Epidemiological and ecological determinants of Zika virus transmission in an urban setting

Exploring Zika's dynamics: A scoping review journey from epidemic to equations through mathematical modelling

Zika virus (ZIKV) infection, along with the concurrent circulation of other arboviruses, presents a great public health challenge, reminding the utilization of mathematical modelling as a crucial tool for explaining its intricate dynamics and interactions with co-circulating pathogens. Through a scoping review, we aimed to discern current mathematical models investigating ZIKV dynamics, focusing on its interplay with other pathogens, and to identify underlying assumptions and deficiencies supporting attention, particularly regarding the epidemiological attributes characterizing Zika outbreaks. Following the PRISMA-Sc guidelines, a systematic search across PubMed, Web of Science, and MathSciNet provided 137 pertinent studies from an initial pool of 2446 papers, showing a diversity of modelling approaches, predominantly centered on vector-host compartmental models, with a notable concentration on the epidemiological landscapes of Colombia and Brazil during the 2015-2016 Zika epidemic. While modelling studies have been important in explaining Zika transmission dynamics and their intersections with diseases such as Dengue, Chikungunya, and COVID-19 so far, future Zika models should prioritize robust data integration and rigorous validation against diverse datasets to improve the accuracy and reliability of epidemic prediction. In addition, models could benefit from adaptable frameworks incorporating human behavior, environmental factors, and stochastic parameters, with an emphasis on open-access tools to foster transparency and research collaboration.

Climate, inter-serotype competition and arboviral interactions shape dengue dynamics in Thailand

The incidence and global spread of dengue are reaching alarming levels. Thailand represents a critical disease epicenter and demands an understanding of the environmental and evolutionary pressures that sustain DENV transmission. Unlike most affected countries experiencing recurrent outbreaks of the same serotype or replacement of one serotype for another, Thailand is an ecological niche for all four serotypes. Favorable climate and mosquito vector availability maintain a landscape defined by stable, endemic circulation of genotypes, with minimal genetic variation attributed to sporadic, external introductions. This equilibrium is achieved through inter-serotype competition, characterized by reproductive fitness levels that maintain infections (Re>1) and elevated evolutionary rates ( ~ 10-4), which steadily increase the genetic diversity of each serotype. This conclusion is reinforced by the identification of numerous positively selected mutations, skewed in the direction of non-structural proteins conferring replication and transmission advantages versus those present in structural proteins evading neutralizing antibodies. Precipitous drops in DENV cases following outbreaks of Chikungunya suggest that interactions with other arboviruses also impact DENV dynamics through vector competition, replication inhibition or partial cross-protection. Thailand is a major exporter of DENV cases and novel emergent lineages gaining fitness here are likely to spread internationally. Surveillance is therefore paramount to monitor diversification trends and take measures to avoid the establishment of similar sustained, local transmission in other countries.

A mathematical model of flavescence dorée in grapevines by considering seasonality

This paper presents a mathematical model to describe the spread of flavescence dorée, a disease caused by the bacterium Candidatus Phytoplasma vitis, which is transmitted by the insect vector Scaphoideus titanus in grapevine crops. The key contribution of this work is the derivation of conditions under which positive periodic solutions exist. These conditions are based on the assumption that key factors such as recruitment rates, disease transmission, and vector infectivity vary periodically, thus reflecting seasonal changes. The existence of these periodic solutions is proven using the degree theory, and numerical examples are provided to support the theoretical findings. This model aims to enhance the understanding of the epidemiological dynamics of flavescence dorée and contribute to developing better control strategies to manage the disease in grapevines.

Exploring the urban arbovirus landscape in Rio de Janeiro, Brazil: transmission dynamics and patterns of disease spread

Background

This study focuses on urban arboviruses, specifically dengue (DENV), chikungunya (CHIKV), and Zika (ZIKV), which pose a significant public health challenge in Rio de Janeiro state, Southeast Brazil. In our research, we highlight critical findings on the transmission dynamics of these arboviruses in Rio de Janeiro, identifying distinct patterns of disease spread.

Methods

By combining genomic data with case reports from the Brazilian Ministry of Health, we have analysed the phylogenetics, prevalence and spatial distribution of these endemic viruses within the state.

Findings

Our results revealed sustained DENV transmission primarily in the northern part of the state, a significant ZIKV epidemic in 2016 affecting all mesoregions, and two major CHIKV outbreaks in 2018 and 2019, predominantly impacting the northern and southern areas. Our analysis suggests an inverse relationship between arboviral case incidence and urban density, with less populous regions experiencing higher transmission rates, potentially attributed to a complex interplay of factors such as the efficacy of vector control measures, environmental conditions, local immunity levels, and human mobility. Furthermore, our investigation unveiled distinct age and gender trends among affected individuals. Notably, dengue cases were predominantly observed in young adults aged 32, while chikungunya cases were more prevalent among individuals over 41. In contrast, cases of ZIKV were concentrated around the 33-year age group. Intriguingly, females accounted for nearly 60% of the cases, suggesting a potential gender-based difference in infection rates.

Interpretation

Our findings underscore the complexity of arbovirus transmission and the need for interventions tailored to different geographical mesoregions. Enhanced surveillance and genomic sequencing will be essential for a deeper, more nuanced understanding of regional arbovirus dynamics. Identifying potential blind spots within the state will be pivotal for developing and implementing more effective public health strategies, specifically designed to address the unique challenges posed by these viruses throughout the state.

Funding

This study was supported by the National Institutes of Health USA grant U01 AI151698 for the United World Arbovirus Research Network (UWARN) and the CRP-ICGEB RESEARCH GRANT 2020 Project CRP/BRA20-03.

Resurgence of Dengue Virus Serotype 3 in Minas Gerais, Brazil: A Case Report

This report provides a detailed overview of the resurgence of DENV-3 in the state of Minas Gerais, Brazil, which is a concerning scenario in the context of dengue, a mosquito-borne viral disease. Historically, Brazil has grappled with dengue epidemics caused primarily by the DENV-1 and DENV-2 serotypes. However, in 2023, a significant shift in this pattern was observed as DENV-3 made a notable resurgence. This resurgence was characterized by the increase in DENV-3 cases within the country and the region of the Americas. Given the absence of sustained DENV-3 circulation in Brazil in previous years, this situation poses a significant risk, making the population highly susceptible to a potential novel epidemic. In November 2023, a 31-year-old male patient in Belo Horizonte exhibited symptoms of acute febrile syndrome. Multiplex RT-qPCR using the Kit Molecular ZC D-Tipagem confirmed DENV-3 infection, suggesting a likely autochthonous case, as the patient reported no travel history. To promptly assess this resurgence, we applied the nanopore sequencing technology. This allowed for the rapid characterization of the initial DENV-3 case isolated in Minas Gerais in 2023, representing a 13-year interval since the serotype's previous documented circulation in that state. This case report underscores the critical importance of proactive monitoring and the swift implementation of targeted control strategies to address the evolving dynamics of dengue, with a specific emphasis on the resurgence of DENV-3 in the state.

Shifting patterns of dengue three years after Zika virus emergence in Brazil

In 2015, the Zika virus (ZIKV) emerged in Brazil, leading to widespread outbreaks in Latin America. Following this, many countries in these regions reported a significant drop in the circulation of dengue virus (DENV), which resurged in 2018-2019. We examine age-specific incidence data to investigate changes in DENV epidemiology before and after the emergence of ZIKV. We observe that incidence of DENV was concentrated in younger individuals during resurgence compared to 2013-2015. This trend was more pronounced in Brazilian states that had experienced larger ZIKV outbreaks. Using a mathematical model, we show that ZIKV-induced cross-protection alone, often invoked to explain DENV decline across Latin America, cannot explain the observed age-shift without also assuming some form of disease enhancement. Our results suggest that a sudden accumulation of population-level immunity to ZIKV could suppress DENV and reduce the mean age of DENV incidence via both protective and disease-enhancing interactions.

Genomic epidemiology unveils the dynamics and spatial corridor behind the Yellow Fever virus outbreak in Southern Brazil

Despite the considerable morbidity and mortality of yellow fever virus (YFV) infections in Brazil, our understanding of disease outbreaks is hampered by limited viral genomic data. Here, through a combination of phylogenetic and epidemiological models, we reconstructed the recent transmission history of YFV within different epidemic seasons in Brazil. A suitability index based on the highly domesticated Aedes aegypti was able to capture the seasonality of reported human infections. Spatial modeling revealed spatial hotspots with both past reporting and low vaccination coverage, which coincided with many of the largest urban centers in the Southeast. Phylodynamic analysis unraveled the circulation of three distinct lineages and provided proof of the directionality of a known spatial corridor that connects the endemic North with the extra-Amazonian basin. This study illustrates that genomics linked with eco-epidemiology can provide new insights into the landscape of YFV transmission, augmenting traditional approaches to infectious disease surveillance and control.

Global transmission suitability maps for dengue virus transmitted by Aedes aegypti from 1981 to 2019

Mosquito-borne viruses increasingly threaten human populations due to accelerating changes in climate, human and mosquito migration, and land use practices. Over the last three decades, the global distribution of dengue has rapidly expanded, causing detrimental health and economic problems in many areas of the world. To develop effective disease control measures and plan for future epidemics, there is an urgent need to map the current and future transmission potential of dengue across both endemic and emerging areas. Expanding and applying Index P, a previously developed mosquito-borne viral suitability measure, we map the global climate-driven transmission potential of dengue virus transmitted by Aedes aegypti mosquitoes from 1981 to 2019. This database of dengue transmission suitability maps and an R package for Index P estimations are offered to the public health community as resources towards the identification of past, current and future transmission hotspots. These resources and the studies they facilitate can contribute to the planning of disease control and prevention strategies, especially in areas where surveillance is unreliable or non-existent.

Mosquito vector competence for dengue is modulated by insect-specific viruses

Aedes aegypti and A. albopictus mosquitoes are the main vectors for dengue virus (DENV) and other arboviruses, including Zika virus (ZIKV). Understanding the factors that affect transmission of arboviruses from mosquitoes to humans is a priority because it could inform public health and targeted interventions. Reasoning that interactions among viruses in the vector insect might affect transmission, we analysed the viromes of 815 urban Aedes mosquitoes collected from 12 countries worldwide. Two mosquito-specific viruses, Phasi Charoen-like virus (PCLV) and Humaita Tubiacanga virus (HTV), were the most abundant in A. aegypti worldwide. Spatiotemporal analyses of virus circulation in an endemic urban area revealed a 200% increase in chances of having DENV in wild A. aegypti mosquitoes when both HTV and PCLV were present. Using a mouse model in the laboratory, we showed that the presence of HTV and PCLV increased the ability of mosquitoes to transmit DENV and ZIKV to a vertebrate host. By transcriptomic analysis, we found that in DENV-infected mosquitoes, HTV and PCLV block the downregulation of histone H4, which we identify as an important proviral host factor in vivo.

Dynamic Hybrid Model to Forecast the Spread of COVID-19 Using LSTM and Behavioral Models Under Uncertainty

To accurately predict the regional spread of coronavirus disease 2019 (COVID-19) infection, this study proposes a novel hybrid model, which combines a long short-term memory (LSTM) artificial recurrent neural network with dynamic behavioral models. Several factors and control strategies affect the virus spread, and the uncertainty arising from confounding variables underlying the spread of the COVID-19 infection is substantial. The proposed model considers the effect of multiple factors to enhance the accuracy in predicting the number of cases and deaths across the top ten most-affected countries at the time of the study. The results show that the proposed model closely replicates the test data, such that not only it provides accurate predictions but it also replicates the daily behavior of the system under uncertainty. The hybrid model outperforms the LSTM model while accounting for data limitation. The parameters of the hybrid models are optimized using a genetic algorithm for each country to improve the prediction power while considering regional properties. Since the proposed model can accurately predict the short-term to medium-term daily spreading of the COVID-19 infection, it is capable of being used for policy assessment, planning, and decision making.

Climate-driven mosquito-borne viral suitability index: measuring risk transmission of dengue, chikungunya and Zika in Mexico

Background

Climate variability influences the population dynamics of the Aedes aegypti mosquito that transmits the viruses that cause dengue, chikungunya and Zika. In recent years these diseases have grown considerably. Dengue is now the fastest-growing mosquito-transmitted disease worldwide, putting 40 per cent of the global population at risk. With no effective antiviral treatments or vaccines widely available, controlling mosquito population remains one of the most effective ways to prevent epidemics. This paper analyses the temporal and spatial dynamics of dengue in Mexico during 2000–2020 and that of chikungunya and Zika since they first appeared in the country in 2014 and 2015, respectively. This study aims to evaluate how seasonal climatological variability affects the potential risk of transmission of these mosquito-borne diseases. Mexico is among the world’s most endemic countries in terms of dengue. Given its high incidence of other mosquito-borne diseases and its size and wide range of climates, it is a good case study.

Methods

We estimate the recently proposed mosquito-borne viral suitability index P, which measures the transmission potential of mosquito-borne pathogens. This index mathematically models how humidity, temperature and precipitation affect the number of new infections generated by a single infected adult female mosquito in a host population. We estimate this suitability index across all Mexico, at small-area level, on a daily basis during 2000–2020.

Results

We find that the index P predicted risk transmission is strongly correlated with the areas and seasons with a high incidence of dengue within the country. This correlation is also high enough for chikungunya and Zika in Mexico. We also show the index P is sensitive to seasonal climatological variability, including extreme weather shocks.

Conclusions

The paper shows the dynamics of dengue, chikungunya and Zika in Mexico are strongly associated with seasonal climatological variability and the index P. This potential risk of transmission index, therefore, is a valuable tool for surveillance for mosquito-borne diseases, particularly in settings with varied climates and limited entomological capacity.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12942-022-00317-0.

Prospective surveillance of Zika virus at the end of the Americas’ outbreak: An unexpected outcome

Objective

The French Polynesia Zika virus (ZIKV) outbreak (2013–2014) broadened the known manifestations of ZIKV disease (ZVD) to include neural and congenital syndromes. A subsequent epidemic in the Americas (2015–2016) caused >685,000 suspected/confirmed cases before seemingly disappearing as fast as it expanded. A study was implemented (2017–2018) to detect ZVD cases in the region (Mexico, Honduras, Colombia and Puerto Rico), with the aim of validating surveillance methodology so as to increase sensitivity in case detection, which would have potential application for future vaccine development endeavors.

Study design and setting

To identify potential cases, we focused on signs/symptoms that were frequently associated with ZVD for confirmation by PCR. Serostatus and seroconversion were evaluated by ZIKV non-structural protein 1 blockade-of-binding enzyme-linked immunosorbent assay (BOB ELISA) and microneutralization assay.

Results

Overall, 2,400 participants aged 15–40 years were enrolled; 959 (40.0%) had signs/symptoms that could be associated with ZVD: axillary temperature ≥37°C (64.3%), myalgia (60.8%) and arthralgia (58.6%). Three suspected cases were virologically confirmed. Zika seroprevalence was high at study initiation (52.6% [BOB ELISA] and 56.0% [microneutralization assay]). In participants who were Zika seronegative, low seroconversion rates were observed after one year follow-up (3.6% [BOB ELISA] and 3.1% [microneutralization assay]).

Conclusion

The ZIKV continued to circulate in the Americas at very low levels following the 2015–2016 outbreak. The epidemiological factors driving Zika’s rapid rise and decline remain poorly understood.

Clinical trial registration

Clinicaltrials.gov: NCT03158233 BARDA (Contract # HHSO100201600039C) WHO Universal Trial Number: U1111-1183-5687.

Spatio-temporal clusters and patterns of spread of dengue, chikungunya, and Zika in Colombia

Background

Colombia has one of the highest burdens of arboviruses in South America. The country was in a state of hyperendemicity between 2014 and 2016, with co-circulation of several Aedes-borne viruses, including a syndemic of dengue, chikungunya, and Zika in 2015.

Methodology/Principal findings

We analyzed the cases of dengue, chikungunya, and Zika notified in Colombia from January 2014 to December 2018 by municipality and week. The trajectory and velocity of spread was studied using trend surface analysis, and spatio-temporal high-risk clusters for each disease in separate and for the three diseases simultaneously (multivariate) were identified using Kulldorff’s scan statistics. During the study period, there were 366,628, 77,345 and 74,793 cases of dengue, chikungunya, and Zika, respectively, in Colombia. The spread patterns for chikungunya and Zika were similar, although Zika’s spread was accelerated. Both chikungunya and Zika mainly spread from the regions on the Atlantic coast and the south-west to the rest of the country. We identified 21, 16, and 13 spatio-temporal clusters of dengue, chikungunya and Zika, respectively, and, from the multivariate analysis, 20 spatio-temporal clusters, among which 7 were simultaneous for the three diseases. For all disease-specific analyses and the multivariate analysis, the most-likely cluster was identified in the south-western region of Colombia, including the Valle del Cauca department.

Conclusions/Significance

The results further our understanding of emerging Aedes-borne diseases in Colombia by providing useful evidence on their potential site of entry and spread trajectory within the country, and identifying spatio-temporal disease-specific and multivariate high-risk clusters of dengue, chikungunya, and Zika, information that can be used to target interventions.

Dengue, chikungunya, and Zika are diseases transmitted to humans by the bite of infected Aedes mosquitoes. Between 2014 and 2016 chikungunya and Zika viruses started causing outbreaks in Colombia, one of the countries historically most affected by dengue. We used case counts of the diseases by municipality and week to study the spread trajectory of chikungunya and Zika within Colombia’s territory, and to identify space-time high-risk clusters, i.e., the areas and time periods that dengue, chikungunya, and Zika were more present. Chikungunya and Zika spread similarly in Colombia, but Zika spread faster. The Atlantic coast, a famous touristic destination in the country, was likely the place of entry of chikungunya and Zika in Colombia. The south-western region was identified as a high-risk cluster for all three diseases in separate and simultaneously. This region has a favorable climate for the Aedes mosquitoes and other characteristics that facilitate the diseases’ transmission, such as social deprivation and high population mobility. Our results provide useful information on the locations that should be prioritized for interventions to prevent the entry of new diseases transmitted by Aedes and to reduce the burden of dengue, chikungunya and Zika where they are established.

Model-Based Projection of Zika Infection Risk with Temperature Effect: A Case Study in Southeast Asia

Zika virus (ZIKV) recently reemerged in the Americas and rapidly expanded in global range. It is posing significant concerns of public health due to its link to birth defects and its complicated transmission routes. Southeast Asia is badly hit by ZIKV, but limited information was found on the transmission potential of ZIKV in the region. In this paper, we develop a new dynamic process-based mathematical model, which incorporates the interactions among humans (sexual transmissibility), and between human and mosquitoes (biting transmissibility), as well as the essential impacts of temperature. The model is first validated by fitting the 2016 ZIKV outbreak in Singapore via Markov chain Monte Carlo method. Based on that, we demonstrate the effects of temperature on mosquito ecology and ZIKV transmission, and further clarify the potential risk of ZIKV outbreak in Southeast Asian countries. The results show that (i) the estimated infection reproduction number [Formula: see text] in Singapore fell from 6.93 (in which the contribution of sexual transmission was 0.89) to 0.24 after the deployment of control strategies; (ii) the optimal temperature for the reproduction of ZIKV infections and adult mosquitoes are estimated to be [Formula: see text]C and [Formula: see text]C, respectively; and (iii) the [Formula: see text] in Southeast Asia could be between 3 and 7, with an inverted-U shape around the year. The large values of [Formula: see text] and the simulative patterns of ZIKV transmission in each country highlights the high risk of ZIKV attack in Southeast Asia.

A Retrospective Overview of Zika Virus Evolution in the Midwest of Brazil

Since the introduction of the Zika virus (ZIKV) into Brazil in 2015, its transmission dynamics have been intensively studied in many parts of the country, although much is still unknown about its circulation in the midwestern states. Here, using nanopore technology, we obtained 23 novel partial and near-complete ZIKV genomes from the state of Goiás, located in the Midwest of Brazil. Genomic, phylogenetic, and epidemiological approaches were used to retrospectively explore the spatiotemporal evolution of the ZIKV-Asian genotype in this region. As a likely consequence of a gradual accumulation of herd immunity, epidemiological data revealed a decline in the number of reported cases over 2018 to 2021. Phylogenetic reconstructions revealed that multiple independent introductions of the Asian lineage have occurred in Goiás over time and revealed a complex transmission dynamic between epidemic seasons. Together, our results highlight the utility of genomic, epidemiological, and evolutionary methods to understand mosquito-borne epidemics. IMPORTANCE Despite the considerable morbidity and mortality of arboviral infections in Brazil, such as Zika, chikungunya, dengue fever, and yellow fever, our understanding of these outbreaks is hampered by the limited availability of genomic data to track and control the epidemic. In this study, we provide a retrospective reconstruction of the Zika virus transmission dynamics in the state of Goiás by analyzing genomic data from areas in Midwest Brazil not covered by other previous studies. Our study provides an understanding of how ZIKV initiates transmission in this region and reveals a complex transmission dynamic between epidemic seasons. Together, our results highlight the utility of genomic, epidemiological, and evolutionary methods to understand mosquito-borne epidemics, revealing how this toolkit can be used to help policymakers prioritize areas to be targeted, especially in the context of finite public health resources.

Facilidades e dificuldades na promoção do direito à saúde de crianças com síndrome congênita do zika

Objetivo: descrever as facilidades e dificuldades na promoção do direito à saúde de crianças com síndrome congênita do vírus zika (SCZ). Materiais e métodos: estudo qualitativo realizado nos serviços onde as crianças com SCZ são acompanhadas, no município de Feira de Santana, Bahia, Brasil. Para a coleta de dados, foram utilizadas a entrevista semiestruturada e a observação sistemática. Os participantes foram constituídos de três grupos: grupo I (sete responsáveis das crianças com SCZ); grupo II (seis profissionais de saúde e dos serviços sociais) e grupo III (oito gestores dos serviços de saúde). Utilizou-se a análise de conteúdo temática. Resultados: emergiram duas categorias empíricas: Facilidades na promoção do direito à saúde, que diz respeito ao direito à saúde ser uma garantia legal, à existência de profissionais comprometidos, ao acesso à informação, à priorização do acesso, à disponibilização de transporte e à existência de uma rede de apoio familiar; Dificuldades na promoção do direito à saúde, que foram a demanda/procura por serviços/consultas/exames ser maior que a oferta, o tempo destinado para as atividades de estimulação precoce e a sua frequência de realização ser menor que a necessária, a inexistência de um espaço de referência para o atendimento interprofissional, a inclusão escolar, o transporte insuficiente, a aquisição de cadeira de rodas, órteses e próteses. Conclusões: a descrição das facilidades e dificuldades na promoção do direito à saúde de crianças com SCZ poderá contribuir para o acesso aos serviços e às práticas de saúde, mediante uma política de saúde efetiva e adequada à realidade apresentada, colaborando para uma maior qualidade de vida.

West Nile virus transmission potential in Portugal

It is unclear whether West Nile virus (WNV) circulates endemically in Portugal. Despite the country’s adequate climate for transmission, Portugal has only reported four human WNV infections so far. We performed a review of WNV-related data (1966–2020), explored mosquito (2016–2019) and land type distributions (1992–2019), and used climate data (1981–2019) to estimate WNV transmission suitability in Portugal. Serological and molecular evidence of WNV circulation from animals and vectors was largely restricted to the south. Land type and climate-driven transmission suitability distributions, but not the distribution of WNV-capable vectors, were compatible with the North-South divide present in serological and molecular evidence of WNV circulation. Our study offers a comprehensive, data-informed perspective and review on the past epidemiology, surveillance and climate-driven transmission suitability of WNV in Portugal, highlighting the south as a subregion of importance. Given the recent WNV outbreaks across Europe, our results support a timely change towards local, active surveillance.

Lourenço et al. review historical data and quantify the transmission potential of West Nile virus in Portugal. They report a North-South divide in infection patterns, a higher ecological capacity in the south, and an increasing positive effect of climate change over the last 40 years.

Is there a relationship between industrial clusters and the prevalence of COVID-19 in the provinces of Morocco?

The main objective of this paper is to verify if there is a relationship between industrial agglomeration and the prevalence of COVID-19 and its diffusion within and between the provinces of Morocco. To do so, we used spatial exploratory analysis and spatial econometrics to show that the preponderance of industrial activity in a province has a significant effect on the number of active COVID-19 cases in that province. On the other hand, we have shown that the spatial diffusion of this effect is not significant, which indicates the appropriateness of the lockdown implemented. We have also shown that age, socio-economic deficits and habitat conditions are not significant determinants in the onset and spread of the pandemic.

Is the ZIKV Congenital Syndrome and Microcephaly Due to Syndemism with Latent Virus Coinfection?

The emergence of the Zika virus (ZIKV) mirrors its evolutionary nature and, thus, its ability to grow in diversity or complexity (i.e., related to genome, host response, environment changes, tropism, and pathogenicity), leading to it recently joining the circle of closed congenital pathogens. The causal relation of ZIKV to microcephaly is still a much-debated issue. The identification of outbreak foci being in certain endemic urban areas characterized by a high-density population emphasizes that mixed infections might spearhead the recent appearance of a wide range of diseases that were initially attributed to ZIKV. Globally, such coinfections may have both positive and negative effects on viral replication, tropism, host response, and the viral genome. In other words, the possibility of coinfection may necessitate revisiting what is considered to be known regarding the pathogenesis and epidemiology of ZIKV diseases. ZIKV viral coinfections are already being reported with other arboviruses (e.g., chikungunya virus (CHIKV) and dengue virus (DENV)) as well as congenital pathogens (e.g., human immunodeficiency virus (HIV) and cytomegalovirus (HCMV)). However, descriptions of human latent viruses and their impacts on ZIKV disease outcomes in hosts are currently lacking. This review proposes to select some interesting human latent viruses (i.e., herpes simplex virus 2 (HSV-2), Epstein-Barr virus (EBV), human herpesvirus 6 (HHV-6), human parvovirus B19 (B19V), and human papillomavirus (HPV)), whose virological features and co-exposition with ZIKV may provide evidence of the syndemism process, shedding some light on the emergence of the ZIKV-induced global congenital syndrome in South America.

Seroprevalence of Chikungunya virus and living conditions in Feira de Santana, Bahia-Brazil

BACKGROUND

Chikungunya is an arbovirus, transmitted by Aedes mosquitoes, which emerged in the Americas in 2013 and spread rapidly to almost every country on this continent. In Brazil, where the first cases were detected in 2014, it currently has reached all regions of this country and more than 900,000 cases were reported. The clinical spectrum of chikungunya ranges from an acute self-limiting form to disabling chronic forms. The purpose of this study was to estimate the seroprevalence of chikungunya infection in a large Brazilian city and investigate the association between viral circulation and living condition.

METHODOLOGY/PRINCIPAL FINDINGS

We conducted a population-based ecological study in selected Sentinel Areas (SA) through household interviews and a serologic survey in 2016/2017. The sample was of 1,981 individuals randomly selected. The CHIKV seroprevalence was 22.1% (17.1 IgG, 2.3 IgM, and 1.4 IgG and IgM) and varied between SA from 2.0% to 70.5%. The seroprevalence was significantly lower in SA with high living conditions compared to SA with low living condition. There was a positive association between CHIKV seroprevalence and population density (r = 0.2389; p = 0.02033).

CONCLUSIONS/SIGNIFICANCE

The seroprevalence in this city was 2.6 times lower than the 57% observed in a study conducted in the epicentre of the CHIKV epidemic of this same urban centre. So, the herd immunity in this general population, after four years of circulation of this agent is relatively low. It indicates that CHIKV transmission may persist in that city, either in endemic form or in the form of a new epidemic, because the vector infestation is persistent. Besides, the significantly lower seroprevalences in SA of higher Living Condition suggest that beyond the surveillance of the disease, vector control and specific actions of basic sanitation, the reduction of the incidence of this infection also depends on the improvement of the general living conditions of the population.

Interactions between timing and transmissibility explain diverse flavivirus dynamics in Fiji

Zika virus (ZIKV) has caused large, brief outbreaks in isolated populations, however ZIKV can also persist at low levels over multiple years. The reasons for these diverse transmission dynamics remain poorly understood. In Fiji, which has experienced multiple large single-season dengue epidemics, there was evidence of multi-year transmission of ZIKV between 2013 and 2017. To identify factors that could explain these differences in dynamics between closely related mosquito-borne flaviviruses, we jointly fit a transmission dynamic model to surveillance, serological and molecular data. We estimate that the observed dynamics of ZIKV were the result of two key factors: strong seasonal effects, which created an ecologically optimal time of year for outbreaks; and introduction of ZIKV after this optimal time, which allowed ZIKV transmission to persist over multiple seasons. The ability to jointly fit to multiple data sources could help identify a similar range of possible outbreak dynamics in other settings.

Real-time seroprevalence and exposure levels of emerging pathogens in infection-naive host populations

For endemic pathogens, seroprevalence mimics overall exposure and is minimally influenced by the time that recent infections take to seroconvert. Simulating spatially-explicit and stochastic outbreaks, we set out to explore how, for emerging pathogens, the mix of exponential growth in infection events and a constant rate for seroconversion events could lead to real-time significant differences in the total numbers of exposed versus seropositive. We find that real-time seroprevalence of an emerging pathogen can underestimate exposure depending on measurement time, epidemic doubling time, duration and natural variation in the time to seroconversion among hosts. We formalise mathematically how underestimation increases non-linearly as the host's time to seroconversion is ever longer than the pathogen's doubling time, and how more variable time to seroconversion among hosts results in lower underestimation. In practice, assuming that real-time seroprevalence reflects the true exposure to emerging pathogens risks overestimating measures of public health importance (e.g. infection fatality ratio) as well as the epidemic size of future waves. These results contribute to a better understanding and interpretation of real-time serological data collected during the emergence of pathogens in infection-naive host populations.

Genomic and Epidemiological Surveillance of Zika Virus in the Amazon Region

Zika virus (ZIKV) has caused an explosive epidemic linked to severe clinical outcomes in the Americas. As of June 2018, 4,929 ZIKV suspected infections and 46 congenital syndrome cases had been reported in Manaus, Amazonas, Brazil. Although Manaus is a key demographic hub in the Amazon region, little is known about the ZIKV epidemic there, in terms of both transmission and viral genetic diversity. Using portable virus genome sequencing, we generated 59 ZIKV genomes in Manaus. Phylogenetic analyses indicated multiple introductions of ZIKV from northeastern Brazil to Manaus. Spatial genomic analysis of virus movement among six areas in Manaus suggested that populous northern neighborhoods acted as sources of virus transmission to other neighborhoods. Our study revealed how the ZIKV epidemic was ignited and maintained within the largest urban metropolis in the Amazon. These results might contribute to improving the public health response to outbreaks in Brazil.

Co-circulation and misdiagnosis led to underestimation of the 2015-2017 Zika epidemic in the Americas

During the 2015-2017 Zika epidemic, dengue and chikungunya-two other viral diseases with the same vector as Zika-were also in circulation. Clinical presentation of these diseases can vary from person to person in terms of symptoms and severity, making it difficult to differentially diagnose them. Under these circumstances, it is possible that numerous cases of Zika could have been misdiagnosed as dengue or chikungunya, or vice versa. Given the importance of surveillance data for informing epidemiological analyses, our aim was to quantify the potential extent of misdiagnosis during this epidemic. Using basic principles of probability and empirical estimates of diagnostic sensitivity and specificity, we generated revised estimates of reported cases of Zika that accounted for the accuracy of diagnoses made on the basis of clinical presentation with or without laboratory confirmation. Applying this method to weekly reported case data from 43 countries throughout Latin America and the Caribbean, we estimated that 944,700 (95% CrI: 884,900-996,400) Zika cases occurred when assuming all confirmed cases were diagnosed using molecular methods versus 608,400 (95% CrI: 442,000-821,800) Zika cases that occurred when assuming all confirmed cases were diagnosed using serological methods. Our results imply that misdiagnosis was more common in countries with proportionally higher reported cases of dengue and chikungunya, such as Brazil. Given that Zika, dengue, and chikungunya appear likely to co-circulate in the Americas and elsewhere for years to come, our methodology has the potential to enhance the interpretation of passive surveillance data for these diseases going forward. Likewise, our methodology could also be used to help resolve transmission dynamics of other co-circulating diseases with similarities in symptomatology and potential for misdiagnosis.

Characterising West Nile virus epidemiology in Israel using a transmission suitability index

Background

Climate is a major factor in the epidemiology of West Nile virus (WNV), a pathogen increasingly pervasive worldwide. Cases increased during 2018 in Israel, the United States and Europe.

Aim

We set to retrospectively understand the spatial and temporal determinants of WNV transmission in Israel, as a case study for the possible effects of climate on virus spread.

Methods

We employed a suitability index to WNV, parameterising it with prior knowledge pertaining to a bird reservoir and Culex species, using local time series of temperature and humidity as inputs. The predicted suitability index was compared with confirmed WNV cases in Israel (2016–2018).

Results

The suitability index was highly associated with WNV cases in Israel, with correlation coefficients of 0.91 (p value = 4 × 10^− 5), 0.68 (p = 0.016) and 0.9 (p = 2 × 10^− 4) in 2016, 2017 and 2018, respectively. The fluctuations in the number of WNV cases between the years were explained by higher area under the index curve. A new WNV seasonal mode was identified in the south-east of Israel, along the Great Rift Valley, characterised by two yearly peaks (spring and autumn), distinct from the already known single summer peak in the rest of Israel.

Conclusions

By producing a detailed geotemporal estimate of transmission potential and its determinants in Israel, our study promotes a better understanding of WNV epidemiology and has the potential to inform future public health responses. The proposed approach further provides opportunities for retrospective and prospective mechanistic modelling of WNV epidemiology and its associated climatic drivers.

Asynchronicity of endemic and emerging mosquito-borne disease outbreaks in the Dominican Republic

Mosquito-borne viruses threaten the Caribbean due to the region's tropical climate and seasonal reception of international tourists. Outbreaks of chikungunya and Zika have demonstrated the rapidity with which these viruses can spread. Concurrently, dengue fever cases have climbed over the past decade. Sustainable disease control measures are urgently needed to quell virus transmission and prevent future outbreaks. Here, to improve upon current control methods, we analyze temporal and spatial patterns of chikungunya, Zika, and dengue outbreaks reported in the Dominican Republic between 2012 and 2018. The viruses that cause these outbreaks are transmitted by Aedes mosquitoes, which are sensitive to seasonal climatological variability. We evaluate whether climate and the spatio-temporal dynamics of dengue outbreaks could explain patterns of emerging disease outbreaks. We find that emerging disease outbreaks were robust to the climatological and spatio-temporal constraints defining seasonal dengue outbreak dynamics, indicating that constant surveillance is required to prevent future health crises.

Mapping the cryptic spread of the 2015-2016 global Zika virus epidemic

BACKGROUND

Zika virus (ZIKV) emerged as a global epidemic in 2015-2016 from Latin America with its true geographical extent remaining unclear due to widely presumed underreporting. The identification of locations with potential and unknown spread of ZIKV is a key yet understudied component for outbreak preparedness. Here, we aim to identify locations at a high risk of cryptic ZIKV spread during 2015-2016 to further the understanding of the global ZIKV epidemiology, which is critical for the mitigation of the risk of future epidemics.

METHODS

We developed an importation simulation model to estimate the weekly number of ZIKV infections imported in each susceptible spatial unit (i.e. location that did not report any autochthonous Zika cases during 2015-2016), integrating epidemiological, demographic, and travel data as model inputs. Thereafter, a global risk model was applied to estimate the weekly ZIKV transmissibility during 2015-2016 for each location. Finally, we assessed the risk of onward ZIKV spread following importation in each susceptible spatial unit to identify locations with a high potential for cryptic ZIKV spread during 2015-2016.

RESULTS

We have found 24 susceptible spatial units that were likely to have experienced cryptic ZIKV spread during 2015-2016, of which 10 continue to have a high risk estimate within a highly conservative scenario, namely, Luanda in Angola, Banten in Indonesia, Maharashtra in India, Lagos in Nigeria, Taiwan and Guangdong in China, Dakar in Senegal, Maputo in Mozambique, Kinshasa in Congo DRC, and Pool in Congo. Notably, among the 24 susceptible spatial units identified, some have reported their first ZIKV outbreaks since 2017, thus adding to the credibility of our results (derived using 2015-2016 data only).

CONCLUSION

Our study has provided valuable insights into the potentially high-risk locations for cryptic ZIKV circulation during the 2015-2016 pandemic and has also laid a foundation for future studies that attempt to further narrow this key knowledge gap. Our modelling framework can be adapted to identify areas with likely unknown spread of other emerging vector-borne diseases, which has important implications for public health readiness especially in resource-limited settings.

Leveraging multiple data types to estimate the size of the Zika epidemic in the Americas

Several hundred thousand Zika cases have been reported across the Americas since 2015. Incidence of infection was likely much higher, however, due to a high frequency of asymptomatic infection and other challenges that surveillance systems faced. Using a hierarchical Bayesian model with empirically-informed priors, we leveraged multiple types of Zika case data from 15 countries to estimate subnational reporting probabilities and infection attack rates (IARs). Zika IAR estimates ranged from 0.084 (95% CrI: 0.067-0.096) in Peru to 0.361 (95% CrI: 0.214-0.514) in Ecuador, with significant subnational variability in every country. Totaling infection estimates across these and 33 other countries and territories, our results suggest that 132.3 million (95% CrI: 111.3-170.2 million) people in the Americas had been infected by the end of 2018. These estimates represent the most extensive attempt to determine the size of the Zika epidemic in the Americas, offering a baseline for assessing the risk of future Zika epidemics in this region.

Inferring change points in the spread of COVID-19 reveals the effectiveness of interventions

As coronavirus disease 2019 (COVID-19) is rapidly spreading across the globe, short-term modeling forecasts provide time-critical information for decisions on containment and mitigation strategies. A major challenge for short-term forecasts is the assessment of key epidemiological parameters and how they change when first interventions show an effect. By combining an established epidemiological model with Bayesian inference, we analyzed the time dependence of the effective growth rate of new infections. Focusing on COVID-19 spread in Germany, we detected change points in the effective growth rate that correlate well with the times of publicly announced interventions. Thereby, we could quantify the effect of interventions and incorporate the corresponding change points into forecasts of future scenarios and case numbers. Our code is freely available and can be readily adapted to any country or region.

Spatial distribution of the relative risk of Zika virus disease in Colombia during the 2015-2016 epidemic from a Bayesian approach

Objective

To determine the spatial distribution of the risk of Zika virus disease in each region of Colombia during the 2015–2016 epidemic.

Methods

An ecological study was designed to estimate the risks for each Colombian region using first‐order neighbors, covariate effects, and three adjacent periods of time (beginning, development, and end of the epidemic) to analyze the spatial distribution of the disease based on a Bayesian hierarchical model.

Results

Spatial distribution of the estimated risks of Zika virus disease showed that it increased in a strip that crosses the central area of the country from west to east. Analysis of the three time periods showed greater risk of the disease in the central and southern zones—Arauca and Santander—where the increase in risk was four times higher during the peak phase compared with the initial phase of the outbreak.

Conclusion

In the identified high‐risk areas, integrated surveillance systems for Zika virus disease and its complications must be strengthened to provide up‐to‐date and accurate epidemiological information. This information would allow those involved in policy and decision making to identify new outbreaks and risk clusters, enabling more focused and accurate measures to target at‐risk populations.

The spatial distribution of the estimated risk of Zika virus disease in Colombia was four times higher during the epidemic phase of the outbreak.

New estimates of the Zika virus epidemic attack rate in Northeastern Brazil from 2015 to 2016: A modelling analysis based on Guillain-Barré Syndrome (GBS) surveillance data

BACKGROUND

Between January 2015 and August 2016, two epidemic waves of Zika virus (ZIKV) disease swept the Northeastern (NE) region of Brazil. As a result, two waves of Guillain-Barré Syndrome (GBS) were observed concurrently. The mandatory reporting of ZIKV disease began region-wide in February 2016, and it is believed that ZIKV cases were significantly under-reported before that. The changing reporting rate has made it difficult to estimate the ZIKV infection attack rate, and studies in the literature vary widely from 17% to > 50%. The same applies to other key epidemiological parameters. In contrast, the diagnosis and reporting of GBS cases were reasonably reliable given the severity and easy recognition of the disease symptoms. In this paper, we aim to estimate the real number of ZIKV cases (i.e., the infection attack rate) and their dynamics in time, by scaling up from GBS surveillance data in NE Brazil.

METHODOLOGY

A mathematical compartmental model is constructed that makes it possible to infer the true epidemic dynamics of ZIKV cases based on surveillance data of excess GBS cases. The model includes the possibility that asymptomatic ZIKV cases are infectious. The model is fitted to the GBS surveillance data and the key epidemiological parameters are inferred by using a plug-and-play likelihood-based estimation. We make use of regional weather data to determine possible climate-driven impacts on the reproductive number [Formula: see text], and to infer the true ZIKV epidemic dynamics.

FINDINGS AND CONCLUSIONS

The GBS surveillance data can be used to study ZIKV epidemics and may be appropriate when ZIKV reporting rates are not well understood. The overall infection attack rate (IAR) of ZIKV is estimated to be 24.1% (95% confidence interval: 17.1%-29.3%) of the population. By examining various asymptomatic scenarios, the IAR is likely to be lower than 33% over the two ZIKV waves. The risk rate from symptomatic ZIKV infection to develop GBS was estimated as ρ = 0.0061% (95% CI: 0.0050%-0.0086%) which is significantly less than current estimates. We found a positive association between local temperature and the basic reproduction number, [Formula: see text]. Our analysis revealed that asymptomatic infections affect the estimation of ZIKV epidemics and need to also be carefully considered in related modelling studies. According to the estimated effective reproduction number and population wide susceptibility, we comment that a ZIKV outbreak would be unlikely in NE Brazil in the near future.

Arbovirus vectors of epidemiological concern in the Americas: A scoping review of entomological studies on Zika, dengue and chikungunya virus vectors

BACKGROUND

Three arthropod-borne viruses (arboviruses) causing human disease have been the focus of a large number of studies in the Americas since 2013 due to their global spread and epidemiological impacts: Zika, dengue, and chikungunya viruses. A large proportion of infections by these viruses are asymptomatic. However, all three viruses are associated with moderate to severe health consequences in a small proportion of cases. Two mosquito species, Aedes aegypti and Aedes albopictus, are among the world's most prominent arboviral vectors, and are known vectors for all three viruses in the Americas.

OBJECTIVES

This review summarizes the state of the entomological literature surrounding the mosquito vectors of Zika, dengue and chikungunya viruses and factors affecting virus transmission. The rationale of the review was to identify and characterize entomological studies that have been conducted in the Americas since the introduction of chikungunya virus in 2013, encompassing a period of arbovirus co-circulation, and guide future research based on identified knowledge gaps.

METHODS

The preliminary search for this review was conducted on PubMed (National Library of Health, Bethesda, MD, United States). The search included the terms 'zika' OR 'dengue' OR 'chikungunya' AND 'vector' OR 'Aedes aegypti' OR 'Aedes albopictus'. The search was conducted on March 1st of 2018, and included all studies since January 1st of 2013.

RESULTS

A total of 96 studies were included in the scoping review after initial screening and subsequent exclusion of out-of-scope studies, secondary data publications, and studies unavailable in English language.

KEY FINDINGS

We observed a steady increase in number of publications, from 2013 to 2018, with half of all studies published from January 2017 to March 2018. Interestingly, information on Zika virus vector species composition was abundant, but sparse on Zika virus transmission dynamics. Few studies examined natural infection rates of Zika virus, vertical transmission, or co-infection with other viruses. This is in contrast to the wealth of research available on natural infection and co-infection for dengue and chikungunya viruses, although vertical transmission research was sparse for all three viruses.

A nanoparticle pseudo pathogen for rapid detection and diagnosis of virus infection

We herein report a new rapid blood test for virus infection detection and diagnosis. A citrate gold nanoparticle is first coated with a virus lysate to form a gold nanoparticle pseudo pathogen. The gold nanoparticle pseudo virus is then mixed with a blood plasma or serum samples. If the blood sample is from a positive patient, the activated immune molecules in the blood such as antibodies, complement proteins and others will react with the nanoparticle pseudo virus, leading to nanoparticle aggregate formation. The nanoparticle aggregate formation is detected and measured using a particle sizing technique called dynamic light scattering. In this study, we applied this test for Zika virus infection detection. We tested blood plasma samples from 85 Zika positive patients, 40 Dengue positive patients, 10 Chikungunya positive patients, and 78 non-patient control samples collected from both endemic and non-endemic locations. The study shows that the new test has a higher sensitivity compared to some existing commercial tests in the market, while maintaining a similar specificity. Within 7 days from the symptom onset, the new test can detect 43% of the infected patients while a commercial anti-Zika IgM test detects only 26% of the infected patients. Within 14 days from the symptom onset, our new test detects 73% of the infected patients while the same commercial anti-Zika IgM test detects 53% of the infected patients. The test is extremely simple, easy to develop, with test results obtained within minutes. This new test platform may be potentially adapted for the detection and diagnosis of a wide range of viral infectious diseases, for example, the currently ongoing COVID-19.

•

A rapid blood test for point-of-care virus infectious disease detection and diagnosis.

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The test uses a gold nanoparticle pseudo virus particle to detect active immune response from patient’s blood.

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The test is a single-step process with results obtained within 20 min.

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The test shows significantly better sensitivity than a commercially available serology test.

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The test platform may be adapted to develop diagnostic tests for different virus infections.

Return of the founder Chikungunya virus to its place of introduction into Brazil is revealed by genomic characterization of exanthematic disease cases

Between June 2017 and August 2018, several municipalities located in Bahia state (Brazil) reported a large increase in the number of patients presenting with febrile illness similar to that of arboviral infections. Using a combination of portable whole genome sequencing, molecular clock and epidemiological analyses, we revealed the return of the CHIKV-ECSA genotype into Bahia. Our results show local persistence of lineages in some municipalities and the re-introduction of new epidemiological strains from different Brazilian regions, highlighting a complex dynamic of transmission between epidemic seasons and sampled locations. Estimated climate-driven transmission potential of CHIKV remained at similar levels throughout the years, such that large reductions in the total number of confirmed cases suggests a slow, but gradual accumulation of herd-immunity over the 4 years of the epidemic in Bahia after its introduction in 2014. Bahia remains a reservoir of the genetic diversity of CHIKV in the Americas, and genomic surveillance strategies are essential to assist in monitoring and understanding arboviral transmission and persistence both locally and over large distances.

Determinants of high residual post-PCV13 pneumococcal vaccine-type carriage in Blantyre, Malawi: a modelling study

BACKGROUND

In November 2011, Malawi introduced the 13-valent pneumococcal conjugate vaccine (PCV13) into the routine infant schedule. Four to 7 years after introduction (2015-2018), rolling prospective nasopharyngeal carriage surveys were performed in the city of Blantyre. Carriage of Streptococcus pneumoniae vaccine serotypes (VT) remained higher than reported in high-income countries, and impact was asymmetric across age groups.

METHODS

A dynamic transmission model was fit to survey data using a Bayesian Markov-chain Monte Carlo approach, to obtain insights into the determinants of post-PCV13 age-specific VT carriage.

RESULTS

Accumulation of naturally acquired immunity with age and age-specific transmission potential were both key to reproducing the observed data. VT carriage reduction peaked sequentially over time, earlier in younger and later in older age groups. Estimated vaccine efficacy (protection against carriage) was 66.87% (95% CI 50.49-82.26%), similar to previous estimates. Ten-year projected vaccine impact (VT carriage reduction) among 0-9 years old was lower than observed in other settings, at 76.23% (CI 95% 68.02-81.96%), with sensitivity analyses demonstrating this to be mainly driven by a high local force of infection.

CONCLUSIONS

There are both vaccine-related and host-related determinants of post-PCV13 pneumococcal VT transmission in Blantyre with vaccine impact determined by an age-specific, local force of infection. These findings are likely to be generalisable to other Sub-Saharan African countries in which PCV impact on carriage (and therefore herd protection) has been lower than desired, and have implications for the interpretation of post-PCV carriage studies and future vaccination programs.

Impact of age-specific immunity on the timing and burden of the next Zika virus outbreak

The 2015-2017 epidemics of Zika virus (ZIKV) in the Americas caused widespread infection, followed by protective immunity. The timing and burden of the next Zika virus outbreak remains unclear. We used an agent-based model to simulate the dynamics of age-specific immunity to ZIKV, and predict the future age-specific risk using data from Managua, Nicaragua. We also investigated the potential impact of a ZIKV vaccine. Assuming lifelong immunity, the risk of a ZIKV outbreak will remain low until 2035 and rise above 50% in 2047. The imbalance in age-specific immunity implies that people in the 15-29 age range will be at highest risk of infection during the next ZIKV outbreak, increasing the expected number of congenital abnormalities. ZIKV vaccine development and licensure are urgent to attain the maximum benefit in reducing the population-level risk of infection and the risk of adverse congenital outcomes. This urgency increases if immunity is not lifelong.

Immunogenicity and Protection Efficacy of a Naked Self-Replicating mRNA-Based Zika Virus Vaccine

To combat emerging infectious diseases like Zika virus (ZIKV), synthetic messenger RNAs (mRNAs) encoding viral antigens are very attractive as they allow a rapid, generic, and flexible production of vaccines. In this work, we engineered a self-replicating mRNA (sr-mRNA) vaccine encoding the pre-membrane and envelope (prM-E) glycoproteins of ZIKV. Intradermal electroporation of as few as 1 µg of this mRNA-based ZIKV vaccine induced potent humoral and cellular immune responses in BALB/c and especially IFNAR1^-/- C57BL/6 mice, resulting in a complete protection of the latter mice against ZIKV infection. In wild-type C57BL/6 mice, the vaccine resulted in very low seroconversion rates and antibody titers. The potency of the vaccine was inversely related to the dose of mRNA used in wild-type BALB/c or C57BL/6 mice, as robust type I interferon (IFN) response was determined in a reporter mice model (IFN-β^+/Δβ-luc). We further investigated the inability of the sr-prM-E-mRNA ZIKV vaccine to raise antibodies in wild-type C57BL/6 mice and found indications that type I IFNs elicited by this naked sr-mRNA vaccine might directly impede the induction of a robust humoral response. Therefore, we assume that the efficacy of sr-mRNA vaccines after intradermal electroporation might be increased by strategies that temper their inherent innate immunogenicity.

MVSE: An R-package that estimates a climate-driven mosquito-borne viral suitability index

Viruses, such as dengue, Zika, yellow fever and chikungunya, depend on mosquitoes for transmission. Their epidemics typically present periodic patterns, linked to the underlying mosquito population dynamics, which are known to be driven by natural climate fluctuations. Understanding how climate dictates the timing and potential of viral transmission is essential for preparedness of public health systems and design of control strategies. While various alternative approaches have been proposed to estimate local transmission potential of such viruses, few open-source, ready to use and freely available software tools exist.We developed the Mosquito-borne Viral Suitability Estimator (MVSE) software package for the R programming environment. MVSE estimates the index P, a novel suitability index based on a climate-driven mathematical expression for the basic reproductive number of mosquito-borne viruses. By accounting for local humidity and temperature, as well as viral, vector and human priors, the index P can be estimated for specific host and viral species in different regions of the globe.We describe the background theory, empirical support and biological interpretation of the index P. Using real-world examples spanning multiple epidemiological contexts, we further demonstrate MVSE's basic functionality, research and educational potentials.

Simple framework for real-time forecast in a data-limited situation: the Zika virus (ZIKV) outbreaks in Brazil from 2015 to 2016 as an example

Background

In 2015–2016, Zika virus (ZIKV) caused serious epidemics in Brazil. The key epidemiological parameters and spatial heterogeneity of ZIKV epidemics in different states in Brazil remain unclear. Early prediction of the final epidemic (or outbreak) size for ZIKV outbreaks is crucial for public health decision-making and mitigation planning. We investigated the spatial heterogeneity in the epidemiological features of ZIKV across eight different Brazilian states by using simple non-linear growth models.

Results

We fitted three different models to the weekly reported ZIKV cases in eight different states and obtained an R² larger than 0.995. The estimated average values of basic reproduction numbers from different states varied from 2.07 to 3.41, with a mean of 2.77. The estimated turning points of the epidemics also varied across different states. The estimation of turning points nevertheless is stable and real-time. The forecast of the final epidemic size (attack rate) is reasonably accurate, shortly after the turning point. The knowledge of the epidemic turning point is crucial for accurate real-time projection of the outbreak.

Conclusions

Our simple models fitted the epidemic reasonably well and thus revealed the spatial heterogeneity in the epidemiological features across Brazilian states. The knowledge of the epidemic turning point is crucial for real-time projection of the outbreak size. Our real-time estimation framework is able to yield a reliable prediction of the final epidemic size.

Electronic supplementary material

The online version of this article (10.1186/s13071-019-3602-9) contains supplementary material, which is available to authorized users.

An update on the aspects of Zika virus infection on male reproductive system

Zika virus (ZIKV) is mainly transmitted through Aedes mosquito bites, but sexual and post-transfusion transmissions have been reported. During acute infection, ZIKV is detectable in most organs and body fluids including human semen. Although it is not currently epidemic, there is a concern that the virus can still reemerge since the male genital tract might harbor persistent reservoirs that could facilitate viral transmission over extended periods, raising concerns among public health and assisted reproductive technologies (ART) experts and professionals. So far, the consensus is that ZIKV infection in the testes or epididymis might affect sperm development and, consequently, male fertility. Still, diagnostic tests have not yet been adapted to resource-restricted countries. This manuscript provides an updated overview of the cellular and molecular mechanisms of ZIKV infection and reviews data on ZIKV persistence in semen and associated risks to the male reproductive system described in human and animal models studies. We provide an updated summary of the impact of the recent ZIKV outbreak on human-ART, weighing on current recommendations and diagnostic approaches, both available and prospective, with special emphasis on mass spectrometry-based biomarker discovery. In the light of the identified gaps in our accumulated knowledge on the subject, we highlight the importance for couples seeking ART to follow the constantly revised guidelines and the need of specific ZIKV diagnosis tools for semen screening to contain ZIKV virus spread and make ART safer.

Outbreak science: recent progress in the detection and response to outbreaks of infectious diseases

The frequency of reported outbreaks of infectious diseases has increased over the past 3 decades, with predictions that this rise will continue. Outbreak response continues to follow nine basic principles: establish the presence of an outbreak, verify the diagnosis, make a case definition, find cases and contacts, conduct basic epidemiology, test hypotheses, institute control measures, communicate the situation and establish ongoing surveillance. Within each of these areas, significant advances have been made over the past 5 years using progress in digital, laboratory, epidemiology and anthropological equipment or techniques. Irrespective of these, future outbreaks of high-consequence are inevitable, and vigilance and preparation must continue in order to prevent significant mortality, morbidity and socio-economic crisis.

Genomic, epidemiological and digital surveillance of Chikungunya virus in the Brazilian Amazon

BACKGROUND

Since its first detection in the Caribbean in late 2013, chikungunya virus (CHIKV) has affected 51 countries in the Americas. The CHIKV epidemic in the Americas was caused by the CHIKV-Asian genotype. In August 2014, local transmission of the CHIKV-Asian genotype was detected in the Brazilian Amazon region. However, a distinct lineage, the CHIKV-East-Central-South-America (ECSA)-genotype, was detected nearly simultaneously in Feira de Santana, Bahia state, northeast Brazil. The genomic diversity and the dynamics of CHIKV in the Brazilian Amazon region remains poorly understood despite its importance to better understand the epidemiological spread and public health impact of CHIKV in the country.

METHODOLOGY/PRINCIPAL FINDINGS

We report a large CHIKV outbreak (5,928 notified cases between August 2014 and August 2018) in Boa vista municipality, capital city of Roraima's state, located in the Brazilian Amazon region. We generated 20 novel CHIKV-ECSA genomes from the Brazilian Amazon region using MinION portable genome sequencing. Phylogenetic analyses revealed that despite an early introduction of the Asian genotype in 2015 in Roraima, the large CHIKV outbreak in 2017 in Boa Vista was caused by an ECSA-lineage most likely introduced from northeastern Brazil. Epidemiological analyses suggest a basic reproductive number of R0 of 1.66, which translates in an estimated 39 (95% CI: 36 to 45) % of Roraima's population infected with CHIKV-ECSA. Finally, we find a strong association between Google search activity and the local laboratory-confirmed CHIKV cases in Roraima.

CONCLUSIONS/SIGNIFICANCE

This study highlights the potential of combining traditional surveillance with portable genome sequencing technologies and digital epidemiology to inform public health surveillance in the Amazon region. Our data reveal a large CHIKV-ECSA outbreak in Boa Vista, limited potential for future CHIKV outbreaks, and indicate a replacement of the Asian genotype by the ECSA genotype in the Amazon region.

A comparison of mosquito densities, weather and infection rates of Aedes aegypti during the first epidemics of Chikungunya (2014) and Zika (2016) in areas with and without vector control in Puerto Rico

In Puerto Rico, the first records of the transmission of Chikungunya (CHIKV) and Zika (ZIKV) viruses were confirmed in May 2014 and December 2015, respectively. Transmission of CHIKV peaked in September 2014, whereas that of ZIKV peaked in August 2016. The emergence of these mosquito-transmitted arboviruses in the context of a lack of human population immunity allowed observations of whether the outbreaks were associated with Aedes aegypti (Diptera: Culicidae) densities and weather. Mosquito density was monitored weekly in four communities using sentinel autocidal gravid ovitraps (AGO traps) during 2016 in order to provide data to be compared with the findings of a previous study carried out during the 2014 CHIKV epidemic. Findings in two communities protected against Ae. aegypti using mass AGO trapping (three traps per house in most houses) were compared with those in two nearby communities without vector control. Mosquito pools were collected to detect viral RNA of ZIKV, CHIKV and dengue virus. In areas without vector control, mosquito densities and rates of ZIKV detection in 2016 were significantly higher, similarly to those observed for CHIKV in 2014. The density of Ae. aegypti in treated sites was less than two females/trap/week, which is similar to the putative adult female threshold for CHIKV transmission. No significant differences in mosquito density or infection rates with ZIKV and CHIKV at the same sites between years were observed. Although 2016 was significantly wetter, mosquito densities were similar.

Impact of recent and future climate change on vector-borne diseases

Climate change is one of the greatest threats to human health in the 21st century. Climate directly impacts health through climatic extremes, air quality, sea-level rise, and multifaceted influences on food production systems and water resources. Climate also affects infectious diseases, which have played a significant role in human history, impacting the rise and fall of civilizations and facilitating the conquest of new territories. Our review highlights significant regional changes in vector and pathogen distribution reported in temperate, peri-Arctic, Arctic, and tropical highland regions during recent decades, changes that have been anticipated by scientists worldwide. Further future changes are likely if we fail to mitigate and adapt to climate change. Many key factors affect the spread and severity of human diseases, including mobility of people, animals, and goods; control measures in place; availability of effective drugs; quality of public health services; human behavior; and political stability and conflicts. With drug and insecticide resistance on the rise, significant funding and research efforts must to be maintained to continue the battle against existing and emerging diseases, particularly those that are vector borne.

Quantifying the risk of local Zika virus transmission in the contiguous US during the 2015-2016 ZIKV epidemic

BACKGROUND

Local mosquito-borne Zika virus (ZIKV) transmission has been reported in two counties in the contiguous United States (US), prompting the issuance of travel, prevention, and testing guidance across the contiguous US. Large uncertainty, however, surrounds the quantification of the actual risk of ZIKV introduction and autochthonous transmission across different areas of the US.

METHODS

We present a framework for the projection of ZIKV autochthonous transmission in the contiguous US during the 2015-2016 epidemic using a data-driven stochastic and spatial epidemic model accounting for seasonal, environmental, and detailed population data. The model generates an ensemble of travel-related case counts and simulates their potential to have triggered local transmission at the individual level in the 2015-2016 ZIKV epidemic.

RESULTS

We estimate the risk of ZIKV introduction and local transmission at the county level and at the 0.025° × 0.025° cell level across the contiguous US. We provide a risk measure based on the probability of observing local transmission in a specific location during a ZIKV epidemic modeled after the epidemic observed during the years 2015-2016. The high spatial and temporal resolution of the model allows us to generate statistical estimates of the number of ZIKV introductions leading to local transmission in each location. We find that the risk was spatially heterogeneously distributed and concentrated in a few specific areas that account for less than 1% of the contiguous US population. Locations in Texas and Florida that have actually experienced local ZIKV transmission were among the places at highest risk according to our results. We also provide an analysis of the key determinants for local transmission and identify the key introduction routes and their contributions to ZIKV transmission in the contiguous US.

CONCLUSIONS

This framework provides quantitative risk estimates, fully captures the stochasticity of ZIKV introduction events, and is not biased by the under-ascertainment of cases due to asymptomatic cases. It provides general information on key risk determinants and data with potential uses in defining public health recommendations and guidance about ZIKV risk in the US.

Screening for Zika virus RNA in sera of suspected cases: a retrospective cross-sectional study

BACKGROUND

Zika virus (ZIKV) became a global human health concern owing to its rapid spread worldwide and its association with congenital and neurological disorders. The current epidemiological profile of arboviruses in Brazil is characterized by widespread co-circulation of Dengue virus, Chikungunya virus, and ZIKV throughout the country. These viruses cause acute diseases frequently with overlapping symptoms, which could result in an inaccurate diagnosis based solely on clinical and epidemiological grounds. Here we conducted a screening for ZIKV RNA in serum samples from patients across Brazil with suspected ZIKV infection.

METHODS

Using RT-qPCR, we investigated ZIKV RNA in 3001 serum samples. Samples were passively acquired through a private laboratory network, between December 2015 and August 2016, from 27 Brazilian Federative Units. We performed descriptive statistics on demographic variables including sex, age, and geographic location.

RESULTS

ZIKV was detected in 11.4% (95%CI = 10.3-12.6%) of the sera. ZIKV RNA was detected in sera collected throughout the country, but during the analyzed period, RNA was more frequently detected in samples from the Southeast, Midwest, and North regions (3.9 to 5.8 times higher) when compared to the Northeast and South regions.

CONCLUSIONS

These data reinforce the importance of laboratory diagnosis, surveillance systems, and further epidemiological studies to understand the dynamics of outbreaks and diseases associated with ZIKV and other arboviruses.

Measuring Mosquito-borne Viral Suitability in Myanmar and Implications for Local Zika Virus Transmission

INTRODUCTION

In South East Asia, mosquito-borne viruses (MBVs) have long been a cause of high disease burden and significant economic costs. While in some SEA countries the epidemiology of MBVs is spatio-temporally well characterised and understood, in others such as Myanmar our understanding is largely incomplete.

MATERIALS AND METHODS

Here, we use a simple mathematical approach to estimate a climate-driven suitability index aiming to better characterise the intrinsic, spatio-temporal potential of MBVs in Myanmar.

RESULTS

Results show that the timing and amplitude of the natural oscillations of our suitability index are highly informative for the temporal patterns of DENV case counts at the country level, and a mosquito-abundance measure at a city level. When projected at fine spatial scales, the suitability index suggests that the time period of highest MBV transmission potential is between June and October independently of geographical location. Higher potential is nonetheless found along the middle axis of the country and in particular in the southern corridor of international borders with Thailand.

DISCUSSION

This research complements and expands our current understanding of MBV transmission potential in Myanmar, by identifying key spatial heterogeneities and temporal windows of importance for surveillance and control. We discuss our findings in the context of Zika virus given its recent worldwide emergence, public health impact, and current lack of information on its epidemiology and transmission potential in Myanmar. The proposed suitability index here demonstrated is applicable to other regions of the world for which surveillance data is missing, either due to lack of resources or absence of an MBV of interest.

Zika outbreak aftermath: status, progress, concerns and new insights

Zika, a neurotrophic virus belonging to Flaviviridae family of viruses and transmitted by vector mosquitoes of Aedes species, took the world by storm during its recent outbreak. Its spread to newer territories, unprecedented pace of transmission, lack of existing therapeutic agents and vaccines and an empty drug pipeline raised an alarm. Uncertainty about full spectrum of diseases and its long-term consequences, newly discovered modes of transmission and controversies over vector status of mosquito species like Culex quinquefasciatus led to layers of complexity and presented new hurdles and challenges in Zika virus research. This review summarizes the progress and updates of efforts, concerns, financial burden and available resources in light of newly acquired knowledge in Zika virus research.

Genomic Epidemiology Reconstructs the Introduction and Spread of Zika Virus in Central America and Mexico

The Zika virus (ZIKV) epidemic in the Americas established ZIKV as a major public health threat and uncovered its association with severe diseases, including microcephaly. However, genetic epidemiology in some at-risk regions, particularly Central America and Mexico, remains limited. We report 61 ZIKV genomes from this region, generated using metagenomic sequencing with ZIKV-specific enrichment, and combine phylogenetic, epidemiological, and environmental data to reconstruct ZIKV transmission. These analyses revealed multiple independent ZIKV introductions to Central America and Mexico. One introduction, likely from Brazil via Honduras, led to most infections and the undetected spread of ZIKV through the region from late 2014. Multiple lines of evidence indicate biannual peaks of ZIKV transmission in the region, likely driven by varying local environmental conditions for mosquito vectors and herd immunity. The spatial and temporal heterogeneity of ZIKV transmission in Central America and Mexico challenges arbovirus surveillance and disease control measures.

Seasonal temperature variation influences climate suitability for dengue, chikungunya, and Zika transmission

Dengue, chikungunya, and Zika virus epidemics transmitted by Aedes aegypti mosquitoes have recently (re)emerged and spread throughout the Americas, Southeast Asia, the Pacific Islands, and elsewhere. Understanding how environmental conditions affect epidemic dynamics is critical for predicting and responding to the geographic and seasonal spread of disease. Specifically, we lack a mechanistic understanding of how seasonal variation in temperature affects epidemic magnitude and duration. Here, we develop a dynamic disease transmission model for dengue virus and Aedes aegypti mosquitoes that integrates mechanistic, empirically parameterized, and independently validated mosquito and virus trait thermal responses under seasonally varying temperatures. We examine the influence of seasonal temperature mean, variation, and temperature at the start of the epidemic on disease dynamics. We find that at both constant and seasonally varying temperatures, warmer temperatures at the start of epidemics promote more rapid epidemics due to faster burnout of the susceptible population. By contrast, intermediate temperatures (24–25°C) at epidemic onset produced the largest epidemics in both constant and seasonally varying temperature regimes. When seasonal temperature variation was low, 25–35°C annual average temperatures produced the largest epidemics, but this range shifted to cooler temperatures as seasonal temperature variation increased (analogous to previous results for diurnal temperature variation). Tropical and sub-tropical cities such as Rio de Janeiro, Fortaleza, and Salvador, Brazil; Cali, Cartagena, and Barranquilla, Colombia; Delhi, India; Guangzhou, China; and Manila, Philippines have mean annual temperatures and seasonal temperature ranges that produced the largest epidemics. However, more temperate cities like Shanghai, China had high epidemic suitability because large seasonal variation offset moderate annual average temperatures. By accounting for seasonal variation in temperature, the model provides a baseline for mechanistically understanding environmental suitability for virus transmission by Aedes aegypti. Overlaying the impact of human activities and socioeconomic factors onto this mechanistic temperature-dependent framework is critical for understanding likelihood and magnitude of outbreaks.

Mosquito-borne viruses like dengue, Zika, and chikungunya have recently caused large epidemics that are partly driven by temperature. Using a mathematical model built from laboratory experimental data for Aedes aegypti mosquitoes and dengue virus, we examine the impact of variation in seasonal temperature regimes on epidemic size and duration. At constant temperatures, both low and high temperatures (20°C and 35°C) produce small epidemics, while intermediate temperatures like 25°C and 30°C produce much larger epidemics. In seasonally varying temperature environments, epidemics peak more rapidly at higher starting temperatures, while intermediate starting temperatures produce the largest epidemics. Seasonal mean temperatures of 25–35°C are most suitable for large epidemics when seasonality is low, but in more variable seasonal environments epidemic suitability peaks at lower annual average temperatures. Tropical and sub-tropical cities have the highest temperature suitability for epidemics, but more temperate cities with high seasonal variation also have the potential for very large epidemics.