Integrating Magnetic-Bead-Based Sample Extraction and Molecular Barcoding for the One-Step Pooled RT-qPCR Assay of Viral Pathogens without Retesting.

Pooling multiple samples prior to real-time reverse-transcription polymerase chain reaction (RT-PCR) analysis has been proposed as a strategy to minimize expenses and boost test throughput during the COVID-19 pandemic. Nevertheless, the traditional pooling approach cannot be effectively deployed in high-prevalence settings due to the need for secondary tests in the case of a positive pool. In this study, we present a pooling test platform with high adaptability and simplicity that allows sample-specific detection of multiple-tagged samples in a single run without the need for retesting. This was accomplished by labeling distinct samples with predefined ID-Primers and identifying tagged pooled samples using one-step RT-PCR followed by melting curve analysis with rationally designed universal fluorescence- and quencher-tagged oligo probes. Using magnetic beads (MBs), nucleic acid targets from different individuals can be tagged and extracted concurrently and then pooled before RT, eliminating the need for extra RNA extraction and separate RT and enzyme digestion steps in the recently developed barcoding strategies. Pools of six samples (positive and negative) were successfully identified by melting temperature values under two fluorescent channels, with a detection sensitivity of 5 copies/µL. We validated the reproducibility of this assay by running it on 40 clinical samples with a hypothetical infection rate of 15%. In addition, to aid the scenario of large-scale pooling tests, we constructed a melting curve autoreadout system (MCARS) for statistical analysis of melting curve plots to eliminate error-prone manual result readout. Our results suggest that this strategy could be a simple and adaptable tool for alleviating existing bottlenecks in diagnostic pooling testing.

A statistical framework for tracking the time-varying superspreading potential of COVID-19 epidemic.

Timely detection of an evolving event of an infectious disease with superspreading potential is imperative for territory-wide disease control as well as preventing future outbreaks. While the reproduction number (R) is a commonly-adopted metric for disease transmissibility, the transmission heterogeneity quantified by dispersion parameter k, a metric for superspreading potential is seldom tracked. In this study, we developed an estimation framework to track the time-varying risk of superspreading events (SSEs) and demonstrated the method using the three epidemic waves of COVID-19 in Hong Kong. Epidemiological contact tracing data of the confirmed COVID-19 cases from 23 January 2020 to 30 September 2021 were obtained. By applying branching process models, we jointly estimated the time-varying R and k. Individual-based outbreak simulations were conducted to compare the time-varying assessment of the superspreading potential with the typical non-time-varying estimate of k over a period of time. We found that the COVID-19 transmission in Hong Kong exhibited substantial superspreading during the initial phase of the epidemics, with only 1 % (95 % Credible interval [CrI]: 0.6-2 %), 5 % (95 % CrI: 3-7 %) and 10 % (95 % CrI: 8-14 %) of the most infectious cases generated 80 % of all transmission for the first, second and third epidemic waves, respectively. After implementing local public health interventions, R estimates dropped gradually and k estimates increased thereby reducing the risk of SSEs to approaching zero. Outbreak simulations indicated that the non-time-varying estimate of k may overlook the possibility of large outbreaks. Hence, an estimation of the time-varying k as a compliment of R as a monitoring of both disease transmissibility and superspreading potential, particularly when public health interventions were relaxed is crucial for minimizing the risk of future outbreaks.

Mass Screening of SARS-CoV-2 With Rapid Antigen Tests in a Receding Omicron Wave: Population-Based Survey for Epidemiologic Evaluation.

BACKGROUND: The COVID-19 Omicron BA.2 epidemic wave in Hong Kong peaked in the first quarter of 2022. Following the implementation of stringent public health measures, the daily number of reported cases fell from over 50,000 to below 2000. Although outbreaks steadily receded, the government rolled out a 3-day "voluntary universal rapid testing" campaign to invite all citizens to self-perform a rapid antigen test (RAT) daily to identify undetected prevalent infections. OBJECTIVE: This study aimed to evaluate the uptake and results of RAT mass screening to estimate the population's residual epidemic burden and assess the risk of further transmission. METHODS: A cross-sectional study comprising an open web-based population-based survey was conducted a week after the RAT campaign. Participants were asked to report their COVID-19 vaccination and infection history and the RAT performance and test result during the period. They were also invited to report their coliving individuals' test performance and results. Reasons for nonuptake were enquired. Testing and positive rates were age-adjusted. Determinants of undergoing RAT were identified using univariable and multivariable logistic regression models. RESULTS: In total, particulars from 21,769 individuals were reported by 8338 participants. The overall age-adjusted testing rate was 74.94% (95% CI 73.71%-76.18%), with over 80% of participants in the age groups between 45-84 years having self-performed RAT during the campaign period. After age-adjustment, 1.03% (95% CI 0.86%-1.21%) of participants tested positive. The positive rates in the age groups between 20-29 years and >84 years exceeded 2%. Taking into account the positive rate and 5819 reported cases during the period, the cases identified in the campaign might account for 7.65% (95% CI 6.47%-9.14%) of all infections. Testers were more likely to be female, older, not previously diagnosed with COVID-19, and have received COVID-19 vaccination. Adjusting for the number of household members, those living with a child aged <12 years and whose household members were also tested were more likely to have self-performed an RAT. Main reasons for not performing an RAT included the absence of symptoms (598/1108, 53.97%), disbelief of the appropriateness of the campaign as an antiepidemic measure (355/1108, 32.04%), and a recent COVID-19 diagnosis (332/1108, 29.96%). CONCLUSIONS: The residual population burden remained substantial in spite of the clear evidence of a receding epidemic wave. Despite caution in generalization to the Hong Kong population, the high participation rate in mass screening indicated that the voluntary RAT was well accepted, making it a feasible option for implementation as a complementary means of public health surveillance.

Three-Dose Primary Series of Inactivated COVID-19 Vaccine for Persons Living with HIV, Hong Kong.

In a cohort of persons living with HIV in Hong Kong, surrogate virus neutralization testing for COVID-19 yielded a median level of 89% after the third dose of an inactivated COVID-19 vaccine, compared with 37% after the second dose. These results support using a 3-dose primary series for enhanced immune protection.

Trajectory patterns of SARS-CoV-2 neutralising antibody response in convalescent COVID-19 patients.

Background: The adaptive immune responses of COVID-19 patients contributes to virus clearance, restoration of health and protection from re-infection. The patterns of and the associated characteristics with longitudinal neutralising antibody (NAb) response following SARS-CoV-2 infection are important in their potential association with the population risks of re-infection. Methods: This is a longitudinal study with blood samples and clinical data collected in adults aged 18 or above following diagnosis of SARS-CoV-2 infection. NAb levels were measured by the SARS-CoV-2 surrogate virus neutralisation test (sVNT). Anonymous clinical and laboratory data were matched with surveillance data for each subject for enabling analyses and applying latent class mixed models for trajectory delineation. Logistic regression models were performed to compare the characteristics between the identified classes. Results: In 2020-2021, 368 convalescent patients in Hong Kong are tested for NAb. Their seroconversion occur within 3 months in 97% symptomatic patients, the level of which are maintained at 97% after 9 months. The NAb trajectories of 200 symptomatic patients are classified by the initial response and subsequent trend into high-persistent and waning classes in latent class mixed models. High-persistent (15.5%) class patients are older and most have chronic illnesses. Waning class patients (84.5%) are largely young adults who are mildly symptomatic including 2 who serorevert after 10 months. Conclusions: Characteristic sub-class variabilities in clinical pattern are noted especially among patients with waning NAb. The heterogeneity of the NAb trajectory patterns and their clinical association can be important for informing vaccination strategy to prevent re-infection.

Surrogate neutralization responses following severe acute respiratory syndrome coronavirus 2 vaccination in people with HIV: comparison between inactivated and mRNA vaccine.

OBJECTIVE: People with HIV (PWH) co-infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are at higher odds of severe diseases. Whereas the immunogenicity of mRNA vaccine and adenovirus-vectored vaccine was similar between PWH in stable condition and healthy adults, the effects of inactivated vaccines are not known. DESIGN: Prospective longitudinal observational study in real-world setting. METHODS: Adult PWH in care and planning to receive either inactivated (day 0 and day 28) or mRNA-based (day 0 and day 21) vaccine against SARS-CoV-2 were recruited, with blood samples collected over 6 months for surrogate virus neutralization test (sVNT). Demographic and clinical data including age, sex, CD4 + cell count, and suppressed viral load (SVL) status were transcribed for analyses, by simple and multivariable linear regression models, and multivariable linear generalized estimating equations (GEE). RESULTS: A total of 611 HIV patients, 91% male patients, were recruited, of whom 423 and 184 have received mRNA-based and inactivated vaccine, respectively. The seroconversion rate was 99% for mRNA-based vs, 86% for inactivated vaccine [odds ratio (OR) = 21.56, P  = 0.004]. At 6 months, mRNA-based vaccine continued to give a higher response (94 vs. 57%, P  < 0.001). The temporal pattern varied between the two vaccines. By GEE, mRNA-based vaccine ( B  = 40.59, P  < 0.001) and latest SVL status ( B  = 10.76, P  = 0.01) were positively associated with sVNT level, but not latest CD4 + cell count. CONCLUSION: In HIV patients, inactivated vaccine gave a lower peak and shorter duration of sVNT responses compared with mRNA vaccine. The results suggested that different strategies may be needed in boosting the immunity in anticipation of the emergence of variants in the community.

User Experience and Usability of Neumorphism and Gamification User Interface Designs in an HIV Self-Test Referral Program for Men Who Have Sex With Men: Prospective Open-Label Parallel-Group Randomized Controlled Trial.

BACKGROUND: Digital interventions have been applied for promoting HIV prevention and care among men who have sex with men (MSM). As user interface (UI) design plays a role in determining usability and user experience (UX), the intervention outcome could be affected. OBJECTIVE: In this study, we hypothesized that 2 UI design styles, namely gamification and neumorphism, could impact usability and be differentially preferred by distinct groups of MSM. METHODS: A prospective parallel-group open-label randomized controlled trial was conducted in Hong Kong. Eligible participants were adult MSM recruited by the research team or referred by enrolled participants, who followed instructions for performing an HIV self-test and promoted its use within their social network. Participants were randomized in a 1:1 ratio into either a gamification or neumorphism arm, with primarily visual differences in the UI only. The primary outcome was usability measured by the System Usability Scale (SUS) between the 2 arms. Distinct characteristics of promoters in the 2 arms who gave an SUS score of 80 or above were identified. RESULTS: Of 463 MSM registered in the study, 232 and 231 were randomized to the gamification and neumorphism arms, respectively. Excluding those who did not request a self-test kit, data from 218 and 216 participants in the gamification and neumorphism arms, respectively, were analyzed (totally 434 participants). With a median SUS score of 80 overall, participants in the neumorphism arm gave a higher score (P<.001), with a higher proportion giving a promoter-level SUS score (P=.002). Promoters used social media for sex networking (P=.02), used pre-exposure prophylaxis in the preceding year (P=.006), had higher satisfaction in UI design (P<.001), and had made a self-test referral (P=.04). In general, higher usability was recorded among participants who were confident in performing the HIV self-test (P<.001), and this was associated with a promoter-level SUS score in both arms. While no other personal characteristics were associated with promoters in the neumorphism arm, those in the gamification arm had higher HIV-related knowledge (P=.01), preferred a specific partner body image type (P=.03), and progressed toward peer referral by completing online training (P=.04). CONCLUSIONS: Both gamified and neumorphic UI designs were well-accepted by MSM. UX and satisfaction of UI were both crucial in influencing the willingness of MSM to promote the application by referring their peers in the community to participate. The simplistic visual design of neumorphism conferred a more general acceptance in the community, whereas gamification was preferred in certain MSM subcommunities. Appropriate UI/UX design should be considered when developing digital interventions targeting the MSM community. TRIAL REGISTRATION: ClinicalTrials.gov NCT04379206; https://clinicaltrials.gov/ct2/show/NCT04379206.

The double-edged impacts of COVID-19 epidemic on influenza vaccination uptake in nurses in Hong Kong.

BACKGROUND: Worldwide, the COVID-19 pandemic has disrupted influenza seasonality and impacted influenza vaccination behaviours. This study examines the patterns of influenza vaccination uptake in nurses during the pre-pandemic seasons and amidst the pandemic in 2020/21 in subtropical Hong Kong. METHODS: In April 2021, a cross-sectional survey was conducted in practising and student nurses. Six patterns were differentiated by their influenza vaccination status in 2020/21 and preceding five seasons: (a) resistance throughout, (b) negative change, (c) decreased tendency, (d) increased tendency (e) positive change, and (f) adherence throughout. Participants' characteristics and reasons for vaccination/non-vaccination and their associations with each vaccination pattern were explored using multivariable multinomial regression. RESULTS: Among 1323 nurses (88% female with a median age of 39 years), no substantial change in vaccination uptake was noted from 2019/20 (41%) to 2020/21 (42%). Some 4% were positive-changers who were older at age of ≥50 years (aOR 4.77) and more likely to anticipate a reduced risk of severe disease with COVID-19/influenza co-infection following vaccination (aOR 8.76). Negative-changers made up 3% and were more inclined to perceive an unlikelihood of widespread influenza outbreaks amidst the pandemic (aOR 3.67). Some 26 and 43% remained adherent and resistant to influenza vaccination throughout respectively notwithstanding the COVID-19 outbreak. CONCLUSIONS: In contrast to the increased uptake elsewhere, the stable influenza vaccination coverage among nurses in Hong Kong could be explained by the ubiquity of strict physical distancing regulations, which have deterred vaccination in some nurses that offsets the new uptakes induced by the mild COVID-19 outbreaks.

Effectiveness of containment strategies in preventing SARS-CoV-2 transmission.

BACKGROUND: Despite substantial resources deployed to curb SARS-CoV-2 transmission, controlling the COVID-19 pandemic has been a major challenge. New variants of the virus are frequently emerging leading to new waves of infection and re-introduction of control measures. In this study, we assessed the effectiveness of containment strategies implemented in the early phase of the pandemic. METHODS: Real-world data for COVID-19 cases was retrieved for the period Jan 1 to May 1, 2020 from a number of different sources, including PubMed, MEDLINE, Facebook, Epidemic Forecasting and Google Mobility Reports. We analyzed data for 18 countries/regions that deployed containment strategies such as travel restrictions, lockdowns, stay-at-home requests, school/public events closure, social distancing, and exposure history information management (digital contact tracing, DCT). Primary outcome measure was the change in the number of new cases over 30 days before and after deployment of a control measure. We also compared the effectiveness of centralized versus decentralized DCT. Time series data for COVID-19 were analyzed using Mann-Kendall (M-K) trend tests to investigate the impact of these measures on changes in the number of new cases. The rate of change in the number of new cases was compared using M-K z-values and Sen's slope. RESULTS: In spite of the widespread implementation of conventional strategies such as lockdowns, travel restrictions, social distancing, school closures, and stay-at-home requests, analysis revealed that these measures could not prevent the spread of the virus. However, countries which adopted DCT with centralized data storage were more likely to contain the spread. CONCLUSIONS: Centralized DCT was more effective in containing the spread of COVID-19. Early implementation of centralized DCT should be considered in future outbreaks. However, challenges such as public acceptance, data security and privacy concerns will need to be addressed.

Shifts of SARS-CoV-2 exposure settings in the transmission clusters of 2 epidemic waves in Hong Kong.

Exposure setting is crucial in the formation and propagation of SARS-CoV-2 transmission clusters. In this cohort study, transmission networks of 2 waves were differentiated by exposure setting using territory-wide surveillance data with clinical and laboratory records in Hong Kong. Characteristically, the first wave had resulted from imported cases followed by local transmissions, while the second wave was constituted primarily by local infections. With a 4-fold higher caseload, the second wave featured predominance of epidemiologically linked, local, older and asymptomatic patients with higher viral loads and shorter inpatient days. The 1028 transmission clusters formed 155 cascades composing at least two clusters. Daily and social activities were exposure settings that bridged clusters while residences usually terminated transmission cascades. Regulatory restrictions on social activities extinguished cluster formation in bars, but shifted to private parties in the second wave. The results confirmed that strategic interventions targeting exposure settings could achieve effective epidemic control.

Effect of prior outbreak work experience to future outbreak responses for nurses in Hong Kong: A cross-sectional study.

Background: During the early phase of the Coronavirus Disease 2019 (COVID-19) epidemic, health care workers had elevated levels of psychological distress. Historical exposure to disease outbreak may shape different pandemic responses among experienced health care workers. Aim: Considering the unique experience of the 2003 SARS outbreak in Hong Kong, this study examined the association between prior epidemic work experience and anxiety levels, and the mediating role of perceived severity of COVID-19 and SARS in nurses. Methods: In March 2020, a cross-sectional survey targeting practising nurses in Hong Kong was conducted during the early phase of the COVID-19 epidemic. The interrelationships among participants' work experience during the SARS outbreak, perceived severity of SARS and COVID-19, and anxiety level were elucidated using structural equation model (SEM). Findings: Of 1,061 eligible nurses, a majority were female (90%) with a median age of 39 years (IQR = 32-49). A significant and negative indirect association was identified between SARS experience and anxiety levels (B=-0.04, p=0.04) in the SEM with a satisfactory fitness (CFI=0.95; RMSEA=0.06). SARS-experienced nurses perceived SARS to be less severe (B=-0.17, p=0.01), translated an equivalent perception to COVID-19 (B=1.29, p<0.001) and resulted in a lower level of anxiety (B=0.19, p<0.001). Conclusions: The less vigorous perception towards the severity of SARS and COVID-19 may explain SARS-experienced nurses' less initial epidemic-induced anxiety. The possible role of outbreak-experienced nurses in supporting outbreak-inexperienced nurses, both emotionally and technically, should be considered when an epidemic commences. Interventions aiming to facilitate the understanding of emerging virus should also be in place.

Impact of pre-event testing and quarantine on reducing the risk of COVID-19 epidemic rebound: a modelling study.

BACKGROUND: With the evolving growth of the COVID-19 epidemic, travel restriction policies would need to be adjusted accordingly. Prohibition of mass event may be relaxed for social and economic benefits when virus transmission stops but could bear the risk of epidemic rebound. Against the background of the varied SARS-CoV-2 prevalence internationally, we modelled the potential impacts of pre-event interventions on epidemic risk of holding a mass event when COVID-19 is under control. METHODS: We developed a mathematical model of SARS-CoV-2 transmission in Guangdong Province, China, where local virus transmission ceased to occur. A large-scale international trade fair was assumed to be held, with influx of people from overseas and rest of China over a short period of time, who participated for 2-week. Scenarios of pre-event intervention (none, quarantine arrangement and polymerase chain reaction (PCR) testing for participants) were compared. The influence of contact pattern, SARS-CoV-2 prevalence outside the province and China, and testing coverage were examined in sensitivity analyses. RESULTS: In basecase scenario (no event), the epidemic has been under control since March 2020. The event would lead to the detection of 1% more confirmed cases by 31 July when community contact rate increases to pre-epidemic level. In event scenario without additional interventions, there would be 599 (93%) more new infections comparing with basecase scenario. To avert new infections, quarantining all participants before the event would be the most effective strategy, followed by quarantining all overseas participants and testing all other participants, and testing all participants before the event and on day 7. However, testing strategy is likely to be affected by the SARS-CoV-2 prevalence outside the event province. CONCLUSIONS: Pre-event interventions are effective for reducing the risk of epidemic rebound caused by an international large-scale event. Universal testing for participants is likely to be an effective and feasible intervention.