Spatio-temporal quantile regression analysis revealing more nuanced patterns of climate change: A study of long-term daily temperature in Australia.

Many studies have considered temperature trends at the global scale, but the literature is commonly associated with an overall increase in mean temperature in a defined past time period and hence lacking in in-depth analysis of the latent trends. For example, in addition to heterogeneity in mean and median values, daily temperature data often exhibit quasi-periodic heterogeneity in variance, which has largely been overlooked in climate research. To this end, we propose a joint model of quantile regression and variability. By accounting appropriately for the heterogeneity in these types of data, our analysis using Australian data reveals that daily maximum temperature is warming by ∼0.21°C per decade and daily minimum temperature by ∼0.13°C per decade. More interestingly, our modeling also shows nuanced patterns of change over space and time depending on location, season, and the percentiles of the temperature series.

Vaccination strategy for preventing the spread of SARS-CoV-2 in the limited supply condition: A mathematical modeling study.

To mitigate SARS-CoV-2 transmission, vaccines have been urgently approved. With their limited availability, it is critical to distribute the vaccines reasonably. We simulated the SARS-CoV-2 transmission for 365 days over four intervention periods: free transmission, structural mitigation, personal mitigation, and vaccination. Sensitivity analyses were performed to obtain robust results. We further evaluated two proposed vaccination allocations, including one-dose-high-coverage and two-doses-low-coverage, when the supply was low. 33.35% (infection rate, 2.68 in 10 million people) and 40.54% (2.36) of confirmed cases could be avoided as the nonpharmaceutical interventions (NPIs) adherence rate rose from 50% to 70%. As the vaccination coverage reached 60% and 80%, the total infections could be reduced by 32.72% and 41.19%, compared to the number without vaccination. When the durations of immunity were 90 and 120 days, the infection rates were 2.67 and 2.38. As the asymptomatic infection rate rose from 30% to 50%, the infection rate increased 0.92 (SD, 0.16) times. Conditioned on 70% adherence rate, with the same amount of limited available vaccines, the 20% and 40% vaccination coverage of one-dose-high-coverage, the infection rates were 2.70 and 2.35; corresponding to the two-doses-low-coverage with 10% and 20% vaccination coverage, the infection rates were 3.22 and 2.92. Our results indicated as the duration of immunity prolonged, the second wave of SARS-CoV-2 would be delayed and the scale would be declined. On average, the total infections in two-doses-low-coverage was 1.48 times (SD, 0.24) as high as that in one-dose-high-coverage. It is crucial to encourage people in order to improve vaccination coverage and establish immune barriers. Particularly when the supply is limited, a wiser strategy to prevent SARS-CoV-2 is equally distributing doses to the same number of individuals. Besides vaccination, NPIs are equally critical to the prevention of widespread of SARS-CoV-2.

A Gonococcal Vaccine Has the Potential to Rapidly Reduce the Incidence of Neisseria gonorrhoeae Infection Among Urban Men Who Have Sex With Men.

BACKGROUND: A gonococcal vaccine is urgently needed due to increasing gonorrhea incidence and emerging multidrug-resistant gonococcal strains worldwide. Men who have sex with men (MSM) have among the highest incidences of gonorrhea and may be a key target population for vaccination when available. METHODS: An individual-based, anatomical site-specific mathematical model was used to simulate Neisseria gonorrhoeae transmission in a population of 10 000 MSM. The impact of vaccination on gonorrhea prevalence was assessed. RESULTS: With a gonococcal vaccine of 100% or 50% protective efficacy, gonorrhea prevalence could be reduced by 94% or 62%, respectively, within 2 years if 30% of MSM are vaccinated on presentation for sexually transmitted infection (STI) testing. Elimination of gonorrhea is possible within 8 years with vaccines of ≥ 50% efficacy lasting 2 years, providing a booster vaccination is available every 3 years on average. A vaccine's impact may be reduced if it is not effective at all anatomical sites. CONCLUSIONS: Our study indicates that with a vaccine of modest efficacy and an immunization strategy that targets MSM presenting for STI screening, the prevalence of gonorrhea in this population could be rapidly and substantially reduced.

Modelling response strategies for controlling gonorrhoea outbreaks in men who have sex with men in Australia.

The ability to treat gonorrhoea with current first-line drugs is threatened by the global spread of extensively drug resistant (XDR) Neisseria gonorrhoeae (NG) strains. In Australia, urban transmission is high among men who have sex with men (MSM) and importation of an XDR NG strain in this population could result in an epidemic that would be difficult and costly to control. An individual-based, anatomical site-specific mathematical model of NG transmission among Australian MSM was developed and used to evaluate the potential for elimination of an imported NG strain under a range of case-based and population-based test-and-treat strategies. When initiated upon detection of the imported strain, these strategies enhance the probability of elimination and reduce the outbreak size compared with current practice (current testing levels and no contact tracing). The most effective strategies combine testing targeted at regular and casual partners with increased rates of population testing. However, even with the most effective strategies, outbreaks can persist for up to 2 years post-detection. Our simulations suggest that local elimination of imported NG strains can be achieved with high probability using combined case-based and population-based test-and-treat strategies. These strategies may be an effective means of preserving current treatments in the event of wider XDR NG emergence.

Spread and Impact of COVID-19 in China: A Systematic Review and Synthesis of Predictions From Transmission-Dynamic Models.

Background: Coronavirus disease 2019 (COVID-19) was first identified in Wuhan, China, in December 2019 and quickly spread throughout China and the rest of the world. Many mathematical models have been developed to understand and predict the infectiousness of COVID-19. We aim to summarize these models to inform efforts to manage the current outbreak. Methods: We searched PubMed, Web of science, EMBASE, bioRxiv, medRxiv, arXiv, Preprints, and National Knowledge Infrastructure (Chinese database) for relevant studies published between 1 December 2019 and 21 February 2020. References were screened for additional publications. Crucial indicators were extracted and analysed. We also built a mathematical model for the evolution of the epidemic in Wuhan that synthesised extracted indicators. Results: Fifty-two articles involving 75 mathematical or statistical models were included in our systematic review. The overall median basic reproduction number (R0) was 3.77 [interquartile range (IQR) 2.78-5.13], which dropped to a controlled reproduction number (Rc) of 1.88 (IQR 1.41-2.24) after city lockdown. The median incubation and infectious periods were 5.90 (IQR 4.78-6.25) and 9.94 (IQR 3.93-13.50) days, respectively. The median case-fatality rate (CFR) was 2.9% (IQR 2.3-5.4%). Our mathematical model showed that, in Wuhan, the peak time of infection is likely to be March 2020 with a median size of 98,333 infected cases (range 55,225-188,284). The earliest elimination of ongoing transmission is likely to be achieved around 7 May 2020. Conclusions: Our analysis found a sustained Rc and prolonged incubation/ infectious periods, suggesting COVID-19 is highly infectious. Although interventions in China have been effective in controlling secondary transmission, sustained global efforts are needed to contain an emerging pandemic. Alternative interventions can be explored using modelling studies to better inform policymaking as the outbreak continues.

Clinical characteristics of coronavirus disease 2019 (COVID-19) in China: A systematic review and meta-analysis.

OBJECTIVE: To better inform efforts to treat and control the current outbreak with a comprehensive characterization of COVID-19. METHODS: We searched PubMed, EMBASE, Web of Science, and CNKI (Chinese Database) for studies published as of March 2, 2020, and we searched references of identified articles. Studies were reviewed for methodological quality. A random-effects model was used to pool results. Heterogeneity was assessed using I2. Publication bias was assessed using Egger's test. RESULTS: 43 studies involving 3600 patients were included. Among COVID-19 patients, fever (83.3% [95% CI 78.4-87.7]), cough (60.3% [54.2-66.3]), and fatigue (38.0% [29.8-46.5]) were the most common clinical symptoms. The most common laboratory abnormalities were elevated C-reactive protein (68.6% [58.2-78.2]), decreased lymphocyte count (57.4% [44.8-69.5]) and increased lactate dehydrogenase (51.6% [31.4-71.6]). Ground-glass opacities (80.0% [67.3-90.4]) and bilateral pneumonia (73.2% [63.4-82.1]) were the most frequently reported findings on computed tomography. The overall estimated proportion of severe cases and case-fatality rate (CFR) was 25.6% (17.4-34.9) and 3.6% (1.1-7.2), respectively. CFR and laboratory abnormalities were higher in severe cases, patients from Wuhan, and older patients, but CFR did not differ by gender. CONCLUSIONS: The majority of COVID-19 cases are symptomatic with a moderate CFR. Patients living in Wuhan, older patients, and those with medical comorbidities tend to have more severe clinical symptoms and higher CFR.

Using Baidu search index to monitor and predict newly diagnosed cases of HIV/AIDS, syphilis and gonorrhea in China: estimates from a vector autoregressive (VAR) model.

OBJECTIVES: Internet search engine data have been widely used to monitor and predict infectious diseases. Existing studies have found correlations between search data and HIV/AIDS epidemics. We aimed to extend the literature through exploring the feasibility of using search data to monitor and predict the number of newly diagnosed cases of HIV/AIDS, syphilis and gonorrhoea in China. METHODS: This paper used vector autoregressive model to combine the number of newly diagnosed cases with Baidu search index to predict monthly newly diagnosed cases of HIV/AIDS, syphilis and gonorrhoea in China. The procedures included: (1) keywords selection and filtering; (2) construction of composite search index; (3) modelling with training data from January 2011 to October 2016 and calculating the prediction performance with validation data from November 2016 to October 2017. RESULTS: The analysis showed that there was a close correlation between the monthly number of newly diagnosed cases and the composite search index (the Spearman's rank correlation coefficients were 0.777 for HIV/AIDS, 0.590 for syphilis and 0.633 for gonorrhoea, p<0.05 for all). The R2 were all more than 85% and the mean absolute percentage errors were less than 11%, showing the good fitting effect and prediction performance of vector autoregressive model in this field. CONCLUSIONS: Our study indicated the potential feasibility of using Baidu search data to monitor and predict the number of newly diagnosed cases of HIV/AIDS, syphilis and gonorrhoea in China.

Anal human papillomavirus among men who have sex with men in three metropolitan cities in southern China: implications for HPV vaccination.

INTRODUCTION: Men who have sex with men (MSM), especially those infected with human immunodeficiency virus (HIV), are at disproportionate risk for human papillomavirus (HPV) infection. Data about anal HPV prevalence among MSM in southern China are limited. METHODS: MSM were recruited between January 1 and August 31, 2017 in three metropolitan cities: Guangzhou, Shenzhen and Wuxi. A self-completed tablet-based questionnaire was used to collect information about socio-demographic/sexual behavioral characteristics, history of sexually transmitted infections (STIs) and recreational drug use. An anal brush was used to collect exfoliated cells for HPV DNA testing and genotyping, and a blood sample was taken for HIV testing. Penile/anal warts were checked by a clinician. RESULTS: A total of 536 MSM were enrolled, including 39 HIV-positive and 497 HIV-negative individuals. Compared with HIV-negative MSM, prevalence of any HPV genotype (79.5% vs 46.7%), any high-risk genotype (64.1% vs 36.6%) and any nonavalent vaccine-preventable genotype (53.9% vs 31.6%) was significantly higher in HIV-positive MSM, with all P < 0.01. HIV infection (adjusted odds ratio [AOR], 4.28; 95% confidence interval [CI], 1.87-9.80), using recreational drugs (AOR, 1.87; 95% CI, 1.22-2.87), having ≥ 3 years of sexual experience (AOR, 1.52; 95% CI, 1.01-2.28), having ≥ 6 lifetime male partners (AOR, 1.92; 95% CI, 1.29-2.86), and engaging receptive anal intercourse (AOR, 2.30; 95% CI, 1.48-3.57) were associated with higher anal HPV prevalence. Any HPV prevalence increased with age, from 24.5% at < 20 years to 55.8% at ≥ 40 years. CONCLUSIONS: Anal HPV prevalence was high among MSM in southern China, significantly associated with HIV status and sexual experience. HPV prevalence increased with age among MSM. A targeted HPV vaccination program for teenage MSM might be necessary. Our findings will inform targeted HPV modelling among MSM in China.