The epidemiology and transmissibility of Zika virus in Girardot and San Andres island, Colombia, September 2015 to January 2016

SPADE4: Sparsity and Delay Embedding Based Forecasting of Epidemics

Predicting the evolution of diseases is challenging, especially when the data availability is scarce and incomplete. The most popular tools for modelling and predicting infectious disease epidemics are compartmental models. They stratify the population into compartments according to health status and model the dynamics of these compartments using dynamical systems. However, these predefined systems may not capture the true dynamics of the epidemic due to the complexity of the disease transmission and human interactions. In order to overcome this drawback, we propose Sparsity and Delay Embedding based Forecasting (SPADE4) for predicting epidemics. SPADE4 predicts the future trajectory of an observable variable without the knowledge of the other variables or the underlying system. We use random features model with sparse regression to handle the data scarcity issue and employ Takens' delay embedding theorem to capture the nature of the underlying system from the observed variable. We show that our approach outperforms compartmental models when applied to both simulated and real data.

Evidence of co-circulation of multiple arboviruses transmitted by Aedes species based on laboratory syndromic surveillance at a health unit in a slum of the Federal District, Brazil

Background

Vector-borne diseases, especially arboviruses transmitted by Aedes sp. mosquitos, should be a health policy priority in Brazil. Despite this urgency, there are significant limitations in the traditional surveillance system, mainly in vulnerable areas. This study aimed to investigate the circulation of dengue (DENV), Zika (ZIKV), and chikungunya viruses (CHIKV) by laboratory syndromic surveillance (LSS) in a slum area of the Federal District of Brazil, comparing the results with traditional surveillance data.

Methods

LSS for acute febrile and/or exanthematous symptoms was developed at a health unit of Cidade Estrutural, in order to identify the circulation of arboviruses transmitted by Aedes sp. mosquitos. Between June 2019 and March 2020, 131 valid participants were identified and sera tested by reverse transcription polymerase chain reaction (RT-PCR) for DENV (by serotype), ZIKV, and CHIKV acute infection and by immunoglobulin M enzyme-inked immunosorbent assay (ELISA-IgM) for DENV and CHIKV 15–21 days after symptom onset, when the participant reported no respiratory signs (cough and/or coryza). The results obtained were compared with traditional surveillance data for the study area and period.

Results

At least three DENV-1 (2.3%), four DENV-2 (3%), and one CHIKV (0.7%) cases were confirmed in the laboratory, showing evidence of hyperendemicity even though LSS had not reached the historic peak dengue fever months in the Federal District (April–May). When the results obtained here were compared with traditional surveillance, a significant discrepancy was observed, including underreporting of CHIKV infection.

Conclusions

In addition to the risks posed to the study population, the area investigated with its respective socio-environmental profile may be a potential site for spread of the virus, given the cosmopolitan presence of Aedes sp. and human mobility in the Federal District. It is also suggested that traditional epidemiological surveillance may be reporting acute viral infections other than DENV as dengue fever, while underreporting other arboviruses transmitted by Aedes sp. mosquitos in the Federal District.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-021-05110-9.

Public Health Response to Zika Virus Exposure of Air Force Members Deployed to Caribbean Islands, 2016

INTRODUCTION

The emergence of Zika virus disease (ZVD) in areas of military operations provided a new opportunity for force health protection. ZVD infection had an estimated 4:1 asymptomatic-to-symptomatic ratio and can cause neurologic sequelae.

MATERIALS AND METHODS

We provide a brief report of a field investigation utilizing laboratory-based surveillance and survey instruments to characterize ZVD risk among personnel deployed to the Dominican Republic in support of Operation NEW HORIZONS (NH). Additionally, we describe a cluster of 3 ZVD cases among 8 aircrew on a short mission to St. Croix (U.S. Virgin Islands).

RESULTS

Following Operation NH, 6 of a total 189 deployed cohort members tested positive for ZVD by immunoglobulin M and confirmatory plaque reduction neutralization test (3.2%). Reverse transcription polymerase chain reaction testing in urine or serum was positive in 4 of those 6 cases. All 6 cases reported at least one symptom, with 5 reporting subjective fever and arthralgia and 4 reporting rash. Cases were less likely to have air-conditioned living quarters (odds ratio = 0.1; 95% confidence interval 0.02-0.77; P < 0.03), but were otherwise similar to non-cases. Likewise, in St. Croix, 3/8 tested positive by immunoglobulin M and plaque reduction neutralization test for an attack rate of 38%. Similar to Operation NH, all three cases were symptomatic with subjective fever (67%), arthralgia (67%), and/or rash (100%).

CONCLUSIONS

This field investigation identified differing, mission location-dependent ZVD attack rates and a 0:9 asymptomatic-to-symptomatic case ratio. As this was unexpected based on a previous report of a 4:1 ratio, it emphasizes the need to be cautious before generalizing outbreak characteristics between populations while also offering additional practical experience for force health protection.

Estimating and interpreting secondary attack risk: Binomial considered biased

The household secondary attack risk (SAR), often called the secondary attack rate or secondary infection risk, is the probability of infectious contact from an infectious household member A to a given household member B, where we define infectious contact to be a contact sufficient to infect B if he or she is susceptible. Estimation of the SAR is an important part of understanding and controlling the transmission of infectious diseases. In practice, it is most often estimated using binomial models such as logistic regression, which implicitly attribute all secondary infections in a household to the primary case. In the simplest case, the number of secondary infections in a household with m susceptibles and a single primary case is modeled as a binomial(m, p) random variable where p is the SAR. Although it has long been understood that transmission within households is not binomial, it is thought that multiple generations of transmission can be neglected safely when p is small. We use probability generating functions and simulations to show that this is a mistake. The proportion of susceptible household members infected can be substantially larger than the SAR even when p is small. As a result, binomial estimates of the SAR are biased upward and their confidence intervals have poor coverage probabilities even if adjusted for clustering. Accurate point and interval estimates of the SAR can be obtained using longitudinal chain binomial models or pairwise survival analysis, which account for multiple generations of transmission within households, the ongoing risk of infection from outside the household, and incomplete follow-up. We illustrate the practical implications of these results in an analysis of household surveillance data collected by the Los Angeles County Department of Public Health during the 2009 influenza A (H1N1) pandemic.

The household secondary attack risk (SAR), often called the secondary attack rate or secondary infection risk, is the probability of infectious contact from an infectious household member A to a given household member B, where we define infectious contact to be a contact sufficient to infect B if he or she is susceptible. The most common statistical models used to estimate the SAR are binomial models such as logistic regression, which implicitly assume that all secondary infections in a household are infected by the primary case. Here, we use analytical calculations and simulations to show that estimation of the SAR must account for multiple generations of transmission within households. As an example, we show that binomial models and statistical models that account for multiple generations of within-household transmission reach different conclusions about the household SAR for 2009 influenza A (H1N1) in Los Angeles County, with the latter models fitting the data better. In an epidemic, accurate estimation of the SAR allows rigorous evaluation of the effectiveness of public health interventions such as social distancing, prophylaxis or treatment, and vaccination.

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.

Modeling the potential of wAu-Wolbachia strain invasion in mosquitoes to control Aedes-borne arboviral infections

Arboviral infections such as dengue, Zika and chikungunya are fast spreading diseases that pose significant health problems globally. In order to control these infections, an intracellular bacterium called Wolbachia has been introduced into wild-type mosquito populations in the hopes of replacing the vector transmitting agent, Aedes aegypti with one that is incapable of transmission. In this study, we developed a Wolbachia transmission model for the novel wAu strain which possesses several favourable traits (e.g., enhanced viral blockage and maintenance at higher temperature) but not cyctoplasmic incompatibility (CI)-when a Wolbachia-infected male mosquito mates with an uninfected female mosquito, producing no viable offspring. This model describes the competitive dynamics between wAu-Wolbachia-infected and uninfected mosquitoes and the role of imperfect maternal transmission. By analysing the system via computing the basic reproduction number(s) and stability properties, the potential of the wAu strain as a viable strategy to control arboviral infections is established. The results of this work show that enhanced maintenance of Wolbachia infection at higher temperatures can overcome the lack of CI induction to support wAu-Wolbachia infected mosquito invasion. This study will support future arboviral control programs, that rely on the introduction of new Wolbachia variants.

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.

Effectiveness of an intervention for Aedes aegypti control scaled-up under an inter-sectoral approach in a Colombian city hyper-endemic for dengue virus

Aedes aegypti transmitted arboviral diseases are of significant importance in Colombia, particularly since the 2014/2015 introduction of chikungunya and Zika in the Americas and the increasing spread of dengue. In response, the Colombian government initiated the scaling-up of a community-based intervention under inter and multi-sector partnerships in two out of four sectors in Girardot, one of the most hyper-endemic dengue cities in the country. Using a quasi-experimental research design a scaled-up community-led Aedes control intervention was assessed for its capacity to reduce dengue from January 2010 to August 2017 in Girardot, Colombia. Reported dengue cases, and associated factors were analysed from available data sets from the Colombian disease surveillance systems. We estimated the reduction in dengue cases before and after the intervention using, Propensity Score Matching and an Autoregressive Moving Average model for robustness. In addition, the differences in dengue incidence among scaling-up phases (pre-implementation vs sustainability) and between treatment groups (intervention and control areas) were modelled. Evidence was found in favour of the intervention, although to maximise impact the scaling-up of the intervention should continue until it covers the remaining sectors. It is expected that a greater impact of the intervention can be documented in the next outbreak of dengue in Girardot.

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.

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 1^st of 2018, and included all studies since January 1^st 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.

Genomic epidemiology supports multiple introductions and cryptic transmission of Zika virus in Colombia

BACKGROUND

Colombia was the second most affected country during the American Zika virus (ZIKV) epidemic, with over 109,000 reported cases. Despite the scale of the outbreak, limited genomic sequence data were available from Colombia. We sought to sequence additional samples and use genomic epidemiology to describe ZIKV dynamics in Colombia.

METHODS

We sequenced ZIKV genomes directly from clinical diagnostic specimens and infected Aedes aegypti samples selected to cover the temporal and geographic breadth of the Colombian outbreak. We performed phylogeographic analysis of these genomes, along with other publicly-available ZIKV genomes from the Americas, to estimate the frequency and timing of ZIKV introductions to Colombia.

RESULTS

We attempted PCR amplification on 184 samples; 19 samples amplified sufficiently to perform sequencing. Of these, 8 samples yielded sequences with at least 50% coverage. Our phylogeographic reconstruction indicates two separate introductions of ZIKV to Colombia, one of which was previously unrecognized. We find that ZIKV was first introduced to Colombia in February 2015 (95%CI: Jan 2015 - Apr 2015), corresponding to 5 to 8 months of cryptic ZIKV transmission prior to confirmation in September 2015. Despite the presence of multiple introductions, we find that the majority of Colombian ZIKV diversity descends from a single introduction. We find evidence for movement of ZIKV from Colombia into bordering countries, including Peru, Ecuador, Panama, and Venezuela.

CONCLUSIONS

Similarly to genomic epidemiological studies of ZIKV dynamics in other countries, we find that ZIKV circulated cryptically in Colombia. More accurately dating when ZIKV was circulating refines our definition of the population at risk. Additionally, our finding that the majority of ZIKV transmission within Colombia was attributable to transmission between individuals, rather than repeated travel-related importations, indicates that improved detection and control might have succeeded in limiting the scale of the outbreak within Colombia.

A systematic review and evaluation of Zika virus forecasting and prediction research during a public health emergency of international concern

INTRODUCTION

Epidemic forecasting and prediction tools have the potential to provide actionable information in the midst of emerging epidemics. While numerous predictive studies were published during the 2016-2017 Zika Virus (ZIKV) pandemic, it remains unknown how timely, reproducible, and actionable the information produced by these studies was.

METHODS

To improve the functional use of mathematical modeling in support of future infectious disease outbreaks, we conducted a systematic review of all ZIKV prediction studies published during the recent ZIKV pandemic using the PRISMA guidelines. Using MEDLINE, EMBASE, and grey literature review, we identified studies that forecasted, predicted, or simulated ecological or epidemiological phenomena related to the Zika pandemic that were published as of March 01, 2017. Eligible studies underwent evaluation of objectives, data sources, methods, timeliness, reproducibility, accessibility, and clarity by independent reviewers.

RESULTS

2034 studies were identified, of which n = 73 met the eligibility criteria. Spatial spread, R0 (basic reproductive number), and epidemic dynamics were most commonly predicted, with few studies predicting Guillain-Barré Syndrome burden (4%), sexual transmission risk (4%), and intervention impact (4%). Most studies specifically examined populations in the Americas (52%), with few African-specific studies (4%). Case count (67%), vector (41%), and demographic data (37%) were the most common data sources. Real-time internet data and pathogen genomic information were used in 7% and 0% of studies, respectively, and social science and behavioral data were typically absent in modeling efforts. Deterministic models were favored over stochastic approaches. Forty percent of studies made model data entirely available, 29% provided all relevant model code, 43% presented uncertainty in all predictions, and 54% provided sufficient methodological detail to allow complete reproducibility. Fifty-one percent of predictions were published after the epidemic peak in the Americas. While the use of preprints improved the accessibility of ZIKV predictions by a median of 119 days sooner than journal publication dates, they were used in only 30% of studies.

CONCLUSIONS

Many ZIKV predictions were published during the 2016-2017 pandemic. The accessibility, reproducibility, timeliness, and incorporation of uncertainty in these published predictions varied and indicates there is substantial room for improvement. To enhance the utility of analytical tools for outbreak response it is essential to improve the sharing of model data, code, and preprints for future outbreaks, epidemics, and pandemics.

Impact of preexisting dengue immunity on Zika virus emergence in a dengue endemic region

The clinical outcomes associated with Zika virus (ZIKV) in the Americas have been well documented, but other aspects of the pandemic, such as attack rates and risk factors, are poorly understood. We prospectively followed a cohort of 1453 urban residents in Salvador, Brazil, and, using an assay that measured immunoglobulin G3 (IgG3) responses against ZIKV NS1 antigen, we estimated that 73% of individuals were infected during the 2015 outbreak. Attack rates were spatially heterogeneous, varying by a factor of 3 within a community spanning 0.17 square kilometers. Preexisting high antibody titers to dengue virus were associated with reduced risk of ZIKV infection and symptoms. The landscape of ZIKV immunity that now exists may affect the risk for future transmission.

Epidemic curves made easy using the R package incidence

The epidemiological curve (epicurve) is one of the simplest yet most useful tools used by field epidemiologists, modellers, and decision makers for assessing the dynamics of infectious disease epidemics. Here, we present the free, open-source package incidence for the R programming language, which allows users to easily compute, handle, and visualise epicurves from unaggregated linelist data. This package was built in accordance with the development guidelines of the R Epidemics Consortium (RECON), which aim to ensure robustness and reliability through extensive automated testing, documentation, and good coding practices. As such, it fills an important gap in the toolbox for outbreak analytics using the R software, and provides a solid building block for further developments in infectious disease modelling. incidence is available from https://www.repidemicsconsortium.org/incidence.

Epidemic potential of Zika virus in Australia: implications for blood transfusion safety

BACKGROUND

Zika virus (ZIKV) is transfusion-transmissible. In Australia the primary vector, Aedes aegypti, is established in the north-east, such that local transmission is possible following importation of an index case, which has the potential to impact on blood transfusion safety and public health. We estimated the basic reproduction number (R ₀ ) to model the epidemic potential of ZIKV in Australian locations, compared this with the ecologically similar dengue viruses (DENV), and examined possible implications for blood transfusion safety.

STUDY DESIGN AND METHODS

Varying estimates of vector control efficiency and extrinsic incubation period, "best-case" and "worst-case" scenarios of monthly R ₀ for ZIKV and DENV were modeled from 1996 to 2015 in 11 areas. We visualized the geographical distribution of blood donors in relation to areas with epidemic potential for ZIKV.

RESULTS

Epidemic potential (R ₀ > 1) existed for ZIKV and DENV throughout the study period in a number of locations in northern Australia (Cairns, Darwin, Rockhampton, Thursday Island, Townsville, and Brisbane) during the warmer months of the year. R ₀ for DENV was greater than ZIKV and was broadly consistent with annual estimates in Cairns. Increased vector control efficiency markedly reduced the epidemic potential and shortened the season of local transmission. Australian locations that provide the greatest number of blood donors did not have epidemic potential for ZIKV.

CONCLUSION

We estimate that areas of north-eastern Australia could sustain local transmission of ZIKV. This early contribution to understanding the epidemic potential of ZIKV may assist in the assessment and management of threats to blood transfusion safety.

A comparison of Zika and dengue outbreaks using national surveillance data in the Dominican Republic

BACKGROUND

Aedes-borne arboviruses continue to precipitate epidemics worldwide. In Dominican Republic, the appearance of Zika virus cases that closely followed a large dengue epidemic provided an opportunity to study the different transmission drivers behind these two flaviviruses. Retrospective datasets were used to collect information on the populations at risk and descriptive statistics were used to describe the outbreaks on a national scale.

METHODOLOGY/ PRINCIPAL FINDINGS

Expectedly, box plots showed that 75% of dengue was reported in those aged <20 years while Zika infections were more widely dispersed among the population. Dengue attack rates were marginally higher among males at 25.9 per 10,000 population vs. 21.5 per 10,000 population for females. Zika infections appeared to be highly clustered among females (73.8% (95% CI 72.6%, 75.0%; p<0.05)); age-adjusted Zika attack rates among females were 7.64 per 10,000 population compared with 2.72 per 10,000 population among males. R0 calculations stratified by sex also showed a significantly higher metric among females: 1.84 (1.82, 1.87; p<0.05) when compared to males at 1.72 (1.69, 1.75; p<0.05). However, GBS attack rates stratified by sex revealed slightly higher risk in males vs. females, at 0.62 and 0.57 per 10,000 population respectively.

CONCLUSIONS/ SIGNIFICANCE

Evidence suggests little impact of existing dengue immunity on reported attack rates of Zika at the population level. Confounding of R0 and incident risk calculations by sex-specific over-reporting can alter the reliability of epidemiological metrics, which could be addressed using associated proxy syndromes or conditions to explore seemingly sex-skewed incidence. The findings indicate that community awareness campaigns, through influencing short-term health seeking behaviour, remain the most plausible mechanism behind increased reporting among women of reproductive age, although biological susceptibility cannot yet be ruled out. Media campaigns and screening are therefore recommended for women of reproductive age during Zika outbreaks. Future research should focus on clinical Zika outcomes among dengue seropositive individuals.

Spatio-Temporal Modeling of Zika and Dengue Infections within Colombia

The aim of this study is to estimate the parallel relative risk of Zika virus disease (ZVD) and dengue using spatio-temporal interaction effects models for one department and one city of Colombia during the 2015–2016 ZVD outbreak. We apply the integrated nested Laplace approximation (INLA) for parameter estimation, using the epidemiological week (EW) as a time measure. At the departmental level, the best model showed that the dengue or ZVD risk in one municipality was highly associated with risk in the same municipality during the preceding EWs, while at the city level, the final model selected established that the high risk of dengue or ZVD in one census sector was highly associated not only with its neighboring census sectors in the same EW, but also with its neighboring sectors in the preceding EW. The spatio-temporal models provided smoothed risk estimates, credible risk intervals, and estimation of the probability of high risk of dengue and ZVD by area and time period. We explore the intricacies of the modeling process and interpretation of the results, advocating for the use of spatio-temporal models of the relative risk of dengue and ZVD in order to generate highly valuable epidemiological information for public health decision making.

Environmental and social determinants of population vulnerability to Zika virus emergence at the local scale

Background

Zika virus (ZIKV) spread rapidly in the Americas in 2015. Targeting effective public health interventions for inhabitants of, and travellers to and from, affected countries depends on understanding the risk of ZIKV emergence (and re-emergence) at the local scale. We explore the extent to which environmental, social and neighbourhood disease intensity variables influenced emergence dynamics. Our objective was to characterise population vulnerability given the potential for sustained autochthonous ZIKV transmission and the timing of emergence. Logistic regression models estimated the probability of reporting at least one case of ZIKV in a given municipality over the course of the study period as an indicator for sustained transmission; while accelerated failure time (AFT) survival models estimated the time to a first reported case of ZIKV in week t for a given municipality as an indicator for timing of emergence.

Results

Sustained autochthonous ZIKV transmission was best described at the temporal scale of the study period (almost one year), such that high levels of study period precipitation and low mean study period temperature reduced the probability. Timing of ZIKV emergence was best described at the weekly scale for precipitation in that high precipitation in the current week delayed reporting. Both modelling approaches detected an effect of high poverty on reducing/slowing case detection, especially when inter-municipal road connectivity was low. We also found that proximity to municipalities reporting ZIKV had an effect to reduce timing of emergence when located, on average, less than 100 km away.

Conclusions

The different modelling approaches help distinguish between large temporal scale factors driving vector habitat suitability and short temporal scale factors affecting the speed of spread. We find evidence for inter-municipal movements of infected people as a local-scale driver of spatial spread. The negative association with poverty suggests reduced case reporting in poorer areas. Overall, relatively simplistic models may be able to predict the vulnerability of populations to autochthonous ZIKV transmission at the local scale.

Electronic supplementary material

The online version of this article (10.1186/s13071-018-2867-8) contains supplementary material, which is available to authorized users.

Surveillance on the endemic of Zika virus infection by meteorological factors in Colombia: a population-based spatial and temporal study

Background

Zika virus (ZIKV) infection is a pandemic and a public health emergency. It is transmitted by mosquitoes, primarily the Aedes genus. In light of no treatment currently, it is crucial to develop effective vector control programs to prevent the spread of ZIKV infection earlier when observing possible risk factors, such as weather conditions enhancing mosquito breeding and surviving.

Methods

This study collected daily meteorological measurements and weekly ZIKV infectious cases among 32 departments of Colombia from January 2015–December 2016. This study applied the distributed lag nonlinear model to estimate the association between the number of ZIKA virus infection and meteorological measurements, controlling for spatial and temporal variations. We examined at most three meteorological factors with 20 lags in weeks in the model.

Results

Average humidity, total rainfall, and maximum temperature were more predictable of ZIKV infection outbreaks than other meteorological factors. Our models can detect significantly lagged effects of average humidity, total rainfall, and maximum temperature on outbreaks up to 15, 14, and 20 weeks, respectively. The spatial analysis identified 12 departments with a significant threat of ZIKV, and eight of those high-risk departments were located between the Equator and 6°N. The outbreak prediction also performed well in identified high-risk departments.

Conclusion

Our results demonstrate that meteorological factors could be used for predicting ZIKV epidemics. Building an early warning surveillance system is important for preventing ZIKV infection, particularly in endemic areas.

Electronic supplementary material

The online version of this article (10.1186/s12879-018-3085-x) contains supplementary material, which is available to authorized users.

Seroprevalence of Dengue Antibodies in Three Urban Settings in Yucatan, Mexico

Dengue transmission in Mexico has become a major public health problem. Few epidemiological studies have examined the seroprevalence of dengue in Mexico, and recent estimates are needed to better understand dengue transmission dynamics. We conducted a dengue seroprevalence survey among 1,668 individuals including all age groups in three urban settings in Yucatan, Mexico. Children (< 19 years old) were selected randomly from schools. The adults (≥ 19 years old) were selected from healthcare facilities. Participants were asked to provide a venous blood sample and to answer a brief questionnaire with demographic information. Previous exposure to dengue was determined using indirect immunoglobulin G enzyme-linked immunosorbent assay. The overall seroprevalence was 73.6%. The age-specific seroprevalence increased with age, going from 51.4% (95% confidence interval [CI] = 45.0-57.9%) in children ≤ 8 years to 72% (95% CI = 66.3-77.2%) in the 9- to 14-years old. The highest seroprevalence was 83.4% (95% CI = 77-82.2%) in adults greater than 50 years. The seroprevalence in Merida was 68.6% (95% CI = 65-72%), in Progreso 68.7% (95% CI = 64.2-72.8%), and in Ticul 85.3% (95% CI = 81.9-88.3%). Ticul had the highest seroprevalence in all age groups. Logistic regression analysis showed that age and city of residence were associated with greater risk of prior dengue exposure. The results highlight the level of past exposure to dengue virus including young children. Similar studies should be conducted elsewhere in Mexico and other endemic countries to better understand the transmission dynamics of dengue.

Quantifying Zika: Advancing the Epidemiology of Zika With Quantitative Models

When Zika virus (ZIKV) emerged in the Americas, little was known about its biology, pathogenesis, and transmission potential, and the scope of the epidemic was largely hidden, owing to generally mild infections and no established surveillance systems. Surges in congenital defects and Guillain-Barré syndrome alerted the world to the danger of ZIKV. In the context of limited data, quantitative models were critical in reducing uncertainties and guiding the global ZIKV response. Here, we review some of the models used to assess the risk of ZIKV-associated severe outcomes, the potential speed and size of ZIKV epidemics, and the geographic distribution of ZIKV risk. These models provide important insights and highlight significant unresolved questions related to ZIKV and other emerging pathogens.

Ecological characterization of Aedes aegypti larval habitats (Diptera: Culicidae) in artificial water containers in Girardot, Colombia

The establishment of habitats for immature Ae. aegypti is regulated by biotic and abiotic factors and interactions between these factors. This study aimed to determine the effects of physico-chemical variables and planktonic algae on immature Ae. aegypti habitats in 101 water tanks (50 of them containing Ae. aegypti pupae and/or larvae) in Girardot, Colombia. Physical data were collected from the water tanks (volume, capacity, material, detritus, and location), along with the physico-chemical variables (temperature, pH, conductivity, redox potential, dissolved oxygen, percentage of oxygen saturation, nitrates, nitrites, and orthophosphates). The richness and abundance of the planktonic organisms were also measured. A chi-square test showed that the occurrence of detritus was greater and the container volume was smaller in the tanks that were positive for larvae. Only Cyanobacteria had a positive correlation with the abundance of immature-stage Ae. aegypti. The results could be important for understanding the vector ecology and envisaging its probable control in the domestic water tanks of Girardot.

Zika virus disease, microcephaly and Guillain-Barré syndrome in Colombia: epidemiological situation during 21 months of the Zika virus outbreak, 2015-2017

Background

The Zika virus disease (ZVD) has had a huge impact on public health in Colombia for the numbers of people affected and the presentation of Guillain-Barre syndrome (GBS) and microcephaly cases associated to ZVD.

Methods

A retrospective descriptive study was carried out, we analyze the epidemiological situation of ZVD and its association with microcephaly and GBS during a 21-month period, from October 2015 to June 2017. The variables studied were: (i) ZVD cases, (ii) ZVD cases in pregnant women, (iii) laboratory-confirmed ZVD in pregnant women, (iv) ZVD cases associated with microcephaly, (v) laboratory-confirmed ZVD associated with microcephaly, and (vi) ZVD associated to GBS cases. Average number of cases, attack rates (AR) and proportions were also calculated. The studied variables were plotted by epidemiological weeks and months. The distribution of ZVD cases in Colombia was mapped across the time using Kernel density estimator and QGIS software; we adopted Kernel Ridge Regression (KRR) and the Gaussian Kernel to estimate the number of Guillain Barre cases given the number of ZVD cases.

Results

One hundred eight thousand eighty-seven ZVD cases had been reported in Colombia, including 19,963 (18.5%) in pregnant women, 710 (0.66%) associated with microcephaly (AR, 4.87 cases per 10,000 live births) and 453 (0.42%) ZVD associated to GBS cases (AR, 41.9 GBS cases per 10,000 ZVD cases). It appears the cases of GBS increased in parallel with the cases of ZVD, cases of microcephaly appeared 5 months after recognition of the outbreak. The kernel density map shows that throughout the study period, the states most affected by the Zika outbreak in Colombia were mainly San Andrés and Providencia islands, Casanare, Norte de Santander, Arauca and Huila. The KRR shows that there is no proportional relationship between the number of GBS and ZVD cases. During the cross validation, the RMSE achieved for the second order polynomial kernel, the linear kernel, the sigmoid kernel, and the Gaussian kernel are 9.15, 9.2, 10.7, and 7.2 respectively.

Conclusions

This study updates the epidemiological analysis of the ZVD situation in Colombia describes the geographical distribution of ZVD and shows the functional relationship between ZVD cases and GBS.

Stratifying the potential local transmission of Zika in municipalities of Antioquia, Colombia

OBJECTIVE

To stratify and understand the potential transmission processes of Zika virus in Colombia, in order to effectively address the efforts on surveillance and disease control.

METHODS

We compare R₀ of Zika for municipalities based on data from the regional surveillance system of Antioquia, Colombia. The basic reproduction number (R₀ ) and its 95% confidence intervals were estimated from an SIR model with implicit vector dynamics, in terms of recovered individuals in each time unit, using an approximate solution. These parameters were estimated fitting the solution of the model to the daily cumulative frequency of each Zika case according to symptoms onset date relative to the index case reported to the local surveillance system.

RESULTS

R₀ was estimated for 20 municipalities with a median of 30 000 inhabitants, all located less than 2200 m above sea level. The reported cases ranged from 17 to 347 between these municipalities within 4 months (January to April of 2016). The results suggest that 15 municipalities had a high transmission potential (R₀  > 1), whereas in five municipality transmissions were potentially not sustaining (R₀  < 1), although the upper bound of the confidence interval of the R₀ for 3 of these 5 was greater than one, indicating the possibility of an outbreak later on.

CONCLUSION

The study identified high-risk municipalities (R₀  > 1) and provide a technique to optimise surveillance and control of Zika. Health authorities should promote the collection, analysis, modelling and sharing of anonymous data onto individual cases to estimate R₀ .

Space and space-time distributions of dengue in a hyper-endemic urban space: the case of Girardot, Colombia

Background

Dengue is a widely spread vector-borne disease. Dengue cases in the Americas have increased over the last few decades, affecting various urban spaces throughout these continents, including the tourism-oriented city of Girardot, Colombia. Interactions among mosquitoes, pathogens and humans have recently been examined using different temporal and spatial scales in attempts to determine the roles that social and ecological systems play in dengue transmission. The current work characterizes the spatial and temporal behaviours of dengue in Girardot and discusses the potential territorial dynamics related to the distribution of this disease.

Methods

Based on officially reported dengue cases (2012–2015) corresponding to epidemic (2013) and inter-epidemic years (2012, 2014, 2015), space (Getis-Ord index) and space-time (Kulldorff’s scan statistics) analyses were performed.

Results

Geocoded dengue cases (n = 2027) were slightly overrepresented by men (52.1%). As expected, the cases were concentrated in the 0- to 15-year-old age group according to the actual trends of Colombia. The incidence rates of dengue during the rainy and dry seasons as well as those for individual years (2012, 2013 and 2014) were significant using the global Getis-Ord index. Local clusters shifted across seasons and years; nevertheless, the incidence rates clustered towards the southwest region of the city under different residential conditions. Space-time clusters shifted from the northeast to the southwest of the city (2012–2014). These clusters represented only 4.25% of the total cases over the same period (n = 1623). A general trend was observed, in which dengue cases increased during the dry seasons, especially between December and February.

Conclusions

Despite study limitations related to official dengue records and available fine-scale demographic information, the spatial analysis results were promising from a geography of health perspective. Dengue did not show linear association with poverty or with vulnerable peripheral spaces in intra-urban settings, supporting the idea that the pathogenic complex of dengue is driven by different factors. A coordinated collaboration of epidemiological, public health and social science expertise is needed to assess the effect of “place” from a relational perspective in which geography has an important role to play.

Electronic supplementary material

The online version of this article (doi:10.1186/s12879-017-2610-7) contains supplementary material, which is available to authorized users.

Spread of Zika virus in the Americas

We use a data-driven global stochastic epidemic model to analyze the spread of the Zika virus (ZIKV) in the Americas. The model has high spatial and temporal resolution and integrates real-world demographic, human mobility, socioeconomic, temperature, and vector density data. We estimate that the first introduction of ZIKV to Brazil likely occurred between August 2013 and April 2014 (90% credible interval). We provide simulated epidemic profiles of incident ZIKV infections for several countries in the Americas through February 2017. The ZIKV epidemic is characterized by slow growth and high spatial and seasonal heterogeneity, attributable to the dynamics of the mosquito vector and to the characteristics and mobility of the human populations. We project the expected timing and number of pregnancies infected with ZIKV during the first trimester and provide estimates of microcephaly cases assuming different levels of risk as reported in empirical retrospective studies. Our approach represents a modeling effort aimed at understanding the potential magnitude and timing of the ZIKV epidemic and it can be potentially used as a template for the analysis of future mosquito-borne epidemics.

Assessing real-time Zika risk in the United States

Background

Confirmed local transmission of Zika Virus (ZIKV) in Texas and Florida have heightened the need for early and accurate indicators of self-sustaining transmission in high risk areas across the southern United States. Given ZIKV’s low reporting rates and the geographic variability in suitable conditions, a cluster of reported cases may reflect diverse scenarios, ranging from independent introductions to a self-sustaining local epidemic.

Methods

We present a quantitative framework for real-time ZIKV risk assessment that captures uncertainty in case reporting, importations, and vector-human transmission dynamics.

Results

We assessed county-level risk throughout Texas, as of summer 2016, and found that importation risk was concentrated in large metropolitan regions, while sustained ZIKV transmission risk is concentrated in the southeastern counties including the Houston metropolitan region and the Texas-Mexico border (where the sole autochthonous cases have occurred in 2016). We found that counties most likely to detect cases are not necessarily the most likely to experience epidemics, and used our framework to identify triggers to signal the start of an epidemic based on a policymakers propensity for risk.

Conclusions

This framework can inform the strategic timing and spatial allocation of public health resources to combat ZIKV throughout the US, and highlights the need to develop methods to obtain reliable estimates of key epidemiological parameters.

Electronic supplementary material

The online version of this article (doi:10.1186/s12879-017-2394-9) contains supplementary material, which is available to authorized users.

Temporal patterns and geographic heterogeneity of Zika virus (ZIKV) outbreaks in French Polynesia and Central America

BACKGROUND

Zika virus (ZIKV) transmission has been reported in 67 countries/territories in the Oceania region and the Americas since 2015, prompting the World Health Organization (WHO) to declare ZIKV as a Public Health Emergency of International Concern in February 2016, due to its strong association with medical complications such as microcephaly and Guillain-Barré Syndrome (GBS). However, a substantial gap in knowledge still exists regarding differing temporal pattern and potential of transmission of ZIKV in different regions of the world.

METHODS

We use a phenomenological model to ascertain the temporal patterns and transmission potential of ZIKV in various countries/territories, by fitting the model to Zika case data from Yap Island and French Polynesia in the Oceania region and 11 countries/territories with confirmed case data, namely, Colombia, Ecuador, French Guiana, Guadeloupe, Guatemala, Mexico, Nicaragua, Panama, Puerto Rico, Saint Martin, and Suriname, to pinpoint the waves of infections in each country/territory and to estimate the respective basic reproduction number R₀.

RESULTS

Six of these time series datasets resulted in statistically significant model fit of at least one wave of reported cases, namely that of French Polynesia, Colombia, Puerto Rico, Guatemala, Suriname and Saint Martin. However, only Colombia and Guatemala exhibited two waves of cases while the others had only one wave. Temporal patterns of the second wave in Colombia and the single wave in Suriname are very similar, with the respective turning points separated by merely a week. Moreover, the mean estimates of R₀ for Colombia, Guatemala and Suriname, all land-based populations, range between 1.05 and 1.75, while the corresponding mean estimates for R₀ of island populations in French Polynesia, Puerto Rico and Saint Martin are significantly lower with a range of 5.70-6.89. We also fit the Richards model to Zika case data from six main archipelagos in French Polynesia, suggesting the outbreak in all six island populations occurred during the same time, albeit with different peak time, with mean R₀ range of 3.09-5.05.

DISCUSSION

Using the same modeling methodology, in this study we found a significant difference between transmissibility (as quantified by R₀) in island populations as opposed to land-based countries/territories, possibly suggesting an important role of geographic heterogeneity in the spread of vector-borne diseases and its future course, which requires further monitoring. Our result has potential implications for planning respective intervention and control policies targeted for island and land-based populations.

Diagnosis of Zika virus infection on a nanotechnology platform

We developed a multiplexed assay on a plasmonic-gold platform for measuring IgG and IgA antibodies and IgG avidity against both Zika virus (ZIKV) and dengue virus (DENV) infections. In contrast to IgM cross-reactivity, IgG and IgA antibodies against ZIKV nonstructural protein 1 (NS1) antigen were specific to ZIKV infection, and IgG avidity revealed recent ZIKV infection and past DENV-2 infection in patients in dengue-endemic regions. This assay could enable specific diagnosis of ZIKV infection over other flaviviral infections.

A comprehensive analysis and immunobiology of autoimmune neurological syndromes during the Zika virus outbreak in Cúcuta, Colombia

We have focused on the epidemiology and immunobiology of Zika virus (ZIKV) infection and factors associated with the development of Guillain-Barré syndrome (GBS) and other neurological syndromes in Cúcuta, the capital of North Santander department, Colombia. Data of patients with ZIKV disease reported to the national population-based surveillance system were used to calculate the basic reproduction number (R₀) and the attack rates (ARs) as well as to develop epidemiological maps. Patients with neurological syndromes were contacted and their diagnoses were confirmed. A case-control study in which 29 patients with GBS associated with ZIKV compared with 74-matched control patients with ZIKV infection alone was undertaken. Antibodies against arboviruses and other infections that may trigger GBS were evaluated. The estimated value of R₀ ranged between 2.68 (95% CI 2.54-2.67) to 4.57 (95% CI 4.18-5.01). The sex-specific ARs were 1306 per 100,000 females, and 552 per 100,000 males. A non-linear interaction between age and gender on the ARs was observed. The incidence of GBS in Cúcuta increased 4.41 times secondary to ZIKV infection. The lag time between ZIKV infection and neurological symptoms was 7 days (interquartile range 2-14.5). Patients with GBS appeared to represent a lower socioeconomic status and were living near to environmentally contaminated areas. All GBS patients were positive for IgG antibodies against both ZIKV and Dengue virus, and 69% were positive for Chikungunya virus. Noteworthy, GBS was associated with a previous infection with M. pneumoniae (OR: 3.95; 95% CI 1.44-13.01; p = 0.006). No differences in antibody levels against C. jejuni, Epstein-Barr virus and cytomegalovirus were observed. High rates of cranial nerves involvement and dysautonomia were present in 82% and 75.9%, respectively. Intensive care unit (ICU) admission was necessary in 69% of the GBS patients. Most of the patients disclosed a high disability condition (Hughes grade 4). Dysautonomia was the main risk factor of poor GBS prognosis (i.e., ICU admission and disability). Thirteen patients were diagnosed with other neurological syndromes different to GBS (6 with transverse myelitis, 3 with encephalitis, 3 with peripheral facial palsy and one with thoraco-lumbosacral myelopathy). Our data confirm an increased transmission of ZIKV in Cúcuta, and provide support to the view that severe neurological syndromes are related to ZIKV disease. The complex ways by which previous infections and socioeconomic status interact to increase the risk of GBS in people infected by ZIKV should be further investigated.

Estimating the subcritical transmissibility of the Zika outbreak in the State of Florida, USA, 2016

BACKGROUND

Florida State has reported autochthonous transmission of Zika virus since late July 2016. Here we assessed the transmissibility associated with the outbreak and generated a short-term forecast.

METHODS

Time-dependent dynamics of imported cases reported in the state of Florida was approximated by a logistic growth equation. We estimated the reproduction number using the renewal equation in order to predict the incidence of local cases arising from both local and imported primary cases. Using a bootstrap method together with the logistic and renewal equations, a short-term forecast of local and imported cases was carried out.

RESULTS

The reproduction number was estimated at 0.16 (95 % Confidence Interval: 0.13, 0.19). Employing the logistic equation to capture a drastic decline in the number of imported cases expected through the course of 2016, together with the low estimate of the local reproduction number in Florida, the expected number of local reported cases was demonstrated to show an evident declining trend for the remainder of 2016.

CONCLUSIONS

The risk of local transmission in the state of Florida is predicted to dramatically decline by the end of 2016.

Assessing the global threat from Zika virus

First discovered in 1947, Zika virus (ZIKV) infection remained a little-known tropical disease until 2015, when its apparent association with a considerable increase in the incidence of microcephaly in Brazil raised alarms worldwide. There is limited information on the key factors that determine the extent of the global threat from ZIKV infection and resulting complications. Here, we review what is known about the epidemiology, natural history, and public health effects of ZIKV infection, the empirical basis for this knowledge, and the critical knowledge gaps that need to be filled.

Zika Fetal Neuropathogenesis: Etiology of a Viral Syndrome

The ongoing Zika virus epidemic in the Americas and the observed association with both fetal abnormalities (primary microcephaly) and adult autoimmune pathology (Guillain-Barré syndrome) has brought attention to this neglected pathogen. While initial case studies generated significant interest in the Zika virus outbreak, larger prospective epidemiology and basic virology studies examining the mechanisms of Zika viral infection and associated pathophysiology are only now starting to be published. In this review, we analyze Zika fetal neuropathogenesis from a comparative pathology perspective, using the historic metaphor of "TORCH" viral pathogenesis to provide context. By drawing parallels to other viral infections of the fetus, we identify common themes and mechanisms that may illuminate the observed pathology. The existing data on the susceptibility of various cells to both Zika and other flavivirus infections are summarized. Finally, we highlight relevant aspects of the known molecular mechanisms of flavivirus replication.