The impact of temperature on the transmissibility potential and virulence of COVID-19 in Tokyo, Japan

Assessing the impact of temperature on COVID-19 epidemiology is critical for implementing non-pharmaceutical interventions. However, few studies have accounted for the nature of contagious diseases, i.e., their dependent happenings. We aimed to quantify the impact of temperature on the transmissibility and virulence of COVID-19 in Tokyo, Japan, employing two epidemiological measurements of transmissibility and severity: the effective reproduction number ($$R_{t}$$ R t ) and case fatality risk (CFR). We estimated the $$R_{t}$$ R t and time-delay adjusted CFR and to subsequently assess the nonlinear and delayed effect of temperature on $$R_{t}$$ R t and time-delay adjusted CFR. For $$R_{t}$$ R t at low temperatures, the cumulative relative risk (RR) at the first temperature percentile (3.3 °C) was 1.3 (95% confidence interval (CI): 1.1–1.7). As for the virulence to humans, moderate cold temperatures were associated with higher CFR, and CFR also increased as the temperature rose. The cumulative RR at the 10th and 99th percentiles of temperature (5.8 °C and 30.8 °C) for CFR were 3.5 (95% CI: 1.3–10.0) and 6.4 (95% CI: 4.1–10.1). Our results suggest the importance to take precautions to avoid infection in both cold and warm seasons to avoid severe cases of COVID-19. The results and our proposed approach will also help in assessing the possible seasonal course of COVID-19 in the future.

Effect of evidence updates on key determinants of measles vaccination impact: a DynaMICE modelling study in ten high-burden countries

Background Model-based estimates of measles burden and the impact of measles-containing vaccine (MCV) are crucial for global health priority setting. Recently, evidence from systematic reviews and database analyses have improved our understanding of key determinants of MCV impact. We explore how representations of these determinants affect model-based estimation of vaccination impact in ten countries with the highest measles burden. Methods Using Dynamic Measles Immunisation Calculation Engine (DynaMICE), we modelled the effect of evidence updates for five determinants of MCV impact: case-fatality risk, contact patterns, age-dependent vaccine efficacy, the delivery of supplementary immunisation activities (SIAs) to zero-dose children, and the basic reproduction number. We assessed the incremental vaccination impact of the first (MCV1) and second (MCV2) doses of routine immunisation and SIAs, using metrics of total vaccine-averted cases, deaths, and disability-adjusted life years (DALYs) over 2000–2050. We also conducted a scenario capturing the effect of COVID-19 related disruptions on measles burden and vaccination impact. Results Incorporated with the updated data sources, DynaMICE projected 253 million measles cases, 3.8 million deaths and 233 million DALYs incurred over 2000–2050 in the ten high-burden countries when MCV1, MCV2, and SIA doses were implemented. Compared to no vaccination, MCV1 contributed to 66% reduction in cumulative measles cases, while MCV2 and SIAs reduced this further to 90%. Among the updated determinants, shifting from fixed to linearly-varying vaccine efficacy by age and from static to time-varying case-fatality risks had the biggest effect on MCV impact. While varying the basic reproduction number showed a limited effect, updates on the other four determinants together resulted in an overall reduction of vaccination impact by 0.58%, 26.2%, and 26.7% for cases, deaths, and DALYs averted, respectively. COVID-19 related disruptions to measles vaccination are not likely to change the influence of these determinants on MCV impact, but may lead to a 3% increase in cases over 2000–2050. Conclusions Incorporating updated evidence particularly on vaccine efficacy and case-fatality risk reduces estimates of vaccination impact moderately, but its overall impact remains considerable. High MCV coverage through both routine immunisation and SIAs remains essential for achieving and maintaining low incidence in high measles burden settings.

Cholera outbreaks in sub-Saharan Africa during 2010-2019: A Descriptive Analysis

Background: Cholera remains a public health threat, but is inequitably distributed, especially affecting areas without universal access to safe water and sanitation, including much of sub-Saharan Africa. Lack of standardized reporting and inconsistent outbreak definitions limit our understanding of cholera outbreak epidemiology. Methods: We curated a database of cholera incidence and mortality from sub-Saharan Africa from 2010 to 2020 and developed methods to reconstruct epidemic curves. We then described the distribution of key outbreak metrics, including outbreak size and duration. Results: We identified 999 suspected cholera outbreaks in 744 unique regions across 25 sub-Saharan Africa countries, and outbreak periods accounted for 1.8 billion person-months (2% of the total during this period) from January 2010 through January 2020. Among the 692 outbreaks reported from second-level administrative units (e.g., districts), the median attack rate was 0.8 per 1,000 people (IQR, 0.3-2.4 per 1,000), the median epidemic duration was 13 weeks (IQR, 8-19), and the median early outbreak reproductive number was 1.8 (range, 1.1-3.5). Rural outbreaks had more than twice the case fatality risk than urban ones (median of 1.8% versus 0.8%). Larger attack rates were associated with longer times to outbreak peak, longer epidemic durations, and lower case fatality risks. Conclusions: Despite reporting gaps and the limitations of analyzing outbreaks by administrative units, this work provides a baseline from which to monitor progress towards cholera control and essential statistics to inform outbreak management and emergency response in sub-Saharan Africa.

Estimating case fatality risk of severe Yellow Fever cases: systematic literature review and meta-analysis

Background Case fatality risk (CFR), commonly referred to as a case fatality ratio or rate, represents the probability of a disease case being fatal. It is often estimated for various diseases through analysis of surveillance data, case reports, or record examinations. Reported CFR values for Yellow Fever vary, offering wide ranges. Estimates have not been found through systematic literature review, which has been used to estimate CFR of other diseases. This study aims to estimate the case fatality risk of severe Yellow Fever cases through a systematic literature review and meta-analysis. Methods A search strategy was implemented in PubMed and Ovid Medline in June 2019 and updated in March 2021, seeking reported severe case counts, defined by fever and either jaundice or hemorrhaging, and the number of those that were fatal. The searches yielded 1,133 studies, and title/abstract review followed by full text review produced 14 articles reporting 32 proportions of fatal cases, 26 of which were suitable for meta-analysis. Four studies with one proportion each were added to include clinical case data from the recent outbreak in Brazil. Data were analyzed through an intercept-only logistic meta-regression with random effects for study. Values of the I2 statistic measured heterogeneity across studies. Results The estimated CFR was 39 % (95 % CI: 31 %, 47 %). Stratifying by continent showed that South America observed a higher CFR than Africa, though fewer studies reported estimates for South America. No difference was seen between studies reporting surveillance data and studies investigating outbreaks, and no difference was seen among different symptom definitions. High heterogeneity was observed across studies. Conclusions Approximately 39 % of severe Yellow Fever cases are estimated to be fatal. This study provides the first systematic literature review to estimate the CFR of Yellow Fever, which can provide insight into outbreak preparedness and estimating underreporting.

Mortality in Escherichia coli bloodstream infections: a multinational population-based cohort study

Background Escherichia coli is the most common cause of bloodstream infections (BSIs) and mortality is an important aspect of burden of disease. Using a multinational population-based cohort of E. coli BSIs, our objectives were to evaluate 30-day case fatality risk and mortality rate, and determine factors associated with each. Methods During 2014–2018, we identified 30-day deaths from all incident E. coli BSIs from surveillance nationally in Finland, and regionally in Sweden (Skaraborg) and Canada (Calgary, Sherbrooke, western interior). We used a multivariable logistic regression model to estimate factors associated with 30-day case fatality risk. The explanatory variables considered for inclusion were year (2014–2018), region (five areas), age (< 70-years-old, ≥70-years-old), sex (female, male), third-generation cephalosporin (3GC) resistance (susceptible, resistant), and location of onset (community-onset, hospital-onset). The European Union 28-country 2018 population was used to directly age and sex standardize mortality rates. We used a multivariable Poisson model to estimate factors associated with mortality rate, and year, region, age and sex were considered for inclusion. Results From 38.7 million person-years of surveillance, we identified 2961 30-day deaths in 30,923 incident E. coli BSIs. The overall 30-day case fatality risk was 9.6% (2961/30923). Calgary, Skaraborg, and western interior had significantly increased odds of 30-day mortality compared to Finland. Hospital-onset and 3GC-resistant E. coli BSIs had significantly increased odds of mortality compared to community-onset and 3GC-susceptible. The significant association between age and odds of mortality varied with sex, and contrasts were used to interpret this interaction relationship. The overall standardized 30-day mortality rate was 8.5 deaths/100,000 person-years. Sherbrooke had a significantly lower 30-day mortality rate compared to Finland. Patients that were either ≥70-years-old or male both experienced significantly higher mortality rates than those < 70-years-old or female. Conclusions In our study populations, region, age, and sex were significantly associated with both 30-day case fatality risk and mortality rate. Additionally, 3GC resistance and location of onset were significantly associated with 30-day case fatality risk. Escherichia coli BSIs caused a considerable burden of disease from 30-day mortality. When analyzing population-based mortality data, it is important to explore mortality through two lenses, mortality rate and case fatality risk.

Estimating age-specific COVID-19 fatality risk and time to death by comparing population diagnosis and death patterns: Australian data

Background Mortality is a key component of the natural history of COVID-19 infection. Surveillance data on COVID-19 deaths and case diagnoses are widely available in the public domain, but they are not used to model time to death because they typically do not link diagnosis and death at an individual level. This paper demonstrates that by comparing the unlinked patterns of new diagnoses and deaths over age and time, age-specific mortality and time to death may be estimated using a statistical method called deconvolution. Methods Age-specific data were analysed on 816 deaths among 6235 cases over age 50 years in Victoria, Australia, from the period January through December 2020. Deconvolution was applied assuming logistic dependence of case fatality risk (CFR) on age and a gamma time to death distribution. Non-parametric deconvolution analyses stratified into separate age groups were used to assess the model assumptions. Results It was found that age-specific CFR rose from 2.9% at age 65 years (95% CI:2.2 – 3.5) to 40.0% at age 95 years (CI: 36.6 – 43.6). The estimated mean time between diagnosis and death was 18.1 days (CI: 16.9 – 19.3) and showed no evidence of varying by age (heterogeneity P = 0.97). The estimated 90% percentile of time to death was 33.3 days (CI: 30.4 – 36.3; heterogeneity P = 0.85). The final age-specific model provided a good fit to the observed age-stratified mortality patterns. Conclusions Deconvolution was demonstrated to be a powerful analysis method that could be applied to extensive data sources worldwide. Such analyses can inform transmission dynamics models and CFR assessment in emerging outbreaks. Based on these Australian data it is concluded that death from COVID-19 occurs within three weeks of diagnosis on average but takes five weeks in 10% of fatal cases. Fatality risk is negligible in the young but rises above 40% in the elderly, while time to death does not seem to vary by age.

The impact of temperature on the transmission potential and virulence of COVID-19 in Tokyo, Japan

Background Assessing the impact of temperature on COVID-19 epidemiology is critical for implementing non-pharmaceutical interventions. However, few studies have accounted for the nature of contagious diseases, i.e., their dependent happenings. Aim We aimed to quantify the impact of temperature on the transmissibility and virulence of COVID-19 in Tokyo, Japan. We employed two epidemiological measurements of transmissibility and severity: the effective reproduction number (Rt) and case fatality risk (CFR). Methods We used empirical surveillance data and meteorological data in Tokyo to estimate the Rt and time-delay adjusted CFR and to subsequently assess the nonlinear and delay effect of temperature on Rt and time-delay adjusted CFR. Results For Rt at low temperatures, the cumulative relative risk (RR) at first temperature percentile (3.3℃) was 1.3 (95% confidence interval (CI): 1.1-1.7). As for the virulence to humans, moderate cold temperatures were associated with higher CFR, and CFR also increased as the temperature rose. The cumulative RR at the 10th and 99th percentiles of temperature (5.8℃ and 30.8℃) for CFR were 3.5 (95%CI: 1.3-10) and 6.4 (95%CI: 4.1-10.1). Conclusions This study provided information on the effects of temperature on the COVID-19 epidemiology using Rt and time-delay adjusted CFR. Our results suggest the importance to take precautions to avoid infection in both cold and warm seasons to avoid severe cases of COVID-19. The results and proposed framework will also help in assessing possible seasonal course of COVID-19 in the future.

Effect of evidence updates on key determinants of measles vaccination impact: a DynaMICE modelling study in ten high-burden countries

Background Model-based estimates of measles burden and the impact of measles-containing vaccine (MCV) are crucial for global health priority setting. Recently, evidence from systematic reviews and database analyses have improved our understanding of key determinants of measles vaccine impact. We explore how updated representations of these determinants affect model-based estimation of MCV impact in ten countries with highest measles burden. Methods Using Dynamic Measles Immunisation Calculation Engine (DynaMICE), an age-structured compartmental model of measles transmission and vaccination, we evaluated the effect of evidence updates for five determinants of MCV impact: case fatality risk, contact patterns, age-dependent vaccine efficacy, the potential of supplementary immunisation activities (SIAs) to reach zero-dose children, and the basic reproduction number. We also evaluated the incremental impact of the first dose (MCV1), second dose (MCV2), and SIA dose of measles vaccines, based on country-specific coverage estimates from the World Health Organization. The MCV impact was assessed by cumulative vaccine-averted cases, deaths, and disability-adjusted life years over 2000-2050. Results Incorporated with the updated data sources, DynaMICE projected 252 million measles cases, 3.7 million deaths and 230 million disability-adjusted life years incurred over 2000-2050 in the ten high-burden countries when MCV1, MCV2, and SIA doses were implemented. Compared to no vaccination, the administration of MCV1 contributed to 66% reduction in cumulative measles burden, while MCV2 and SIAs reduced this further to 89%. With routine and supplementary vaccination, India and countries with high vaccination coverage could maintain measles incidence below 1 per million. Among the updated determinants, shifting from fixed to linearly-varying vaccine efficacy by age and from static to time-varying case fatality risks had the biggest effect on the model projections of MCV impact. While varying the basic reproduction number showed a limited effect on vaccine-averted burden, updates on the other four determinants together led to an overall reduction of MCV impact by 0.87-26.7%. Conclusions High coverage of measles vaccine through both routine and SIA delivery platforms are essential for achieving and maintaining low incidence in high-measles burden settings. Incorporating updated evidence particularly on vaccine efficacy and case fatality risk reduces estimates of the impact of vaccination slightly, but its overall impact remains considerable.

Delay-Adjusted Age-Specific COVID-19 Case Fatality Rates in a High Testing Setting: South Korea, February 2020 to February 2021

In South Korea, a country with a high coronavirus disease 19 (COVID-19) testing rate, a total of 87,324 COVID-19 cases, including 1562 deaths, have been recorded as of 23 February 2021. This study assessed the delay-adjusted COVID-19 case fatality risk (CFR), including data from the second and third waves. A statistical method was applied to the data from 20 February 2021 through 23 February 2021 to minimize bias in the crude CFR, accounting for the survival interval as the lag time between disease onset and death. The resulting overall delay-adjusted CFR was 1.97% (95% credible interval: 1.94–2.00%). The delay-adjusted CFR was highest among adults aged ≥80 years and 70–79 years (22.88% and 7.09%, respectively). The cumulative incidence rate was highest among individuals aged ≥80 years and 60–69 years. The cumulative mortality rate was highest among individuals aged ≥80 years and 70–79 years (47 and 12 per million, respectively). In South Korea, older adults are being disproportionately affected by COVID-19 with a high death rate, although the incidence rate among younger individuals is relatively high. Interventions to prevent COVID-19 should target older adults to minimize the number of deaths.