Benjamin J Cowling

The University of Hong Kong | HKU · School of Public Health

Forecasting of influenza activity in tropical and subtropical regions such as Hong Kong is challenging due to irregular seasonality with high variability in the onset of influenza epidemics, and potential summer activity. To overcome this challenge, we develop a diverse set of statistical, machine learning and deep learning approaches to forecast i...

Since the emergence of SARS-CoV-2, different variants and subvariants successively emerged to dominate global virus circulation as a result of immune evasion, replication fitness or both. COVID-19 vaccines continue to be updated in response to the emergence of antigenically divergent viruses, the first being the bivalent RNA vaccines that encodes f...

From 2020 to December 2022, China implemented strict measures to contain the spread of severe acute respiratory syndrome coronavirus 2. However, despite these efforts, sustained outbreaks of the Omicron variants occurred in 2022. We extracted COVID-19 case numbers from May 2021 to October 2022 to identify outbreaks of the Delta and Omicron variants...

Background We assessed the performance of three different multiplex lateral flow assays which provide results for influenza, respiratory syncytial virus (RSV) and SARS-CoV-2. Methods Ambulatory patients 6 months and older presenting with two or more symptoms or signs of an acute respiratory illness were enrolled in an outpatient clinic in Hong Kon...

Influenza A virus (IAV) infection establishes a more diverse immunological memory to different viral proteins compared to vaccination. We hypothesized that the relative abundance of pre-existing immune memory to different viral antigens could skew post-infection antibody responses. To explore this, we generated mouse models with either an IAV hemag...

Background: The hemagglutination inhibition antibody (HAI) titer mediates only a part of vaccine-induced protection against influenza virus infections. Using causal mediation analysis, we quantified the proportion of vaccine efficacy mediated by post-vaccination HAI titers. Methods: Causal mediation analyses were conducted using data collected f...

Since the emergence of SARS-CoV-2, different variants and subvariants successively emerged to dominate global virus circulation as a result of immune evasion, replication fitness or both. COVID-19 vaccines continue to be updated in response to the emergence of antigenically divergent viruses, the first being the bivalent RNA vaccines that encodes f...

Seroprevalence studies assessing community exposure to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Ghana concluded that population-level immunity remained low as of February 2021. Thus, it is important to demonstrate how increasing vaccine coverage reduces the economic and public health impacts associated with SARS-CoV-2 transmi...

Background Waning of COVID-19 vaccine efficacy/effectiveness (VE) has been observed across settings and epidemiological contexts. We conducted a systematic review of COVID-19 VE studies and performed a meta-regression analysis to improve understanding of determinants of waning. Methods Systematic review of PubMed, medRxiv and the WHO-International...

Seasonal influenza vaccine (SIV) significantly reduces influenza-related illnesses among school-aged children, yet parental vaccine hesitancy remains a persistent challenge. Two types of SIV are available for children in Hong Kong and other locations: inactivated influenza vaccine (IIV), administered through intramuscular injection, and live attenu...

To support the ongoing management of viral respiratory diseases while transitioning out of the acute phase of the COVID-19 pandemic, many countries are moving toward an integrated model of surveillance for SARS-CoV-2, influenza virus, and other respiratory pathogens. Although many surveillance approaches catalyzed by the COVID-19 pandemic provide n...

We evaluated the population-level benefits of expanding treatment with the antiviral drug Paxlovid (nirmatrelvir/ritonavir) in the United States for SARS-CoV-2 Omicron variant infections. Using a multiscale mathematical model, we found that treating 20% of symptomatic case-patients with Paxlovid over a period of 300 days beginning in January 2022 r...

Background Seasonal influenza resurged in China in February 2023, causing a large number of hospitalizations. While influenza epidemics occurred across China during the coronavirus disease 2019 (COVID-19) pandemic, the relaxation of COVID-19 containment measures in December 2022 may have contributed to the spread of acute respiratory infections in...

Background: The COVID-19 pandemic caused over 6.94 million deaths and significant social and economic hardship as of 7 June 2023. An antiviral drug, Paxlovid, was authorized for emergency use in the US in December 2021 following clinical trials indicating its safety and efficacy in rapidly reducing viral load. However, the potential public health i...

Background Recognising the importance of attaining high vaccine coverage to mitigate the COVID-19 impact, a Vaccine Pass scheme was implemented during and after the first large Omicron wave in Hong Kong in early 2022 requiring three doses by June 2022. We evaluated the impact of the Vaccine Pass policy on vaccine uptake in adults. Methods We analy...

We compared the effectiveness and interactions of molnupiravir and nirmatrelvir/ritonavir and 2 vaccines, CoronaVac and Comirnaty, in a large population of inpatients with COVID-19 in Hong Kong. Both the oral antiviral drugs and vaccines were associated with lower risks for all-cause mortality and progression to serious/critical/fatal conditions (s...

Background Despite the early demonstrated safety and effectiveness of COVID-19 vaccines in children, uptake was slow throughout the pandemic and remains low globally. Understanding vaccine refusal could provide insights to improving vaccine uptake in future pandemics. Methods In a population-wide registry of all COVID-19 paediatric vaccination app...

Background Hong Kong contained COVID-19 for two years but experienced a large epidemic of Omicron BA.2 in early 2022 and endemic transmission of Omicron subvariants thereafter. We reflected on pandemic preparedness and responses by assessing COVID-19 transmission and associated disease burden in the context of implementation of various public healt...

Background Annual influenza vaccination is recommended for older adults but repeated vaccination with standard-dose influenza vaccine has been linked to reduced immunogenicity and effectiveness, especially against A(H3N2) viruses. Methods Community-dwelling Hong Kong adults aged 65-82 years were randomly allocated to receive 2017/18 standard-dose...

To date there is a lack of randomized trial data examining the use of the antiviral nirmatrelvir/ritonavir in SARS-CoV-2-infected pregnant persons. This target trial emulation study aims to address this gap by evaluating the use of nirmatrelvir/ritonavir in non-hospitalized pregnant women with symptomatic SARS-CoV-2 Omicron variant infection. Among...

Soon after a mask mandate was relaxed (March 1, 2023), the first post-COVID-19 influenza season in Hong Kong lasted 12 weeks. After other preventive measures were accounted for, mask wearing was associated with an estimated 25% reduction in influenza transmission. Influenza resurgence probably resulted from relaxation of mask mandates and other mea...

Importance Hong Kong was held as an exemplar for pandemic response until it recorded the world’s highest daily COVID-19 mortality, which was likely due to vaccine refusal. To prevent this high mortality in future pandemics, information on underlying reasons for vaccine refusal is necessary. Objectives To track the evolution of COVID-19 vaccination...

In March-June 2023 we conducted a test negative study in 1671 children who were hospitalized with acute respiratory illness in Hong Kong. 286 (17.2%) tested positive for influenza virus including 188 with A(H1N1). We estimated influenza vaccine effectiveness against influenza-associated hospitalization as 69.6% (95% confidence interval: 49.3%, 81.7...

The time-varying effective reproduction number (Rt at time t) measures the transmissibility of SARS-CoV-2 and is conventionally based on daily case counts which may suffer from time-varying ascertainment. We analyzed Rt estimates from case counts, and severe COVID-19 (ICU admissions, severe or critical cases, and mortality) across 2022 in Hong Kong...

We introduce the angular reproduction number Ω, which measures time-varying changes in epidemic transmissibility resulting from variations in both the effective reproduction number R, and generation time distribution w. Predominant approaches for tracking pathogen spread infer either R or the epidemic growth rate r. However, R is biased by mismatch...

Promoting high vaccine uptake is a primary public health policy in mitigating the profound impact of COVID-19 pandemic. The evolution of the COVID-19 pandemic requires a dynamic evaluation of factors that are associated with COVID-19 vaccination uptake to inform a strategic plan on vaccination programmes. Using real-time population-based data that...

Background: Assessment of viral kinetics of SARS-CoV-2 can inform on host immune responses to the virus and on the viral transmission potential. We aimed to characterise viral shedding kinetics by age, virus type, and clinical outcome, and to examine the potential effect of vaccination on viral shedding. Methods: In this retrospective observatio...

In this cohort study conducted in Hong Kong where both bivalent and monovalent formulations of BNT162b2 were available, there was no significant differences in the mortality or hospitalization between those who received bivalent and monovalent mRNA as second boosters. Bivalent and monovalent mRNA boosters appear equally protective against clinical...

As the pandemic's dynamics changed, many municipalities lifted face wearing requirement in school which was initially implemented to mitigate the transmission of COVID-19. This study examines the effects of lifting mask mandates on COVID-19 transmission within Massachusetts school districts. We first replicated previous research by Cowger et al. (2...

Social distancing measures (SDMs) are community-level interventions that aim to reduce person-to-person contacts in the community. SDMs were a major part of the responses first to contain, then to mitigate, the spread of SARS-CoV-2 in the community. Common SDMs included limiting the size of gatherings, closing schools and/or workplaces, implementin...

We administered BNT162b2 as a third dose to 314 adults ≥30 years of age who had previously received 2 doses of inactivated vaccine. We collected blood samples before the third dose and again after 1, 6 and 12 months, and found stable levels of antibody responses to the ancestral strain and Omicron BA.2 at 6-12 months after receipt of the BNT162b2 t...

Test negative studies have been used extensively for the estimation of COVID-19 vaccine effectiveness (VE). Such studies are able to estimate VE against medically-attended illness under certain assumptions. Selection bias may be present if the probability of participation is associated with vaccination or COVID-19, but this can be mitigated through...

China announced a slight easing of its zero-COVID rules on November 11, 2022, and then a major relaxation on December 7, 2022. We estimate that the ensuing wave of SARS-CoV-2 infections caused 1.41 million deaths in China during December 2022-February 2023, substantially higher than that reported through official channels.

There has long been controversy over the potential for asymptomatic cases of the influenza virus to have the capacity for onward transmission, but recognition of asymptomatic transmission of COVID-19 stimulates further research into this topic. Here, we develop a Bayesian methodology to analyze detailed data from a large cohort of 727 households an...

As influenza A virus (IAV) infection establishes a more diverse immunological memory to different viral proteins compared to vaccination, we hypothesize that this could skew antibody responses to immunizing antigens after infection. To explore this, we generated mouse models that possess either an IAV hemagglutinin (HA)- or neuraminidase (NA)-biase...

Background: Few trials have compared homologous and heterologous third doses of COVID-19 vaccination with inactivated vaccines and mRNA vaccines. The aim of this study was to assess immune responses, safety, and efficacy against SARS-CoV-2 infection following homologous or heterologous third-dose COVID-19 vaccination with either one dose of Corona...

Background: High COVID-19 vaccination uptake rates across all age groups are important for achieving herd immunity. However, age disparity in vaccination acceptance was consistently identified. Objective: Taking cues from tenets of socioemotional selectivity theory, this study examined how the contextual and psychosocial factors contributed to a...

We show that school closures reduced COVID-19 incidence rates in children by 31%-46% in Hong Kong in 2022. After school reopening accompanied by mask mandates, daily rapid testing, and vaccination requirements, school-reported cases correlated with community incidence rates. Safe school reopening is possible when appropriate preventive measures are...

COVID-19 measures influenced respiratory virus epidemiology in Hong Kong. Rhinoviruses/enteroviruses became dominant as measures eased, with HRV genotypes A and C persisting in children. A resurgence of HRV A cases occurred during relaxation of measures, while strict measures reduced virus circulation but increased overall diversity. HRV genotypes...

Background: Elevations in alanine aminotransferase (ALT) and aspartate aminotransferase (AST) were reported as adverse events of nirmatrelvir/ritonavir users in the EPIC-HR trial. Aim: To quantify the risk and severity of acute liver injury (ALI) associated with nirmatrelvir/ritonavir use. Methods: This self-controlled case-series study was co...

Background: Understanding severity of infections with SARS-CoV-2 and its variants is crucial to inform public health measures. Here we used COVID-19 patient data from Hong Kong to characterise the severity profile of COVID-19. Methods: Time-varying and age-specific effective severity measured by case-hospitalization risk and hospitalization-fata...

Background: Hong Kong contained COVID-19 for two years, but experienced a large epidemic of Omicron BA.2 in early 2022 and endemic transmission of Omicron subvariants thereafter. Methods: We examined the use and impact of pandemic controls in Hong Kong by analysing data on more than 1.7 million confirmed COVID-19 cases and characterizing non-pharma...

Background: Hong Kong experienced four epidemic waves caused by the ancestral strain of SARS-CoV-2 in 2020-2021 and a large Omicron wave in 2022. Few studies have assessed antibacterial drug prescribing for COVID-19 inpatients throughout the pandemic. Objectives: To describe inpatient antibacterial drug prescribing for COVID-19 patients throughout...

The antiviral drug Paxlovid has been shown to rapidly reduce viral load. Coupled with vaccination, timely administration of safe and effective antivirals could provide a path towards managing COVID-19 without restrictive non-pharmaceutical measures. Here, we estimate the population-level impacts of expanding treatment with Paxlovid in the US using...

To support the ongoing management of viral respiratory diseases, many countries are moving towards an integrated model of surveillance for SARS-CoV-2, influenza, and other respiratory pathogens. While many surveillance approaches catalysed by the COVID-19 pandemic provide novel epidemiological insight, continuing them as implemented during the pand...

Background: Understanding factors associated with SARS-CoV-2 exposure risk in the hospital setting may help improve infection control measures for prevention. Aim: To monitor SARS-CoV-2 exposure risk among healthcare workers and to identify risk factors associated with SARS-CoV-2 detection. Methods: Surface and air samples were collected longi...

Background: People with substance use disorder have a high risk of SARS-CoV-2 infection and subsequent poor outcomes. Few studies have evaluated COVID-19 vaccine effectiveness among people with substance use disorder. We aimed to estimate the vaccine effectiveness of BNT162b2 (Fosun-BioNTech) and CoronaVac (Sinovac) against SARS-CoV-2 omicron (B.1...

Importance: Diabetes and COVID-19 are both global pandemics, and type 2 diabetes is a common comorbidity in patients with acute COVID-19 and is proven to be a key determinant of COVID-19 prognosis. Molnupiravir and nirmatrelvir-ritonavir are oral antiviral medications recently approved for nonhospitalized patients with mild to moderate COVID-19, f...

Hong Kong experienced a surge of Omicron BA.2 infections in early 2022, resulting in one of the highest per-capita death rates of COVID-19. The outbreak occurred in a dense population with low immunity towards natural SARS-CoV-2 infection, high vaccine hesitancy in vulnerable populations, comprehensive disease surveillance and the capacity for stri...

We described the frequency of residential case clusters and the efficiency of compulsory testing in identifying cases using buildings targeted in compulsory testing and locally infected COVID-19 cases matched by residence in Hong Kong. Most of the buildings (4246/7688, 55.2%) with COVID-19 cases identified had only one reported case and 13% of the...

Background: School-located influenza vaccination programme (SIVP) can effectively promote childhood seasonal influenza vaccination (SIV). However, the longitudinal effects of continuation and discontinuation of the SIVP on parents' vaccine hesitancy remained unknown. Methods: A two-wave longitudinal study recruited adult parents who had at least...

Test negative studies have been used extensively for the estimation of COVID-19 vaccine effectiveness (VE). Such studies are able to estimate VE against medically-attended illness under certain assumptions. Selection bias may be present if the probability of participation is associated with vaccination or COVID-19, but this can be mitigated through...

Purpose of review: Initial response strategies to the COVID-19 pandemic were heavily reliant on nonpharmaceutical interventions (NPIs), a set of measures implemented to slow or even stop the spread of infection. Here, we reviewed key measures used during the COVID-19 pandemic. Recent findings: Some NPIs were successful in reducing the transmissi...

The two nearby Amazonian cities of Iquitos and Manaus endured explosive COVID-19 epidemics and may well have suffered the world's highest infection and death rates over 2020, the first year of the pandemic. State-of-the-art epidemiological and modeling studies estimated that the populations of both cities came close to attaining herd immunity (>70%...

Background: Understanding severity of infections with SARS-CoV-2 and its variants is crucial to inform public health measures. Here we used COVID-19 patient data from Hong Kong to characterise the severity profile of COVID-19 and to examine factors associated with fatality of infection. Methods: Time-varying and age-specific effective severity meas...

Background: Coronavirus disease 2019 (COVID-19) continues to be a major global public health crisis that exacts significant human and economic costs. Booster vaccination of individuals can improve waning immunity and reduce the impact of community epidemics. Methods: Using an epidemiological model that incorporates population-level severe acute...

The COVID-19 pandemic has highlighted important considerations for modeling future pandemics.

Background: Viral rebound after nirmatrelvir-ritonavir treatment has implications for the clinical management and isolation of patients with COVID-19. We evaluated an unselected, population-wide cohort to identify the incidence of viral burden rebound and associated risk factors and clinical outcomes. Methods: We did a retrospective cohort study...

In randomized controlled trials of influenza vaccination, 550 children received trivalent-inactivated influenza vaccine, permitting us to explore relationship between vaccine response and host single nucleotide polymorphisms (SNPs) in 23 candidate genes with adjustment of multiple testing. For host SNPs in TLR7–1817G/T (rs5741880), genotype GT was...

What is already known about this topic? People are likely to engage in collective behaviors online during extreme events, such as the coronavirus disease 2019 (COVID-19) crisis, to express awareness, take action, and work through concerns. What is added by this report? This study offers a framework for evaluating interactions among individuals’ em...

A SARS-CoV-2 Omicron BA.5 outbreak occurred in Macau from mid-June through July 2022. Out of >1,800 laboratory-confirmed cases, most were mild or asymptomatic; only 6 deaths were recorded. The outbreak was controlled through stringent public health and social measures, such as repeated universal testing and a stay-at-home order lasting 2 weeks.

Influenza imprinting reduces risks of influenza A virus clinical infection by 40-90% estimated from surveillance data in western countries. We analyzed surveillance data from 2010-2019 in Hong Kong. Based on the best model included HA group-level imprinting, we estimated that individuals imprinted to H1N1 or H2N2 had a 17% (95% CI: 3%, 28%) lower r...

Background: Influenza causes considerable disease burden each year, particularly in children. Monitoring school absenteeism has long been proposed as a surveillance tool of influenza activity in the community, but the practice of school absenteeism could be varying, and the potential of such usage remains unclear. Objective: The aim of this pape...

Background On-arrival quarantine has been one of the primary measures to prevent the introduction of SARS-CoV-2 into Hong Kong since the start of the pandemic. Most on-arrival quarantines have been done in hotels, with the duration of quarantine and testing frequency during quarantine modified over time along with other pandemic control measures. H...

Background Hong Kong followed a strict COVID-19 elimination strategy in 2020. We estimated the impact of the COVID-19 pandemic responses on all-cause and cause-specific hospitalizations and deaths in 2020. Methods Interrupted time-series analysis using negative binomial regression accounting for seasonality and long-term trend was used on weekly 2...

Background Accurate estimation of household secondary attack rate (SAR) is crucial to understand the transmissibility of SARS-CoV-2. The impact of population-level factors, such as transmission intensity in the community on SAR estimates are however rarely explored. Methods In this study, we included articles with original data to compute the hous...