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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.

AIM: To compare the clinical features of Middle East respiratory syndrome coronavirus (MERS-CoV) infection between paediatric and adult cases. METHODS: Using multiple public data sources, we created an enhanced open-source surveillance dataset of all MERS-CoV cases between 20 September 2012 and 31 December 2018 in Saudi Arabia including available risk factor data. RESULTS: Of the 1791 cases of MERS-CoV identified, 30 cases (1.7%) were aged under 18 years and 1725 cases (96.3%) were aged 18 years and over. Three paediatric cases were fatal, aged 0, 2 and 15 years. The odds of asymptomatic MERS-CoV infection among cases under 18 years (n = 10/23; 44%) was significantly higher (odds ratio (OR) = 4.98; 95% confidence interval (CI): 2.15-11.51; P = 0.001) compared to adults (n = 199/1487; 13%). The odds of hospitalisation were significantly lower (OR = 0.17; 95% CI: 0.08-0.39; P < 0.001) among cases under 18 years (n = 12/24; 50%) compared to adults (n = 1231/1443; 85%). Children were more likely to have a known source of exposure compared to adults (OR = 2.68; 95% CI: 1.29-5.56; P = 0.008). CONCLUSIONS: Clinically severe illness is less common in children, although death can occur, and the proportion of paediatric cases (1.7%) is similar to that reported for COVID-19. Age-specific differences in the clinical presentation of MERS-CoV cases could have implications for transmission for other betacoronaviruses including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Children may be at risk within the household with an infected adult. More studies are required on the role of children in transmission of betacoronaviruses.

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 A large cluster of 59 cases were linked to a single flight with 146 passengers from New Delhi to Hong Kong in April 2021. This outbreak coincided with early reports of exponential pandemic growth in New Delhi, which reached a peak of > 400 000 newly confirmed cases on 7 May 2021. Methods Epidemiological information including date of symptom onset, date of positive-sample detection and travel and contact history for individual cases from this flight were collected. Whole genome sequencing was performed, and sequences were classified based on the dynamic Pango nomenclature system. Maximum-likelihood phylogenetic analysis compared sequences from this flight alongside other cases imported from India to Hong Kong on 26 flights between June 2020 and April 2021, as well as sequences from India or associated with India-related travel from February to April 2021 and 1217 reference sequences. Results Sequence analysis identified six lineages of SARS-CoV-2 belonging to two variants of concern (Alpha and Delta) and one variant of public health interest (Kappa) involved in this outbreak. Phylogenetic analysis confirmed at least three independent sub-lineages of Alpha with limited onward transmission, a superspreading event comprising 37 cases of Kappa and transmission of Delta to only one passenger. Additional analysis of another 26 flights from India to Hong Kong confirmed widespread circulation of all three variants in India since early March 2021. Conclusions The broad spectrum of disease severity and long incubation period of SARS-CoV-2 pose a challenge for surveillance and control. As illustrated by this particular outbreak, opportunistic infections of SARS-CoV-2 can occur irrespective of variant lineage, and requiring a nucleic acid test within 72 hours of departure may be insufficient to prevent importation or in-flight transmission.

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.

Superspreading events (SSEs) have characterized previous epidemics of severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) infections1–6. For SARS-CoV-2, the degree to which SSEs are involved in transmission remains unclear, but there is growing evidence that SSEs might be a typical feature of COVID-197,8. Using contact tracing data from 1,038 SARS-CoV-2 cases confirmed between 23 January and 28 April 2020 in Hong Kong, we identified and characterized all local clusters of infection. We identified 4–7 SSEs across 51 clusters (n = 309 cases) and estimated that 19% (95% confidence interval, 15–24%) of cases seeded 80% of all local transmission. Transmission in social settings was associated with more secondary cases than households when controlling for age (P = 0.002). Decreasing the delay between symptom onset and case confirmation did not result in fewer secondary cases (P = 0.98), although the odds that an individual being quarantined as a contact interrupted transmission was 14.4 (95% CI, 1.9–107.2). Public health authorities should focus on rapidly tracing and quarantining contacts, along with implementing restrictions targeting social settings to reduce the risk of SSEs and suppress SARS-CoV-2 transmission. Cases linked to superspreading events are estimated to account for 80% of all local transmission of SARS-CoV-2 in Hong Kong in a study with implications for public health policies.

Superspreading events have characterised previous epidemics of severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) infections. Using contact tracing data, we identified and characterized SARS-CoV-2 clusters in Hong Kong. Given a superspreading threshold of 6-8 secondary cases, we identified 5-7 probable superspreading events and evidence of substantial overdispersion in transmissibility, and estimated that 20% of cases were responsible for 80% of local transmission. Among terminal cluster cases, 27% (45/167) ended in quarantine. Social exposures produced a greater number of secondary cases compared to family or work exposures (p

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 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

Objective Compare the adoption and adherence to health protection behaviours prior to and during travel among international Australian travellers who return to Australia with notified chikungunya or malaria infection. This information could inform targeted health promotion and intervention strategies to limit the establishment of these diseases within Australia. Results Seeking travel advice prior to departure was moderate (46%, N = 21/46) yet compliance with a range of recommended anti-vectorial prevention measures was low among both chikungunya and malaria infected groups (16%, N = 7/45). Reasons for not seeking advice between groups was similar and included ‘previous overseas travel with no problems’ (45%, N = 9/20) and ‘no perceived risk of disease’ (20%, N = 4/20). Most chikungunya cases (65%, N = 13/20) travelled to Indonesia and a further 25% (N = 5/20) visited India, however most malaria cases (62%, N = 16/26) travelled to continental Africa with only 12% (N = 3/26) travelling to India. The majority (50%, N = 10/20) of chikungunya cases reported ‘holiday’ as their primary purpose of travel, compared to malaria cases who most frequently reported travel to visit friends and family (VFR; 42%, N = 11/26). These results provide import data that may be used to support distinct public health promotion and intervention strategies of two important vector-borne infectious diseases of concern for Australia. Electronic supplementary material The online version of this article (10.1186/s13104-018-3695-9) contains supplementary material, which is available to authorized users.

An increase in the number of Acute Flaccid Myelitis (AFM) cases reported in the USA was detected in August 2018. The CDC has confirmed 186 cases of AFM in 2018 making this the largest outbreak of AFM reported in the USA. The cause however remains unknown. In this watching brief we review key features of the current outbreak in context, describe what is known about AFM, and consider probable causes. A two-year epidemic cycle of AFM appears to be emerging, and most current evidence implicates both EV-A71 and EV-D68 as the probable cause of the current outbreak yet key questions remain.