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.

The emergence of SARS-CoV-2 lineages and associated saliva antibody responses among asymptomatic individuals in a large university community.

SARS-CoV-2 (CoV2) infected, asymptomatic individuals are an important contributor to COVID transmission. CoV2-specific immunoglobulin (Ig)-as generated by the immune system following infection or vaccination-has helped limit CoV2 transmission from asymptomatic individuals to susceptible populations (e.g. elderly). Here, we describe the relationships between COVID incidence and CoV2 lineage, viral load, saliva Ig levels (CoV2-specific IgM, IgA and IgG), and ACE2 binding inhibition capacity in asymptomatic individuals between January 2021 and May 2022. These data were generated as part of a large university COVID monitoring program in Ohio, United States of America, and demonstrate that COVID incidence among asymptomatic individuals occurred in waves which mirrored those in surrounding regions, with saliva CoV2 viral loads becoming progressively higher in our community until vaccine mandates were established. Among the unvaccinated, infection with each CoV2 lineage (pre-Omicron) resulted in saliva Spike-specific IgM, IgA, and IgG responses, the latter increasing significantly post-infection and being more pronounced than N-specific IgG responses. Vaccination resulted in significantly higher Spike-specific IgG levels compared to unvaccinated infected individuals, and uninfected vaccinees' saliva was more capable of inhibiting Spike function. Vaccinees with breakthrough Delta infections had Spike-specific IgG levels comparable to those of uninfected vaccinees; however, their ability to inhibit Spike binding was diminished. These data are consistent with COVID vaccines having achieved hoped-for effects in our community, including the generation of mucosal antibodies that inhibit Spike and lower community viral loads, and suggest breakthrough Delta infections were not due to an absence of vaccine-elicited Ig, but instead limited Spike binding activity in the face of high community viral loads.

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.

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.

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.

Inequalities in Household Catastrophic Health Expenditure and Impoverishment Associated With Noncommunicable Diseases in Chi Linh, Hai Duong, Vietnam.

A costly modern-day double burden, the expenses of noncommunicable diseases (NCDs) are becoming a devastating epidemic. The World Health Organization estimates $7 trillion in economic losses from NCDs in 2011-2025. Although regarded as affluent diseases, the burden of NCDs is shifting into poorer groups. In this study, we assessed the socioeconomic inequalities in catastrophic health expenditure and impoverishment associated with NCDs in Northern Vietnam. We also identified associated factors for catastrophic health expenditure and impoverishment. Households self-reporting NCD diagnoses had the highest association with both catastrophic health expenditure and impoverishment, followed by those in urban areas. Such households were likely poorer according to our calculations estimating socioeconomic inequalities. Households with at least 1 member older than 60 years were also more likely to suffer catastrophic health expenditures. These findings suggest that targeted policy to prevent or subsidize care for NCDs could prevent catastrophic health expenditure and impoverishment among those already most disadvantaged.

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.

Trends in childhood measles vaccination highlight socioeconomic inequalities in Vietnam.

OBJECTIVES: To describe trends in measles vaccine coverage rates and their association with socioeconomic characteristics among children from age 12 to 23 months in Vietnam from the year 2000 to 2014. METHODS: Data were drawn from the Vietnam Multiple Indicator Cluster Surveys in years 2000, 2006, 2011, and 2014. Concentration indices were used to determine the magnitude of socioeconomic inequalities in measles vaccine coverage. Associations between measles vaccine coverage and relevant social factors were assessed using logistic regression. RESULTS: Socioeconomic inequalities in measles vaccine coverage rates decreased during 2000-2014. Children belonging to ethnic minority groups, having mothers with lower education, and belonging to the poorest group were less likely to receive measles vaccine; although, their vaccine coverage rates did increase with time. Measles vaccine coverage declined among children of mothers with more education and belonging to the wealthiest socioeconomic group. CONCLUSIONS: Understanding the social factors influencing adherence to recommend childhood vaccination protocols is essential. Attempts to regain and retain herd immunity must be guided by an understanding of these social factors if they are to succeed.

Estimated global exportations of Zika virus infections via travellers from Brazil from 2014 to 2015.

The ongoing Zika pandemic in Latin America illustrates a potential source for further globalized spread. Here, we assessed global travel-related Zika virus exportations from Brazil during the initial year of the epidemic. Similar to subsequent national notifications, we estimated 584-1786 exported Zika cases from Brazil occurred September 2014-August 2015.

Dissecting Japan's Dengue Outbreak in 2014.

Despite Japan's temperate climate, a dengue outbreak occurred in Tokyo for the first time in over 70 years in 2014. We dissected this dengue outbreak based on phylogenetic analysis, travel interconnectivity, and environmental drivers for dengue epidemics. Comparing the available dengue virus 1 (DENV1) E gene sequence from this outbreak with 3,282 unique DENV1 sequences in National Center for Biotechnology Information suggested that the DENV might have been imported from China, Indonesia, Singapore, or Vietnam. With travelers arriving into Japan, Guangzhou (China) may have been the source of DENV introduction, given that Guangzhou also reported a large-scale dengue outbreak in 2014. Coinciding with the 2014 outbreak, Tokyo's climate conditions permitted the amplification of Aedes vectors and the annual peak of vectorial capacity. Given suitable vectors and climate conditions in addition to increasing interconnectivity with endemic areas of Asia, Tokyo's 2014 outbreak did not come as a surprise and may foretell more to come.

Estimating air travel-associated importations of dengue virus into Italy.

BACKGROUND: Southern Europe is increasingly at risk for dengue emergence, given the seasonal presence of relevant mosquito vectors and suitable climatic conditions. For example, Aedes mosquitoes, the main vector for both dengue and chikungunya, are abundant in Italy, and Italy experienced the first ever outbreak of chikungunya in Europe in 2007. We set out to estimate the extent of dengue virus importations into Italy via air travelers. METHODS: We attempted to quantify the number of dengue virus importations based on modeling of published estimates on dengue incidence in the countries of disembarkation and analysis of data on comprehensive air travel from these countries into Italy's largest international airport in Rome. RESULTS: From 2005 to 2012, more than 7.3 million air passengers departing from 100 dengue-endemic countries arrived in Rome. Our Importation Model, which included air traveler volume, estimated the incidence of dengue infections in the countries of disembarkation, and the probability of infection coinciding with travel accounted for an average of 2,320 (1,621-3,255) imported dengue virus infections per year, of which 572 (381-858) were "apparent" dengue infections and 1,747 (1,240-2,397) "inapparent." CONCLUSIONS: Between 2005 and 2012, we found an increasing trend of dengue virus infections imported into Rome via air travel, which may pose a potential threat for future emergence of dengue in Italy, given that the reoccurring pattern of peak importations corresponds seasonally with periods of relevant mosquito vector activity. The observed increasing annual trends of dengue importation and the consistent peaks in late summer underpin the urgency in determining the threshold levels for the vector and infected human populations that could facilitate novel autochthonous transmission of dengue in Europe.

Epidemiology of dengue: past, present and future prospects.

Dengue is currently regarded globally as the most important mosquito-borne viral disease. A history of symptoms compatible with dengue can be traced back to the Chin Dynasty of 265-420 AD. The virus and its vectors have now become widely distributed throughout tropical and subtropical regions of the world, particularly over the last half-century. Significant geographic expansion has been coupled with rapid increases in incident cases, epidemics, and hyperendemicity, leading to the more severe forms of dengue. Transmission of dengue is now present in every World Health Organization (WHO) region of the world and more than 125 countries are known to be dengue endemic. The true impact of dengue globally is difficult to ascertain due to factors such as inadequate disease surveillance, misdiagnosis, and low levels of reporting. Currently available data likely grossly underestimates the social, economic, and disease burden. Estimates of the global incidence of dengue infections per year have ranged between 50 million and 200 million; however, recent estimates using cartographic approaches suggest this number is closer to almost 400 million. The expansion of dengue is expected to increase due to factors such as the modern dynamics of climate change, globalization, travel, trade, socioeconomics, settlement and also viral evolution. No vaccine or specific antiviral therapy currently exists to address the growing threat of dengue. Prompt case detection and appropriate clinical management can reduce the mortality from severe dengue. Effective vector control is the mainstay of dengue prevention and control. Surveillance and improved reporting of dengue cases is also essential to gauge the true global situation as indicated in the objectives of the WHO Global Strategy for Dengue Prevention and Control, 2012-2020. More accurate data will inform the prioritization of research, health policy, and financial resources toward reducing this poorly controlled disease. The objective of this paper is to review historical and current epidemiology of dengue worldwide and, additionally, reflect on some potential reasons for expansion of dengue into the future.