals started within the first 4 days of illness enhance viral clearance.

An audit of risk factors for wound infection in patients undergoing coronary artery bypass grafting or valve replacement.

OBJECTIVES: To investigate the epidemiology of surgical site infection in cardiac surgery patients operated on in 2006. DESIGN: Retrospective study of a case-control sample. SETTING: Cardiac surgery unit of a university teaching hospital in Hong Kong. PATIENTS: Cardiac surgery patients with surgical site infection were matched by procedure type, sex, and year of surgery with non-infected patients. MAIN OUTCOME MEASURES: Identification of risk factors for surgical site infection. RESULTS: The infected and non-infected cardiac surgery patients did not differ in age, sex, or smoking history; however, patients with surgical site infection were significantly heavier (mean body mass index, 26.6 vs 23.9 kg/m2, P < 0.046). Almost 41% of the subjects had a history of diabetes mellitus, there being a significantly greater proportion among infected than non-infected patients (53.1% vs 28.1%, P < 0.042). All 37 of the patients without a diagnosis of diabetes had normal (ie < 8 mmol/L) preoperative glucose levels, but 99% of them yielded evidence of subsequent glycaemic dysfunction during or after surgery. Overall, 50% of the patients had a blood transfusion during the operation, with infected patients significantly more likely to have been transfused than the non-infected ones (65.6% vs 34.4%, P < 0.008). CONCLUSIONS: There appears to be a relationship between surgical site infection in cardiac surgery patients and pre-existing (diagnosed and covert) diabetes mellitus and blood transfusion. Future studies should consider these factors in relation to surgical site infections, both in the wider surgical population and from a risk-minimisation perspective.

Longitudinally tracking fluoroquinolone resistance and its determinants in penicillin-susceptible and -nonsusceptible Streptococcus pneumoniae isolates in Hong Kong, 2000 to 2005.

Of 1,388 Streptococcus pneumoniae isolates collected from 2000 to 2005, 10.5% had a ciprofloxacin MIC of >/=4.0 mug/ml and 1.6% (range, 0.8% to 4.3% per year) had a levofloxacin MIC of >/=4.0 mug/ml. Molecular characterization indicated that fluoroquinolone resistance occurred independently in our prevalent Spain(23F)-1 clone, expressing serotypes 23F, 19F, and 14. Rates of resistance to levofloxacin in S. pneumoniae have remained stable at a Hong Kong hospital.

Streptococcus suis in Hong Kong.

Streptococcus suis was isolated from 6.1% of raw pork meat from 3 of the 6 wet markets in 6 districts in Hong Kong. S. suis was particularly isolated in sites from the tongue, tonsil, bone, and tail, but not from lean meat/minced pork or internal organs. Isolates were confirmed by polymerase chain reaction using S. suis-specific primers, did not belong to serotype 2 using serotype 2-specific antiserum, and were clustered closely with other known serotypes by phylogenetic analysis. Ten strains from patients admitted to Hong Kong hospitals with sepsis or meningitis in the past 10 years all belonged to type 2, with closely related pulsed-field gel electrophoresis types that were distinct from the S. suis strains isolated from pork in this study. These methods may serve as useful tools in studying and enhancing our understanding of these infections in Hong Kong.

Molecular epidemiology and household transmission of community-associated methicillin-resistant Staphylococcus aureus in Hong Kong.

This study evaluated the clinical and epidemiologic features of individuals with community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) in Hong Kong from January 2004 through December 2005. Twenty-four episodes of skin and soft tissue infections and 1 episode of meningitis due to CA-MRSA were identified. CA-MRSA infections or carriage was found in 6 (13%) of 46 household contacts. A total of 29 isolates were analyzed by the Staphylococcus cassette chromosome mec (SCCmec) typing, pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing. In addition, polymerase chain reaction detection of the genes encoding Panton-Valentine leukocidin was also carried out. It was observed that 24 had SCCmec IV/IVA and 5 had SCCmec V, and 23 were pvl positive. PFGE analysis clustered all except 1 isolate into 3 pulsed-field types (PFTs), HKU100 through HKU300. The HKU100 isolates had genotype ST30-IV identical to the Southwest Pacific clone. The HKU200 isolates belonged to ST59-V and were multiresistant, including an ermB-mediated macrolide resistance trait, which is characteristic of the predominant CA-MRSA clone in Taiwan. The HKU300 isolates had unique features (ST8, Panton-Valentine leukocidin negative, and SCCmec IVA) typical of CA-MRSA in Japan. In conclusion, CA-MRSA has a propensity to spread within families. Our findings showed that CA-MRSA strains in Hong Kong have diverse genetic backgrounds.