Impact of the coronavirus disease 2019 interventions on the incidence of hand, foot, and mouth disease in mainland China

Background

In early 2020, non-pharmaceutical interventions (NPIs) were implemented in China to reduce and contain the coronavirus disease 2019 (COVID-19) transmission. These NPIs might have also reduced the incidence of hand, foot, and mouth disease (HFMD).

Methods

The weekly numbers of HFMD cases and meteorological factors in 31 provincial capital cities and municipalities in mainland China were obtained from Chinese Center for Disease Control and Prevention (CCDC) and National Meteorological Information Center of China from 2016 to 2020. The NPI data were collected from local CDCs. The incidence rate ratios (IRRs) were calculated for the entire year of 2020, and for January-July 2020 and August-December 2020. The expected case numbers were estimated using seasonal autoregressive integrated moving average models. The relationships between kindergarten closures and incidence of HFMD were quantified using a generalized additive model. The estimated associations from all cities were pooled using a multivariate meta-regression model.

Findings

Stringent NPIs were widely implemented for COVID-19 control from January to July 2020, and the IRRs for HFMD were less than 1 in all 31 cities, and less than 0·1 for 23 cities. Overall, the proportion of HFMD cases reduced by 52·9% (95% CI: 49·3-55·5%) after the implementation of kindergarten closures in 2020, and this effect was generally consistent across subgroups.

Interpretation

The decrease in HFMD incidence was strongly associated with the NPIs for COVID-19. HFMD epidemic peaks were either absent or delayed, and the final epidemic size was reduced. Kindergarten closure is an intervention to prevent HFMD outbreaks.

Funding

This research was supported by the National Natural Science Foundation of China (81973102 & 81773487), Public Health Talents Training Program of Shanghai Municipality (GWV-10.2-XD21), the Shanghai New Three-year Action Plan for Public Health (GWV-10.1-XK16), the Major Project of Scientific and Technical Winter Olympics from National Key Research and Development Program of China (2021YFF0306000), 13th Five-Year National Science and Technology Major Project for Infectious Diseases (2018ZX10725-509) and Key projects of the PLA logistics Scientific research Program (BHJ17J013).

Challenges in the control of COVID-19 outbreaks caused by the delta variant during periods of low humidity: an observational study in Sydney, Australia

Background

Since the appearance of severe acute respiratory coronavirus 2 (SARS-CoV-2) and the coronavirus disease 2019 (COVID-19) pandemic, a growing body of evidence has suggested that weather factors, particularly temperature and humidity, influence transmission. This relationship might differ for the recently emerged B.1.617.2 (delta) variant of SARS-CoV-2. Here we use data from an outbreak in Sydney, Australia that commenced in winter and time-series analysis to investigate the association between reported cases and temperature and relative humidity.

Methods

Between 16 June and 10 September 2021, the peak of the outbreak, there were 31,662 locally-acquired cases reported in five local health districts of Sydney, Australia. The associations between daily 9:00 am and 3:00 pm temperature (°C), relative humidity (%) and their difference, and a time series of reported daily cases were assessed using univariable and multivariable generalized additive models and a 14-day exponential moving average. Akaike information criterion (AIC) and the likelihood ratio statistic were used to compare different models and determine the best fitting model. A sensitivity analysis was performed by modifying the exponential moving average.

Results

During the 87-day time-series, relative humidity ranged widely (< 30–98%) and temperatures were mild (approximately 11–17 °C). The best-fitting (AIC: 1,119.64) generalized additive model included 14-day exponential moving averages of 9:00 am temperature (P < 0.001) and 9:00 am relative humidity (P < 0.001), and the interaction between these two weather variables (P < 0.001). Humidity was negatively associated with cases no matter whether temperature was high or low. The effect of lower relative humidity on increased cases was more pronounced below relative humidity of about 70%; below this threshold, not only were the effects of humidity pronounced but also the relationship between temperature and cases of the delta variant becomes apparent.

Conclusions

We suggest that the control of COVID-19 outbreaks, specifically those due to the delta variant, is particularly challenging during periods of the year with lower relative humidity and warmer temperatures. In addition to vaccination, stronger implementation of other interventions such as mask-wearing and social distancing might need to be considered during these higher risk periods.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s40249-021-00926-0.

What Would You Do? Types of Ethical Challenging Situations Depicted in Vignettes Published in the Veterinary Literature from 1990 to 2020

Veterinary team members encounter a wide range of ethically challenging situations (ECS) in their work. Inability to resolve ECS in accordance with their values may negatively impact the wellbeing of veterinary team members. We sought to determine the types of ECS described in published ethical vignettes in the veterinary literature. We performed a strategic literature search, followed by a thematic analysis of vignettes published in the veterinary literature from 1990–2020. We identified 567 published vignettes in 544 publications. In the majority of vignettes, the protagonist was a veterinarian (61.6%) and the most common categories of animal involved were dogs (28.0%), livestock in general (10.8%), and cattle (10.6%). The primary type of ECS was coded for each scenario, generating 29 themes. These findings extend knowledge about types of ECS that may be encountered by veterinary team members. These themes can help to inform curricula and better prepare veterinary team members to navigate ECS. They may also highlight factors that contribute to ECS that can be addressed on a broad scale, such as through regulation, continuing professional development, or stakeholder education. Knowing that others may experience similar ECS may help veterinary team members feel part of a moral community.

Evaluation of reticulorumen temperature boluses for the diagnosis of subclinical cases of bovine respiratory disease in feedlot cattle

Bovine respiratory disease (BRD) is the most important and costly health issue of the feedlot industry worldwide. Remote monitoring of reticulorumen temperature has been suggested as a potential tool to improve the diagnostic accuracy of BRD. The present study aimed to evaluate 1) the difference and degree of reticulorumen hyperthermia episodes between healthy and subclinical BRD feedlot steers, and 2) determine the correlation between reticulorumen hyperthermia and lung pathology, performance, and carcass traits. Mixed-breed feedlot steers (n = 148) with a mean arrival weight of 321 ± 3.34 kg were administered a reticulorumen bolus at feedlot entry and monitored for visual and audible signs of BRD until slaughter when lungs were examined and scored for lesions indicative of BRD. Post-slaughter animals with no record of BRD treatment were assigned to one of three case definitions. Healthy steers had no visual or audible signs of BRD (i.e., CIS=1), and total lung consolidation score < 5% or pleurisy score < 3 at slaughter. Subclinical BRD cases had a CIS of 1, and a lung consolidation score ≥ 5% or a pleurisy score of 3 at slaughter. Mild CIS cases had at least one CIS of 2, and a lung consolidation score < 5% and a pleurisy score < 3 at slaughter. Subclinical BRD and mild CIS cases had longer total duration of reticulorumen hyperthermia, more episodes and longer average episode duration above 40.0 °C compared to healthy steers (P < 0.05). A moderate positive correlation was found between lung consolidation and total duration (r = 0.27, P < 0.001), episode duration (r = 0.29, P < 0.001), and number of episodes (r = 0.20, P < 0.05). Pleurisy score was also found to be moderately and positively correlated with total duration (r = 0.23, P < 0.01), episode duration (r = 0.37, P < 0.001), and number of episodes (r = 0.26, P < 0.01). Moderate negative correlations were found between reticulorumen hyperthermia and carcass traits including hot standard carcass weight (HSCW) (-0.22 ≤ r ≤ -0.23, P < 0.05) and P8-fat depth (-0.18 ≤ r ≤ -0.32, P < 0.05). Subclinical BRD reduced carcass weight by 22 kg and average daily gain (ADG) by 0.44 kg/day compared to healthy steers (P < 0.05), but mild CIS cases had no effect on performance (P > 0.05). The reticulorumen bolus technology appears promising for detection of subclinical BRD cases in feedlot cattle as defined by lung pathology at slaughter.

Meta-analysis and adjusted estimation of COVID-19 case fatality risk in India and its association with the underlying comorbidities

Management of coronavirus disease 2019 (COVID-19) in India is a top government priority. However, there is a lack of COVID-19 adjusted case fatality risk (aCFR) estimates and information on states with high aCFR. Data on COVID-19 cases and deaths in the first pandemic wave and 17 state-specific geodemographic, socio-economic, health and comorbidity-related factors were collected. State-specific aCFRs were estimated, using a 13-day lag for fatality. To estimate country-level aCFR in the first wave, state estimates were meta-analysed based on inverse-variance weighting and aCFR as either a fixed- or random-effect. Multiple correspondence analyses, followed by univariable logistic regression, were conducted to understand the association between aCFR and geodemographic, health and social indicators. Based on health indicators, states likely to report a higher aCFR were identified. Using random- and fixed-effects models, cumulative aCFRs in the first pandemic wave on 27 July 2020 in India were 1.42% (95% CI 1.19%-1.70%) and 2.97% (95% CI 2.94%-3.00%), respectively. At the end of the first wave, as of 15 February 2021, a cumulative aCFR of 1.18% (95% CI 0.99%-1.41%) using random and 1.64% (95% CI 1.64%-1.65%) using fixed-effects models was estimated. Based on high heterogeneity among states, we inferred that the random-effects model likely provided more accurate estimates of the aCFR for India. The aCFR was grouped with the incidence of diabetes, hypertension, cardiovascular diseases and acute respiratory infections in the first and second dimensions of multiple correspondence analyses. Univariable logistic regression confirmed associations between the aCFR and the proportion of urban population, and between aCFR and the number of persons diagnosed with diabetes, hypertension, cardiovascular diseases and stroke per 10,000 population that had visited NCD (Non-communicable disease) clinics. Incidence of pneumonia was also associated with COVID-19 aCFR. Based on predictor variables, we categorised 10, 17 and one Indian state(s) expected to have a high, medium and low aCFR risk, respectively. The current study demonstrated the value of using meta-analysis to estimate aCFR. To decrease COVID-19 associated fatalities, states estimated to have a high aCFR must take steps to reduce co-morbidities.

Risk Factors Associated With Increased Ethically Challenging Situations Encountered by Veterinary Team Members During the COVID-19 Pandemic

Ethically challenging situations (ECS) are commonly encountered in veterinary settings. The number of ECS encountered by some veterinary team members may increase during a crisis, such as the COVID-19 pandemic. This study aimed to determine the risk factors for experiencing an increase in the frequency of ECS in the months following the beginning of the COVID-19 pandemic, utilizing data from a global survey of veterinarians, veterinary nurses and animal health technicians collected from May to July 2020. In this study, descriptive analyses were performed to characterize veterinary team members who responded to the survey (n = 540). Binomial logistic regression analyses were performed to determine factors associated with an increase in ECS encountered since the beginning of the COVID-19 pandemic. Being a veterinary nurse or animal health technician, working with companion animals, working in the USA or Canada, and being not confident or underconfident in dealing with ECS in the workplace were factors associated with an increase in ECS encountered since the beginning of the COVID-19 pandemic. Results suggest a need to explore the ECS encountered by veterinary team members, particularly veterinary nurses and animal health technicians working in companion animal practice, in depth. Identification of risk factors may facilitate better preparation of veterinary team members for managing ECS, and minimizing the negative impact of ECS on the well-being of those who care for animals.

Early-life patterns of growth are linked to levels of phenotypic trait covariance and postfledging mortality across avian species

Life history studies have established that trade-offs between growth and survival are common both within and among species. Identifying the factor(s) that mediate this trade-off has proven difficult, however, especially at the among-species level. In this study, we examined a series of potentially interrelated traits in a community of temperate-zone passerine birds to help understand the putative causes and consequences of variation in early-life growth among species. First, we examined whether nest predation risk (a proven driver of interspecific variation in growth and development rates) was correlated with species-level patterns of incubation duration and nestling period length. We then assessed whether proxies for growth rate covaried with mean trait covariance strength (i.e., phenotypic correlations ( rp), which can be a marker of early-life stress) among body mass, tarsus length, and wing length at fledging. Finally, we examined whether trait covariance strength at fledging was related to postfledging survival. We found that higher nest predation risk was correlated with faster skeletal growth and that our proxies for growth corresponded with increased trait covariance strength ( rp), which subsequently, correlated with higher mortality in the next life stage (postfledging period). These results provide an indication that extrinsic pressures (nest predation) impact rates of growth, and that there are costs of rapid growth across species, expressed as higher mean rp and elevated postfledging mortality. The link between higher levels of trait covariance at fledging and increased mortality is unclear, but increased trait covariance strength may reflect reduced phenotypic flexibility (i.e., phenotypic canalization), which may limit an organism's capacity for coping with environmental or ecological variability.

Distribution of mortality patterns in cats with naturally occurring trauma: A Veterinary Committee on Trauma registry study

A greater understanding of the prognostic variables that affect the timing of death for cats with trauma may help clinicians select treatments and monitoring plans. This study investigated the mortality rate and its distribution pattern in a large population of cats to identify variables associated with the timing of trauma-related deaths. Clinical data was retrieved from the Veterinary Committee on Trauma database to determine mortality rates and timing of deaths, defined as early death (ED; <1 day post-presentation) or delayed death (DD; ≥1 day post-presentation). Multivariable logistic regression analyses were performed to identify characteristics and interventions that best predicted timing of death. Overall mortality rate for 6703 feline trauma patients with complete records was 17.2%, with 7.6% due to natural death and 92.3% due to euthanasia. Among the subset of 543 cats with trauma that died after presentation or required euthanasia due to a grave prognosis (representing an 8.1% mortality rate), EDs were more common (71.7%) than DD and the cause of death was not significantly associated with the timing of death. Clinical pathology parameters were unable to identify animals more likely to die or to require euthanasia due to a poor prognosis during hospitalisation. Factors that were significantly different for cats with ED vs. DD included the median cumulative results for the Modified Glasgow Coma Scale (MGCS) score and the Animal Trauma Triage (ATT) score, the presence of spinal trauma, administration of blood products and undertaking surgical procedures. An increased likelihood of DD rather than ED was associated with the administration of blood products (odds ratio [OR], 3.959; P = 0.019) vs. not, performing a surgical procedure (OR, 6.055; P < 0.001) vs. not, and a cumulative MGCS of 15-17 or 18 (OR, 1.947 and 3.115; P = 0.031 and P = 0.01, respectively) vs. a cumulative MGCS ≤ 11.

Inherent virus characteristics and host range drive the zoonotic and emerging potential of viruses

Understanding the zoonotic and emerging potential of viruses is critical to prevent and control spread that can cause disease epidemics or pandemics. We developed a database using the most up-to-date information from the International Committee on Taxonomy of Viruses (4958 virus species) and identified 1479 vertebrate virus species and their host ranges. Viral traits and host ranges were then used as predictors in generalized linear mixed models for three host-associated outcomes - confirmed zoonotic, potential zoonotic and disease emergence. We identified significant interactions between host range and viral characteristics, not previously reported, that influence the zoonotic and emergence potential of viruses. Bat- and livestock-adapted viruses posed high risk, and the risk increased substantially if these viruses were also present in other vertebrates or were not reported from invertebrates. Our model predicted 39 viruses of interest that have never been reported to have zoonotic potential (27) or to potentially become emerging human viruses (12). We conclude that nucleic acid type is important in identifying the zoonotic and emerging potential of viruses. We recommend enhanced surveillance and monitoring of these virus species identified with a zoonotic and emerging potential to mitigate disease outbreaks and future epidemics.

Communication challenges experienced by veterinary professionals during the COVID-19 pandemic

The COVID-19 pandemic and associated restrictions have caused major changes in veterinary practice. Utilising a subset of qualitative data from a global survey of 540 veterinarians, veterinary nurses and animal health technicians, we highlight the impact of these changes on communication in veterinary clinical practice. Communication challenges experienced by veterinary team members included lack of face-to-face contact with clients; increased difficulty in communicating in general; inability to demonstrate physical examination, diagnostic findings or treatment information to clients; difficulty in communicating while wearing personal protective equipment; increased 'miscommunication' and challenges in convincing clients of the importance of pandemic-associated protocols. These findings suggest a need for veterinary teams to modify and adapt their communication strategies to facilitate effective communication where social distancing and noncontact consultations are required.

Etiological and epidemiological features of acute respiratory infections in China

Nationwide prospective surveillance of all-age patients with acute respiratory infections was conducted in China between 2009‒2019. Here we report the etiological and epidemiological features of the 231,107 eligible patients enrolled in this analysis. Children <5 years old and school-age children have the highest viral positivity rate (46.9%) and bacterial positivity rate (30.9%). Influenza virus, respiratory syncytial virus and human rhinovirus are the three leading viral pathogens with proportions of 28.5%, 16.8% and 16.7%, and Streptococcus pneumoniae, Mycoplasma pneumoniae and Klebsiella pneumoniae are the three leading bacterial pathogens (29.9%, 18.6% and 15.8%). Negative interactions between viruses and positive interactions between viral and bacterial pathogens are common. A Join-Point analysis reveals the age-specific positivity rate and how this varied for individual pathogens. These data indicate that differential priorities for diagnosis, prevention and control should be highlighted in terms of acute respiratory tract infection patients' demography, geographic locations and season of illness in China.

Multiple diagnostic tests demonstrate an increased risk of canine heartworm disease in northern Queensland, Australia

Background

Canine heartworm (Dirofilaria immitis) is a life-threatening infection of dogs with a global distribution. Information on the prevalence of D. immitis and associated risk factors for canine heartworm antigen positivity—and thus disease—in Australia is scarce or outdated. The current reference method for D. immitis diagnosis in dogs is via the detection of heartworm antigen in blood using commercially available microwell-based enzyme-linked immunosorbent assays (ELISAs). Heat treatment of canine plasma prior to testing has been suggested to increase test sensitivity. The aim of the current study was to estimate the prevalence of D. immitis in dogs confined to shelters in Queensland, Australia. The impact of heat treatment on antigen test results was also assessed.

Methods

Blood samples (n = 166) were collected directly from dogs in seven shelters across Queensland (latitudinal span of approx. 1700 km) into EDTA blood collection tubes. A commercially available ELISA (DiroCHEK®) was used to detect canine heartworm antigen in untreated and heat-treated plasma. Whole blood was concurrently tested for the presence of microfilariae and D. immitis DNA using a modified Knott’s test and real-time PCR, respectively. Risk factors (age, gender, source, location) associated with the odds of positivity for canine heartworm were assessed using binary logistic regression models.

Results

A total of 16 dogs (9.6%; 95% confidence interval [CI]: 5.9–15.2%) were positive for canine heartworm based on combined test results. Heat treatment did not impact on the positivity of D. immitis antigen within samples (Cohen’s kappa = 0.98), but the optical density was significantly increased in paired plasma samples for D. immitis antigen-positive samples (Wilcoxon matched-pairs signed rank test, two-tailed P < 0.01). Location of the dog in a shelter in northern Queensland was the only risk factor significantly associated with the odds of a dog being more likely to be D. immitis antigen positive (odds ratio: 4.39; 95% CI: 1.26–13.51). All samples positive for the modified Knott’s test were also positive for D. immitis DNA by PCR.

Conclusions

This study demonstrated the presence of heartworm-positive dogs in shelters in Queensland, with positive animals significantly more likely to occur in northern Queensland than southern Queensland. Sustained testing for the presence of D. immitis microfilariae and antigen remain important diagnostic tools in areas with known and re-emerging canine heartworm activity.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-021-04896-y.

Investigation into clinicopathological and pathological findings, prognosis, and aetiology of lorikeet paralysis syndrome in rainbow lorikeets (Trichoglossus haematodus)

Objective

To report the temporal and spatial distribution of rainbow lorikeets presenting with lorikeet paralysis syndrome (LPS) and their clinicopathologic and pathologic findings, exposure to toxins, and response to treatment.

Methods

Records of lorikeets admitted in 2017 and 2018 to facilities in south‐east Queensland (QLD) were reviewed and LPS and non‐LPS cases were mapped and their distribution compared. Plasma biochemistries and complete blood counts were done on 20 representative lorikeets from south‐east QLD and Grafton, New South Wales (NSW). Tissues from 28 lorikeets were examined histologically. Samples were tested for pesticides (n = 19), toxic elements (n = 23), botulism (n = 15) and alcohol (n = 5).

Results

LPS occurred in warmer months. Affected lorikeets were found across south‐east QLD. Hotspots were identified in Brisbane and the Sunshine Coast. Lorikeets had a heterophilic leucocytosis, elevated muscle enzymes, uric acid and sodium and chloride. Specific lesions were not found. Exposure to cadmium was common in LPS and non‐LPS lorikeets. Treated lorikeets had a 60–93% See Table 2 depending on severity of signs.

Clinical significance

The primary differential diagnosis for lorikeets presenting with lower motor neuron signs during spring, summer and autumn in northern NSW and south‐east Queensland should be LPS. With supportive care, prognosis is fair to good.

The impact of African swine fever virus on smallholder village pig production: An outbreak investigation in Lao PDR

African swine fever virus (ASFV) causes a deadly disease of pigs which spread through southeast Asia in 2019. We investigated one of the first outbreaks of ASFV in Lao People's Democratic Republic amongst smallholder villages of Thapangtong District, Savannakhet Province. In this study, two ASFV affected villages were compared to two unaffected villages. Evidence of ASFV‐like clinical signs appeared in pig herds as early as May 2019, with median epidemic days on 1 and 18 June in the two villages, respectively. Using participatory epidemiology mapping techniques, we found statistically significant spatial clustering in both outbreaks (p < 0.001). Villagers reported known risk factors for ASFV transmission – such as free‐ranging management systems and wild boar access – in all four villages. The villagers reported increased pig trader activity from Vietnam before the outbreaks; however, the survey did not determine a single outbreak source. The outbreak caused substantial household financial losses with an average of nine pigs lost to the disease, and Monte Carlo analysis estimated this to be USD 215 per household. ASFV poses a significant threat to food and financial security in smallholder communities such as Thapangtong, where 40.6% of the district's population are affected by poverty. This study shows ASFV management in the region will require increased local government resources, knowledge of informal trader activity and wild boar monitoring alongside education and support to address intra‐village risk factors such as free‐ranging, incorrect waste disposal and swill feeding.

Estimation of the Rural Dog Population Within a Mega-City: An Example in Jiading District, Shanghai

Rural dog populations have long been recognized to be inadequately managed in terms of disease control and prevention. In this study we consider dog management in rural Shanghai and its implications for rabies control in the entire metropolitan area of Shanghai. The prerequisite to improve rabies vaccination coverage in rural Shanghai depends on a proper enumeration of the total rural dog population. In this study we selected one of the nine administrative districts in Shanghai (Jiading), within which there are 7 towns and 2 industrial zones (township-level division) that contain agricultural areas. A total of 9 villages (rabies model villages) were chosen from each township-level division in Jiading, and an additional 3 non-model villages were also included in the study. A household questionnaire survey was implemented in all 12 villages recruited. In 3 of the model villages and the 3 non-model villages chosen as a comparison, two methods of enumeration—a sight-resight survey and a household census survey—were implemented. Results from the household survey in these 6 villages showed that among the total 1,560 owned dogs, 80.4% were Chinese Garden Dogs, 69.1% were aged 1 to 3 years, 49.2% were homebred, and 88.3% were kept for the purpose of guarding the house. However, only 3.7% of the owned dogs were desexed. There was a higher proportion of chained or confined dogs in model compared to non-model villages. The model villages had an absolute rabies vaccination coverage of 100% among its owned dog population and a smaller number of stray dogs. It was also identified that the two enumeration methods yielded similar counts (P = 0.12), particularly within smaller villages. From the questionnaire survey implemented within all 12 villages and based on the average human-to-dog ratio, the total rural dog population of Jiading district was estimated to be 24,058. This study generated information on the general demographics of the rural dog population in Jiading, and demonstrates an approach to the study of rural dog populations within the context of a megacity. In such a context, rural dog populations need to be considered as a critical component of animal and public health.

Meteorological conditions are heterogeneous factors for COVID-19 risk in China

Whether meteorological factors influence COVID-19 transmission is an issue of major public health concern, but available evidence remains unclear and limited for several reasons, including the use of report date which can lag date of symptom onset by a considerable period. We aimed to generate reliable and robust evidence of this relationship based on date of onset of symptoms. We evaluated important meteorological factors associated with daily COVID-19 counts and effective reproduction number (R_t) in China using a two-stage approach with overdispersed generalized additive models and random-effects meta-analysis. Spatial heterogeneity and stratified analyses by sex and age groups were quantified and potential effect modification was analyzed. Nationwide, there was no evidence that temperature and relative humidity affected COVID-19 incidence and R_t. However, there were heterogeneous impacts on COVID-19 risk across different regions. Importantly, there was a negative association between relative humidity and COVID-19 incidence in Central China: a 1% increase in relative humidity was associated with a 3.92% (95% CI, 1.98%-5.82%) decrease in daily counts. Older population appeared to be more sensitive to meteorological conditions, but there was no obvious difference between sexes. Linear relationships were found between meteorological variables and COVID-19 incidence. Sensitivity analysis confirmed the robustness of the association and the results based on report date were biased. Meteorological factors play heterogenous roles on COVID-19 transmission, increasing the possibility of seasonality and suggesting the epidemic is far from over. Considering potential climatic associations, we should maintain, not ease, current control measures and surveillance.

Semi-quantitative food safety risk profile of the Australian red meat industry

In 2017-18, the Australian red meat (beef, sheep and goat species) industry generated more than $AUD 13 billion in export trade alone and is therefore of substantial importance to the Australian GDP. With both relatively high amounts of domestic red meat consumption and dependence on international markets, food safety risk is constantly reassessed so as to maintain a resilient industry sector. The current study aimed to conduct a food safety risk rating for the Australian red meat industry. In 2002, a food safety risk profile was developed for the Australian red meat industry. It included raw and processed meat products of cattle, sheep and goats and considered microbiological, chemical and physical hazards. The current risk rating was undertaken during 2017 and 2018. The first step was to conduct a hazard characterization, which involved a review of literature and data on foodborne outbreaks, pathogen surveillance and product recalls, and an expert elicitation process with 15 Australian food safety experts. This process identified the Hazard:Product:Process combinations to be considered and the likelihood of contamination at the point of consumption. These likelihood ratings were then combined with hazard severity ratings to qualitatively estimate the relative risk posed by each combination. Combinations with a moderate-to-high risk were included in the semi-quantitative risk rating using Risk Ranger v2, a tool that allows an estimation of the public health risk of hazard: product combinations and a ranking of this risk. The Risk Ranger tool provides a risk ranking (RR), ranging from 0 (no risk) to 100 (every member of the population eats a meal that contains a lethal dose of the hazard every day). STEC E. coli O157 (RR 35-39) and Salmonella spp. (RR 33-37) in undercooked hamburgers and Listeria monocytogenes in ready-to-eat products (RR 35-38) were combinations which had the highest (moderate) risk for the general and susceptible populations. In addition, Toxoplasma gondii in undercooked lamb was identified as posing a high risk among pregnant women (RR 49). The study provides an updated food safety risk profile for the Australian red meat industry which, considering the available information, suggests red meat products do not pose a high food safety risk. The methodology developed in this study provides an easy to implement approach to profile and prioritise food safety risk and relies on data that can generated in most situations.

Hybridisation between dingoes and domestic dogs in proximity to Indigenous communities in northern Australia

In northern Australia, wild dog populations potentially interact with domestic dogs from remote communities, which would create opportunities for disease transmission at the wild-domestic interface. An example is rabies, in the event of an incursion into northern Australia. However, the likelihood of such wild-domestic interactions is ambiguous. Hybridisation analyses based on 23 microsatellite DNA markers were performed on canine-origin scats collected in bushland areas around remote Indigenous communities in the Northern Peninsula Area, Queensland. Sufficient DNA was extracted from 6 of 41 scats to assess the percentage of dingo purity. These scats most likely originated from two 'pure' domestic dogs (0% dingo purity), one hybrid (20% dingo purity) and three 'pure' dingoes (92%-98% dingo purity). The two domestic dog samples were collected in the vicinity of communities. The location of two of the dingo-origin samples provides genetic evidence that dingoes are present in areas close to the communities. The availability of anthropogenic food resources likely creates opportunities for interactions with domestic dogs in the region. The hybrid sample demonstrates the occurrence of antecedent contacts between both populations by means of mating and supports the likelihood of a spatio-temporal overlap at the wild-domestic interface. This represents the first genetic survey involving a wild dog population of equatorial northern Queensland, with evidence of dingo purity. Our results have implications for potential disease transmission within a priority area for biosecurity in northern Australia.

The differential demographic pattern of coronavirus disease 2019 fatality outside Hubei and from six hospitals in Hubei, China: a descriptive analysis

BACKGROUND

The coronavirus disease 2019 (COVID-19) epidemic has been largely controlled in China, to the point where case fatality rate (CFR) data can be comprehensively evaluated.

METHODS

Data on confirmed patients, with a final outcome reported as of 29 March 2020, were obtained from official websites and other internet sources. The hospitalized CFR (HCFR) was estimated, epidemiological features described, and risk factors for a fatal outcome identified.

RESULTS

The overall HCFR in China was estimated to be 4.6% (95% CI 4.5-4.8%, P < 0.001). It increased with age and was higher in males than females. Although the highest HCFR observed was in male patients ≥70 years old, the relative risks for death outcome by sex varied across age groups, and the greatest HCFR risk ratio for males vs. females was shown in the age group of 50-60 years, higher than age groups of 60-70 and ≥ 70 years. Differential age/sex HCFR patterns across geographical regions were found: the age effect on HCFR was greater in other provinces outside Hubei than in Wuhan. An effect of longer interval from symptom onset to admission was only observed outside Hubei, not in Wuhan. By performing multivariate analysis and survival analysis, the higher HCFR was associated with older age (both P < 0.001), and male sex (both P < 0.001). Only in regions outside Hubei, longer interval from symptom onset to admission, were associated with higher HCFR.

CONCLUSIONS

This up-to-date and comprehensive picture of COVID-19 HCFR and its drivers will help healthcare givers target limited medical resources to patients with high risk of fatality.

Web-scraping applied to acquire difficult to access animal disease outbreak information, using African Swine Fever in Europe as an example

Surveillance data are key to informing decisions on the control and prevention of transboundary and emerging diseases. Here, we describe new methods for acquiring difficult to access, publicly available disease surveillance data. We use World Organisation for Animal Heath (OIE) data on African Swine Fever (ASF) outbreaks in European countries to showcase the importance of adequate disease surveillance data to inform decision-making. The data acquired using these methods allow for large scale, geospatial outbreak mapping and estimation of summary statistics for any listed terrestrial disease in the OIE World Animal Health Information System (WAHIS) database. These techniques will make valuable epidemiological data more accessible to the scientific community, aiding further insight into the occurrence and spread of transboundary and emerging diseases in a timely manner, fulfilling an important function of disease surveillance.

African Swine Fever spread across Asia, 2018-2019

African Swine Fever Virus (ASFV) is a highly contagious pathogen that causes disease in pigs, commonly characterized by acute haemorrhagic fever. Prior to August 2018, African Swine Fever (ASF) had not been reported in Asia, but has since spread throughout China, Mongolia, Korea, Vietnam, Laos, Cambodia, Myanmar, the Philippines, Hong Kong, Indonesia, Timor-Leste and Papua New Guinea. Using data collated from reports of confirmed cases, we applied spatio-temporal analysis to describe ASFV spread throughout Asia during its early phase-from 1 August 2018 (reported start date) to 31 December 2019-to provide an overview and comparative analysis. Analysis revealed a propagating epidemic of ASFV throughout Asia, with peaks corresponding to increased reports from China, Vietnam and Laos. Two clusters of reported outbreaks were found. During the epidemic, ASFV primarily spread from the North-East to the South-East: A larger, secondary cluster in the North-East represented earlier reports, while the smaller, primary cluster in the South-East was characterized by later reports. Significant differences in country-specific epidemics, morbidity, mortality and unit types were discovered. The initial number of outbreaks and enterprise size are likely predictors of the speed of spread and the effectiveness of ASFV stamping out procedures. Biosecurity methods, wild boar populations and the transportation of pigs and movement of infected fomites are discussed as likely risk factors for facilitating ASFV spread across Asia.