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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 coronavirus disease 2019 (COVID-19) cases matched by residence in Hong Kong. Most of the buildings (4246 of 7688, 55.2%) with COVID-19 cases identified had only 1 reported case, and 13% of the daily reported cases were detected through compulsory testing. Compulsory testing notices could be essential in attempting to eliminate infections (“zero COVID”) and have an impact early in an epidemic, but they appear to be relatively inefficient in response to sustained community transmission.

Objectives: Rhinoviruses (RV) represent the most common aetiological agent of all acute respiratory tract infections across all age groups and a significant burden of disease among children. Recent studies have shown that RV-A and RV-C species are associated with increased disease severity. In order to better understand the potential associations between RV species and clinical features among paediatric cases, this study aimed to integrate genetic and epidemiological data using Bayesian phylogenetic methods. Methods: Potential associations between RV species and subtypes, and clinical disease severity using a matched dataset of 52 RV isolates sampled from children (< 18 years) in Sydney, Australia, between 2006 and 2009 were uncovered using epidemiological and phylogenetic methods. Results: It was found that RV-C was significantly more likely to be isolated from paediatric cases aged < 2 years compared with RV-A, although no significant differences in recorded symptoms were observed. Significant phylogenetic-trait associations between age and the VP4/VP2 capsid protein phylogeny suggest that age-specific variations in infectivity among subtypes may may be possible. Conclusion: This study adds to the growing body of epidemiological evidence concerning RV. Improving surveillance and testing for RV, including routine whole genome sequencing, may improve understanding of the varied disease outcomes of RV species and subtypes. Future studies could aim to identify specific genetic markers associated with age-specific infectivity of RV, which could inform treatment practices and public health surveillance of RV.

Summary Objectives mask-wearing outside the home has been almost universal in Hong Kong since late January 2020 with very high compliance. Nevertheless, community spread of COVID-19 has still occurred. We aimed to assess the settings where COVID-19 transmission occurred and determine the fraction of transmission events that occurred in settings where masks are not usually worn. Methods we reviewed detailed information provided by the Hong Kong Department of Health on local COVID-19 cases diagnosed up to 30 September 2020 to determine the most likely settings in which transmission occurred. We classified them in probably mask-on or mask-of and compared the prevalence of asymptomatic infections in these settings. Results among the 2425 cases (65.3%, 2425/3711) with information on transmission setting, 77.6% of the transmission occurred in household and social settings where face masks are not usually worn. Infections that occurred in mask-on settings were more likely to be asymptomatic (adjusted odds ratio 1.33; 95% confidence interval: 1.04, 1.68). Conclusions we conclude that universal mask-wearing can reduce transmission, but transmission can continue to occur in settings where face masks are not usually worn. The higher proportion of asymptomatic cases in mask-on settings could be related to a milder disease presentation or earlier case detection.

Background Testing of an entire community has been used as an approach to control coronavirus disease 2019 (COVID-19). In Hong Kong, a universal community testing program (UCTP) was implemented at the fadeout phase of a community epidemic in July to September 2020. We described the utility of the UCTP in finding unrecognized infections and analyzed data from the UCTP and other sources to characterize transmission dynamics. Methods We described the characteristics of people participating in the UCTP and compared the clinical and epidemiological characteristics of COVID-19 cases detected by the UCTP versus those detected by clinical diagnosis and public health surveillance (CDPHS). We developed a Bayesian model to estimate the age-specific incidence of infection and the proportion of cases detected by CDPHS. Results In total, 1.77 million people, 24% of the Hong Kong population, participated in the UCTP from 1 to 14 September 2020. The UCTP identified 32 new infections (1.8 per 100000 samples tested), consisting of 29% of all local cases reported during the two-week UCTP period. Compared with the CDPHS, the UCTP detected a higher proportion of sporadic cases (62% vs 27%, P Conclusions We reported empirical evidence of the utility of population-wide COVID-19 testing in detecting unrecognized infections and clusters. Around three quarters of infections have not been identified through existing surveillance approaches including contact tracing.

Background In December 2019, we ran Pacific Eclipse, a pandemic tabletop exercise using smallpox originating in Fiji as a case study. Pacific Eclipse brought together international stakeholders from health, defence, law enforcement, emergency management and a range of other organisations. Aim To review potential gaps in preparedness and identify modifiable factors which could prevent a pandemic or mitigate the impact of a pandemic. Methods Pacific Eclipse was held on December 9–10 in Washington DC, Phoenix and Honolulu simultaneously. The scenario began in Fiji and becomes a pandemic. Mathematical modelling of smallpox transmission was used to simulate the epidemic under different conditions and to test the effect of interventions. Live polling, using Poll Everywhere software that participants downloaded onto their smart phones, was used to gather participant decisions as the scenario unfolded. Stakeholders from state and federal government and non-government organisations from The United States, The United Kingdom, Australia, New Zealand, Canada, as well as industry and non-government organisations attended. Results The scenario progressed in three phases and participants were able to make decisions during each phase using live polling. The polling showed very diverse and sometimes conflicting decision making. Factors influential to pandemic severity were identified and categorised as modifiable or unmodifiable. A series of recommendations were made on the modifiable determinants of pandemic severity and how these can be incorporated into pandemic planning. These included preventing an attack through intelligence, law enforcement and legislation, improved speed of diagnosis, speed and completeness of case finding and case isolation, speed and security of vaccination response (including stockpiling), speed and completeness of contact tracing, protecting critical infrastructure and business continuity, non-pharmaceutical interventions (social distancing, PPE, border control) and protecting first responders. Discussion Pacific Eclipse illustrated the impact of a pandemic of smallpox under different response scenarios, which were validated to some extent by the COVID-19 pandemic. The framework developed from the scenario draws out modifiable determinants of pandemic severity which can inform pandemic planning for the ongoing COVID-19 pandemic and for future pandemics.

Background Disparities were marked in previous pandemics, usually with higher attack rates reported for those in lower socioeconomic positions and for ethnic minorities. Methods We examined characteristics of laboratory-confirmed coronavirus disease 2019 (COVID-19) cases in Hong Kong, assessed associations between incidence and population-level characteristics at the level of small geographic areas, and evaluated relations between socioeconomics and work-from-home (WFH) arrangements. Results The largest source of COVID-19 importations switched from students studying overseas in the second wave to foreign domestic helpers in the third. The local cases were mostly individuals not in formal employment (retirees and homemakers) and production workers who were unable to WFH. For every 10% increase in the proportion of population employed as executives or professionals in a given geographic region, there was an 84% (95% confidence interval [CI], 1–97%) reduction in the incidence of COVID-19 during the third wave. In contrast, in the first 2 waves, the same was associated with 3.69 times (95% CI, 1.02–13.33) higher incidence. Executives and professionals were more likely to implement WFH and experienced frequent changes in WFH practice compared with production workers. Conclusions Consistent findings on the reversed socioeconomic patterning of COVID-19 burden between infection waves in Hong Kong in both individual- and population-level analyses indicated that risks of infections may be related to occupations involving high exposure frequency and WFH flexibility. Contextual determinants should be taken into account in policy planning aiming at mitigating such disparities., Disparities in COVID-19 burden in Hong Kong suggested that the risk of infection may be associated with frequencies of occupation-related general exposure and the flexibility of arranging working from home in the population.

This study compared the phylogeography of MERS-CoV between hospital outbreak-associated cases and sporadic cases in Saudi Arabia. We collected complete genome sequences from human samples in Saudi Arabia and data on the multiple risk factors of human MERS-CoV in Saudi Arabia reported from 2012 to 2018. By matching each sequence to human cases, we identified isolates as hospital outbreak-associated cases or sporadic cases. We used Bayesian phylogenetic methods including temporal, discrete trait analysis and phylogeography to uncover transmission routes of MERS-CoV isolates between hospital outbreaks and sporadic cases. Of the 120 sequences collected between 19 June 2012 and 23 January 2017, there were 64 isolates from hospital outbreak-associated cases and 56 from sporadic cases. Overall, MERS-CoV is fast evolving at 7.43 &times, 10&minus, 4 substitutions per site per year. Isolates from hospital outbreaks showed unusually fast evolutionary speed in a shorter time-frame than sporadic cases. Multiple introductions of different MERS-CoV strains occurred in three separate hospital outbreaks. MERS-CoV appears to be mutating in humans. The impact of mutations on viruses transmissibility in humans is unknown.

Avian influenza H5N1 subtype has caused a global public health concern due to its high pathogenicity in poultry and high case fatality rates in humans. The recently emerged H7N9 is a growing pandemic risk due to its sustained high rates of human infections, and recently acquired high pathogenicity in poultry. Here, we used Bayesian phylogeography on 265 H5N1 and 371 H7N9 haemagglutinin sequences isolated from humans, animals and the environment, to identify and compare migration patterns and factors predictive of H5N1 and H7N9 diffusion rates in China. H7N9 diffusion dynamics and predictor contributions differ from H5N1. Key determinants of spatial diffusion included: proximity between locations (for H5N1 and H7N9), and lower rural population densities (H5N1 only). For H7N9, additional predictors included low avian influenza vaccination rates, low percentage of nature reserves and high humidity levels. For both H5N1 and H7N9, we found viral migration rates from Guangdong to Guangxi and Guangdong to Hunan were highly supported transmission routes (Bayes Factor > 30). We show fundamental differences in wide-scale transmission dynamics between H5N1 and H7N9. Importantly, this indicates that avian influenza initiatives designed to control H5N1 may not be sufficient for controlling the H7N9 epidemic. We suggest control and prevention activities to specifically target poultry transportation networks between Central, Pan-Pearl River Delta and South-West regions.

The risk and benefits of gain‐of‐function studies on influenza A have been widely debated since 2012 when the methods to create two respiratory transmissible H5N1 mutant isolates were published. Opponents of gain‐of‐function studies argue the biosecurity risk is unacceptable, while proponents cite potential uses for pandemic surveillance, preparedness and mitigation. In this commentary, we provide an overview of the background and applications of gain‐of‐function research and argue that the anticipated benefits have yet to materialize while the significant risks remain.

Background Over the last two decades, Australia has experienced four severe influenza seasons caused by a predominance of influenza A (A/H3N2): 2003, 2007, 2012, and 2017. Methods We compared the epidemiology, genetics, and transmission dynamics of severe A/H3N2 seasons in Australia from 2003 to 2017. Results Since 2003, the proportion of notifications in 0‐4 years old has decreased, while it has increased in the age group >80 years old (P

The clinical severity and observed case fatality ratio of influenza A/H1N1pdm09 in India, particularly in 2015 and 2017 far exceeds current global estimates. Reasons for these frequent and severe epidemic waves remain unclear. We used Bayesian phylodynamic methods to uncover possible genetic explanations for this, while also identifying the transmission dynamics of A/H1N1pdm09 between 2009 and 2017 to inform future public health interventions. We reveal a disproportionate selection at haemagglutinin residue positions associated with increased morbidity and mortality in India such as position 222 and clade 6B characteristic residues, relative to equivalent isolates circulating globally. We also identify for the first time, increased selection at position 186 as potentially explaining the severity of recent A/H1N1pdm09 epidemics in India. We reveal national routes of A/H1N1pdm09 transmission, identifying Maharashtra as the most important state for the spread throughout India, while quantifying climactic, ecological, and transport factors as drivers of within-country transmission. Together these results have important implications for future A/H1N1pdm09 surveillance and control within India, but also for epidemic and pandemic risk prediction around the world.

Background It appears inter‐seasonal influenza notifications have been increasing in summer months in Australia. This study aims to determine changes in inter‐seasonal influenza activity in Australia over time. Methods Routine influenza surveillance data and hospitalisations data were analysed to study the epidemiology of inter‐seasonal influenza and to examine the impact of inter‐seasonal influenza on morbidity in Australia at a national level. To adjust for changes in testing over time, we calculated a ratio of summer‐to‐winter notifications for each year in the study. A P‐value of