Reviewing estimates of the basic reproduction number for dengue, Zika and chikungunya across global climate zones.

BACKGROUND: Globally, dengue, Zika virus, and chikungunya are important viral mosquito-borne diseases that infect millions of people annually. Their geographic range includes not only tropical areas but also sub-tropical and temperate zones such as Japan and Italy. The relative severity of these arboviral disease outbreaks can vary depending on the setting. In this study we explore variation in the epidemiologic potential of outbreaks amongst these climatic zones and arboviruses in order to elucidate potential reasons behind such differences. METHODOLOGY: We reviewed the peer-reviewed literature (PubMed) to obtain basic reproduction number (R0) estimates for dengue, Zika virus, and chikungunya from tropical, sub-tropical and temperate regions. We also computed R0 estimates for temperate and sub-tropical climate zones, based on the outbreak curves in the initial outbreak phase. Lastly we compared these estimates across climate zones, defined by latitude. RESULTS: Of 2115 studies, we reviewed the full text of 128 studies and included 65 studies in our analysis. Our results suggest that the R0 of an arboviral outbreak depends on climate zone, with lower R0 estimates, on average, in temperate zones (R0 = 2.03) compared to tropical (R0 = 3.44) and sub-tropical zones (R0 = 10.29). The variation in R0 was considerable, ranging from 0.16 to 65. The largest R0 was for dengue (65) and was estimated by the Ross-Macdonald model in the tropical zone, whereas the smallest R0 (0.16) was for Zika virus and was estimated statistically from an outbreak curve in the sub-tropical zone. CONCLUSIONS: The results indicate climate zone to be an important determinant of the basic reproduction number, R0, for dengue, Zika virus, and chikungunya. The role of other factors as determinants of R0, such as methods, environmental and social conditions, and disease control, should be further investigated. The results suggest that R0 may increase in temperate regions in response to global warming, and highlight the increasing need for strengthening preparedness and control activities.

Identification of SARS-CoV-2 variants in indoor dust.

Environmental surveillance of pathogens underlying infectious disease is critical to ensure public health. Recent efforts to track SARS-CoV-2 have utilized wastewater sampling to infer community trends in viral abundance and variant composition. Indoor dust has also been used for building-level inferences, though to date no sequencing data providing variant-scale resolution have been reported from dust samples, and strategies to monitor circulating variants in dust are needed to help inform public health decisions. In this study, we demonstrate that SARS-CoV-2 lineages can be detected and sequenced from indoor bulk dust samples. We collected 93 vacuum bags from April 2021 to March 2022 from buildings on The Ohio State University's (OSU) Columbus campus, and the dust was used to develop and apply an amplicon-based whole-genome sequencing protocol to identify the variants present and estimate their relative abundances. Three variants of concern were detected in the dust: Alpha, Delta, and Omicron. Alpha was found in our earliest sample in April 2021 with an estimated frequency of 100%. Delta was the primary variant present from October of 2021 to January 2022, with an average estimated frequency of 91% (±1.3%). Omicron became the primary variant in January 2022 and was the dominant strain in circulation through March with an estimated frequency of 87% (±3.2%). The detection of these variants on OSU's campus correlates with the circulation of these variants in the surrounding population (Delta p<0.0001 and Omicron p = 0.02). Overall, these results support the hypothesis that dust can be used to track COVID-19 variants in buildings.

Global burden for dengue and the evolving pattern in the past 30 years.

BACKGROUND: Dengue is the most prevalent and rapidly spreading mosquito-borne viral disease. We present the global, regional and national burden of dengue from 1990 to 2019 based on the findings from the Global Burden of Diseases, Injuries, and Risk Factors Study 2019 (GBD 2019). METHODS: Based upon GBD 2019 dengue data on age-standardized incidence rate (ASIR), age-standardized death rate (ASDR) and age-standardized disability-adjusted life years (DALYs) rate, this study estimates and presents annual percentage change (EAPC) to quantify trends over time to assess potential correlates of increased dengue activity, such as global travel and warming. RESULTS: Globally from 1990 to 2019, dengue incident cases, deaths and DALYs gradually increased. Those under 5 years of age, once accounting for the largest portion of deaths and DALYs in 1990, were eclipsed by those who were 15-49 years old in 2019. Age standardized incidence [ASIR: EAPC: 3.16, 95% confidence interval (CI): 2.90-3.43], death (ASDR: EAPC: 5.42, 95% CI: 2.64-8.28) and DALY rates (EAPC: 2.31, 95% CI: 2.00-2.62) accelerated most among high-middle and high sociodemographic index (SDI) regions. South-East Asia and South Asia had most of the dengue incident cases, deaths and DALYs, but East Asia had the fastest rise in ASIR (EAPC: 4.57, 95% CI: 4.31, 4.82), while Tropical Latin America led in ASDR (EAPC: 11.32, 95% CI: 9.11, 13.58) and age-standardized DALYs rate (EAPC: 4.13, 95% CI: 2.98, 5.29). SDI showed consistent bell-shaped relationship with ASIR, ASDR and age-standardized DALYs rate. Global land-ocean temperature index and air passenger travel metrics were found to be remarkably positively correlated with dengue burden. CONCLUSIONS: The burden of dengue has become heavier from 1990 to 2019, amidst the three decades of urbanization, warming climates and increased human mobility in much of the world. South-East Asia and South Asia remain as regions of concern, especially in conjunction with the Americas' swift rise in dengue burden.

The evolutionary dynamics of DENV 4 genotype I over a 60-year period.

Dengue virus serotype 4 (DENV 4) has had a relatively low prevalence worldwide for decades; however, likely due to data paucity, no study has investigated the epidemiology and evolutionary dynamics of DENV 4 genotype I (DENV 4-I). This study aims to understand the diversity, epidemiology and dynamics of DENV 4-I. We collected 404 full length DENV4-1 envelope (E) gene sequences from 14 countries using two sources: Yunnan Province in China (15 strains during 2013-2016) and GenBank (489 strains up to 2018-01-11). Conducting phylogenetic and phylogeographical analyses, we estimated the virus spread, population dynamics, and selection pressures using different statistical analysis methods (substitution saturation, likelihood mapping, Bayesian coalescent inference, and maximum likelihood estimation). Our results show that during the last 60 years (1956-2016), DENV 4-I was present in mainland and maritime Southeast Asia, the Indian subcontinent, the southern provinces of China, parts of Brazil and Australia. The recent spread of DENV 4-I likely originated in the Philippines and later spread to Thailand. From Thailand, it spread to adjacent countries and eventually the Indian subcontinent. Apparently diverging around years 1957, 1963, 1976 and 1990, the different Clades (Clade I-V) were defined. The mean overall evolution rate of DENV 4-I was 9.74 (95% HPD: 8.68-10.82) × 10-4 nucleotide substitutions/site/year. The most recent common ancestor for DENV 4-I traces back to 1956. While the demographic history of DENV 4-I fluctuated, peaks appeared around 1982 and 2006. While purifying selection dominated the majority of E-gene evolution of DENV 4-I, positive selection characterized Clade III (Vietnam). DENV 4-I evolved in situ in Southeast Asia and the Indian subcontinent. Thailand and Indian acted as the main and secondary virus distribution hubs globally and regionally. Our phylogenetic analysis highlights the need for strengthened regional cooperation on surveillance and sharing of sample sequences to improve global dengue control and cross-border transmission prevention efforts.

Assessing Greenhouse Gas Emissions and Health Co-Benefits: A Structured Review of Lifestyle-Related Climate Change Mitigation Strategies.

This is the first structured review to identify and summarize research on lifestyle choices that improve health and have the greatest potential to mitigate climate change. Two literature searches were conducted on: (1) active transport health co-benefits, and (2) dietary health co-benefits. Articles needed to quantify both greenhouse gas emissions and health or nutrition outcomes resulting from active transport or diet changes. A data extraction tool (PRISMA) was created for article selection and evaluation. A rubric was devised to assess the biases, limitations and uncertainties of included articles. For active transport 790 articles were retrieved, nine meeting the inclusion criteria. For diet 2524 articles were retrieved, 23 meeting the inclusion criteria. A total of 31 articles were reviewed and assessed using the rubric, as one article met the inclusion criteria for both active transport and diet co-benefits. Methods used to estimate the effect of diet or active transport modification vary greatly precluding meta-analysis. The scale of impact on health and greenhouse gas emissions (GHGE) outcomes depends predominately on the aggressiveness of the diet or active transport scenario modelled, versus the modelling technique. Effective mitigation policies, infrastructure that supports active transport and low GHGE food delivery, plus community engagement are integral in achieving optimal health and GHGE outcomes. Variation in culture, nutritional and health status, plus geographic density will determine which mitigation scenario(s) best suit individual communities.