Analytical sensitivity of the Rapid Antigen Test kits for detection of SARS-CoV-2 Omicron variant BA.2 sublineage.

The severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) Omicron was classified as a variant of concern in November 2021. The sublineage BA.2 spreads rapidly worldwide. Currently, there is a lack of data for the parallel comparison of Rapid Antigen Test (RAT) Kits to detect SARS-CoV-2 Omicron BA.2. We evaluated the analytical sensitivity of 12 RAT kits to detect Omicron BA.2 in the present study. Analytical sensitivity was determined by means of the limit of detection (LOD). We prepared a dilution set using a respiratory specimen collected from a COVID-19 patient infected by Omicron BA.2. The reverse transcription-polymerase chain reaction was used as a reference method. The LOD results showed that all 12 RAT kits had comparable analytical sensitivity to detect Omicron BA.2. The RAT kits selected in the current study may be used for the first-line screening of the rapid spreading Omicron BA.2.

The surveillance of spike protein for patients with COVID-19 detected in Hong Kong in 2020.

In 2020, numerous fast-spreading severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have been reported. These variants had unusually high genetic changes in the spike (S) protein. In an attempt to understand the genetic background of SARS-CoV-2 viruses in Hong Kong, especially before vaccination, the purpose of this study is to summarize the S protein mutations detected among coronavirus disease 2019 (COVID-19) patients in Hong Kong in 2020. COVID-19 cases were selected every month in 2020. One virus from each case was analyzed. The full encoding region of the S proteins was sequenced. From January 2020 to December 2020, a total of 340 COVID-19 viruses were sequenced. The amino acids of the S protein for 44 (12.9%) were identical to the reference sequence, WIV04 (GenBank accession MN996528). For the remaining 296 sequences (87.1%), a total of 43 nonsynonymous substitution patterns were found. Of the nonsynonymous substitutions found, some of them were only detected at specific time intervals and then they disappeared. The ongoing genetic surveillance system is important. It would facilitate early detection of mutations that can increase infectivity as well as mutations that are selected for the virus to escape immunological restraint.

Non-specific signals in real-time RT-PCR for detecting respiratory viruses.

We describe our experiences in investigating the origin of non-specific signals during the development phase of a multiplex PCR assay for respiratory viruses. After ruling out various sources of error, eventually we discovered the non-specific signal was related to the particular lot of the PCR kit.

Optimizing heat inactivation for SARS-CoV-2 at 95 °C and its implications: A standardized approach.

Background: Standardized and validated heat inactivation procedure for Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are not available. For heat inactivation, various protocols were reported to prepare External Quality Assessment Programme (EQAP) samples without direct comparison between different durations. Objective: To assess the heat inactivation procedures against SARS-CoV-2. The efficacy of the optimized condition was reflected by the results from laboratories testing the EQAP samples. Study design: The SARS-CoV-2 strain was exposed to 95 °C in a water bath for three different time intervals, 5 min, 10 min and 15 min, respectively. The efficacy of inactivation was confirmed by the absence of cytopathic effects and decreasing viral load in 3 successive cell line passages. The viral stock inactivated by the optimal time interval was dispatched to EQAP participants and the result returned were analyzed. Results: All of the three conditions were capable of inactivating the SARS-CoV-2 of viral load at around cycle threshold value of 10. When the 95 °C 10 min condition was chosen to prepare SARS-CoV-2 EQAP samples, they showed sufficient homogeneity and stability. High degree of consensus was observed among EQAP participants in all samples dispatched. Conclusions: The conditions evaluated in the present study could be helpful for laboratories in preparing SARS-CoV-2 EQAP samples.

Assessment of SARS-CoV-2 viral loads in combined nasal-and-throat swabs collected from COVID-19 individuals under the Universal Community Testing Programme in Hong Kong.

BACKGROUND: Combined nasal-and-throat swabs (CNTS) is less invasive and easy to execute. CNTS also induces lower risk to healthcare workers upon collection. However, there is a lack of data on viral load assessment for population-wide testing. OBJECTIVE: This study assessed if CNTS is suitable as an alternative specimen type for the detection of SARS-CoV-2. METHODS: We assessed the viral load of SARS-CoV-2 in CNTS collected from COVID-19 individuals through the 2-week period of the Universal Community Testing Programme (UCTP) conducted in Hong Kong. In addition, we compared viral loads of SARS-CoV-2 for the paired CNTS and non-CNTS specimens among these individuals. RESULTS: This UCTP identified 48 COVID-19 individuals from nearly 2 million specimens collected. The viral loads of SARS-CoV-2 varied widely, cycle threshold values Ct 16.28-36.94, among symptoms and asymptomatic individuals. The viral loads for the paired CNTS and non-CNTS specimens were comparable. CONCLUSIONS: This study demonstrated that CNTS could be a specimen of choice for diagnosis of SARS-CoV-2.

Early detection of community acquired of SARS-CoV-2 lineage B.1.351 in Hong Kong.

Background: Prior to this report, variants of concern for SARS-CoV-2 were only detected from imported cases in Hong Kong. Objective: Multiple cases of SARS-CoV-2 lineage B.1.351 have been identified in local community. We reported the phylogenetic relationship of these cases. Study design: SARS-CoV-2 cases were screened for the key non-synonymous substitutions in spike protein by different assays. Preliminary positive cases were further tested by whole genome sequencing. Results: From Dec 2020 to May 2021, 55 SARS-CoV-2 cases belonged to lineage B.1.351. Among them, eight genomes were clustered together, all of them were local cases with epidemiological link. Conclusions: To track variants of SARS-CoV-2 and to allow early implementation of control measures, SARS-CoV-2 genomic surveillance must be consistently performed.

Evaluation of rapid antigen detection kit from the WHO Emergency Use List for detecting SARS-CoV-2.

BACKGROUND: Currently, there are two rapid antigen detection (RAD) kits from the WHO Emergency Use List for detecting SARS-CoV-2. OBJECTIVE: The Panbio COVID-19 Ag Rapid Test Device was selected to evaluate the performance for detecting SARS-CoV-2. STUDY DESIGN: Analytical sensitivity for the detection of SARS-CoV-2 virus was determined by limit of detection (LOD) using RT-PCR as a reference method. Clinical sensitivity was evaluated by using respiratory specimens collected from confirmed COVID-19 patients. RESULTS: The LOD results showed that the RAD kit was 100 fold less sensitive than RT-PCR. Clinical sensitivity of the RAD kit was 68.6 % for detecting specimens from COVID-19 patients. CONCLUSIONS: The RAD kit evaluated in the present study shared similar performance with another kit from the WHO Emergency Use List, the Standard Q COVID-19 Ag. Understanding the clinical characteristics of RAD kits can guide us to decide different testing strategies in different settings.

Evaluation of automated antigen detection test for detection of SARS-CoV-2.

RT-PCR is the gold standard to detect SARS-CoV-2, however, its capacity is limited. We evaluated an automated antigen detection (AAD) test, Elecsys SARS-CoV-2 Antigen (Roche, Germany), for detecting SARS-CoV-2. We compared the limit of detection (LOD) between AAD test, rapid antigen detection (RAD) test; SARS-CoV-2 Rapid Antigen Test (SD Biosensor, Korea), and in-house RT-PCR test. LOD results showed that the AAD test was 100 fold more sensitive than the RAD test, while the sensitivity of the AAD test was comparable to the RT-PCR test. The AAD test detected between 85.7% and 88.6% of RT-PCR-positive specimens collected from COVID-19 patients, false negative results were observed for specimens with Ct values >30. Although clinical sensitivity for the AAD test was not superior or comparable to the RT-PCR test in the present study, the AAD test may be an alternative to RT-PCR test in terms of turn-around time and throughput.

Sero-immunity and serologic response to pandemic influenza A (H1N1) 2009 virus in Hong Kong.

To study the serologic response to the new pandemic influenza A (H1N1) 2009 virus in Hong Kong, the level of immunity was measured before and after the occurrence of the outbreak, and the titer of antibody to the pandemic influenza A (H1N1) 2009 virus in serum samples of laboratory confirmed cases. The presence of pre-outbreak pandemic influenza A (H1N1) 2009 virus antibodies in 37% of individuals older than >65 years suggested previous exposures to heterologous virus strains may have elicited cross-reacting antibody. Following large outbreaks of pandemic influenza A 2009 virus that peaked in September 2009, there is a change in immunity level in various age groups consistent with the attack rates among population in Hong Kong. Among individuals with mild clinical presentation, the antibody response to pandemic influenza A (H1N1) 2009 virus was stronger in those individuals aged ≤ 24 years but took more time to reach a titer of 40 when compared with those aged >24 years; however, the antibody level declined slower among individuals aged ≤ 24 years. Regardless of age, the antibody response rose rapidly and reached much higher titer among individuals with severe clinical presentation. Further study is required to collect additional data on antibody persistence and determine how much protection is conferred by previous exposure to seasonal influenza A (H1N1) viruses.

Epidemiology and genetic diversity of methicillin-resistant Staphylococcus aureus strains in residential care homes for elderly persons in Hong Kong.

OBJECTIVE: To determine the prevalence and molecular epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) strains among residents in residential care homes for the elderly in Hong Kong. DESIGN: Cross-sectional and descriptive study. PARTICIPANTS: A total of 949 residents in 13 residential care homes for elderly persons in Hong Kong in January 2005. METHODS: MRSA colonization was assessed by culture of swab specimens from anterior nares and active skin lesions. Characteristics of residents were obtained by a standard questionnaire. All MRSA isolates were analyzed by polymerase chain reaction for their staphylococcal cassette chromosome (SCC) mec content and were typed by pulsed-field gel electrophoresis (PFGE) and multilocus sequencing. RESULTS: MRSA colonization was detected in 27 residents (2.8%). No MRSA was found in 2 facilities. The rate of MRSA carriage in the other 11 facilities ranged from 1.9% to 4.2%. In univariate analysis, functional immobility (odds ratio [OR], 1.4), history of hospital admission (OR, 2.3), and the use of nebulized medication (OR, 5.4) were significantly associated with MRSA colonization. The isolates had 11 unique antibiograms, with 14 isolates susceptible to all but 1 or 2 of the non- beta -lactam antimicrobial agents tested. The isolates exhibited SCCmec types I (1 isolate), II (2 isolates), III (1 isolate), IV/IVA (10 isolates), and V (13 isolates). No isolates had the Panton-Valentine leukocidin genes. PFGE analysis clustered all except 1 isolate into 7 PFGE types, designated HKU10 to HKU70. Between 1 and 4 unique PFGE types were found in the individual residential care facilities. CONCLUSION: This study documented the emergence of SCCmec types IV and V among genetically diverse MRSA strains in residential care homes for elderly persons in Hong Kong.

Antimicrobial resistance in Escherichia coli outpatient urinary isolates from women: emerging multidrug resistance phenotypes.

This study evaluated the antimicrobial resistance profile of outpatient urinary Escherichia coli isolated from women obtained throughout Hong Kong during 2004-2005. Of 1067 single patient isolates analyzed, 60.1% were resistant to ampicillin, 34% were resistant to co-trimoxazole, and 22.1% were resistant to ciprofloxacin. Thirty-four (6.6%) of 519 isolates in 2004 and 55 (10%) of 548 isolates in 2005 were extended-spectrum beta-lactamase (ESBL) producers with a CTX-M phenotype. Rates of non-beta-lactam resistance and ESBL production were strongly influenced by patient age. The age-stratified rates for dual co-trimoxazole and ciprofloxacin resistance and for ESBL production were 10.9% and 7.6% in women aged 18-35 years, 13% and 6.9% in women aged 36-50 years, 20.4% and 8.8% in women aged 51-64 years, and 23.7% and 11.8% in women aged > or =65 years, respectively. Nitrofurantoin and fosfomycin remain active against >90% of the isolates, irrespective of the resistance phenotypes for other drugs. Our results documented the emergence of problematic resistance phenotypes among community urinary E. coli and highlight the need to explore strategies for their containment.

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.

Escherichia coli producing CTX-M beta-lactamases in food animals in Hong Kong.

A study was conducted to evaluate the occurrence of extended-spectrum beta-lactamases (ESBLs)-producing Escherichia coli from fecal samples of healthy food animals in Hong Kong. Rectal or cloacal swabs were obtained from cattle, pigs, chicken, ducks, geese, and pigeons in slaughterhouses or wholesale markets over a 5- month period in 2002. Antibiotic-containing medium was used for selective isolation of potentially ESBL-producing E. coli. Of 734 samples analyzed, six (2%) from pigs, three (3.1%) from cattle, and one (3%) from pigeons had E. coli strains with the ESBL phenotype. The ESBL content for the 10 isolates include CTXM- 3 (n = 4), CTX-M-13 (n = 3), CTX-M-14 (n = 2), and CTX-M-24 (n = 1). In five isolates, the bla (CTX-M) gene was encoded on transferable plasmids (60 or 90 kb), and the gene was found to transfer to E. coli (J53 or JP995) with frequencies of 10(7) to 10(3) per donor cells. The ten isolates had five distinct pulsotypes with some clonal spread. However, the isolates from the different kinds of animals were not clonally related. These findings imply that bacteria of animal origins may serve as reservoirs of some ESBL genes.