Feb 28, 2020
Metabiota Risk Report No. 3: Monitoring and risk analytics for the 2019 Novel Coronavirus (COVID-19) EpidemicSince January 2, 2020, Metabiota has been closely monitoring and analyzing the COVID-19 epidemic. New cases continue to be reported, indicating the epidemic is not yet contained. Metabiota is tracking and analyzing this outbreak in several ways, including through a true-to-source digital surveillance system and a global disease spread model. Metabiota created a near-term forecasting model of disease spread, which incorporates the current known characteristics of the virus. Our forecasting model estimates, for March 3rd, a median… Download full PDF report here
Feb 21, 2019
Using Social Media to Estimate Zika's Impact on Tourism: #babymoon, 2014-2017Abstract: Zika virus infection during pregnancy can cause microcephaly and other birth defects. We hypothesized that the Latin America Zika epidemic resulted in pregnant women and their partners adopting behavioral changes to limit risk, leading them to forego travel to Zika-affected locations. We evaluated this hypothesis by studying travelers’ intent and behavior through Twitter data related to babymoon: a holiday taken by parents-to-be before their baby is born. We found the odds of mentioning representative Zika-affected locations in #babymoon tweets dropped significantly (Odds ratio: 0.29, 95% CI: 0.20–0.40) after the Zika-microcephaly association became well-known. This result was further corroborated through a content analysis of #babymoon tweets mentioning Zika-affected locations, which identified if the Twitter user was physically present in the Zika-affected locations. Conversely, we found a small but statistically insignificant increase in the odds of mentioning Zika-free locations from #babymoon tweets (Odds Ratio: 1.11, 95% CI: 0.97–1.27) after the Zika-microcephaly association became well-known.
Jan 31, 2019
Assessing global preparedness for the next pandemic: development and application of an Epidemic Preparedness IndexAbstract and Introduction: Robust metrics for national-level preparedness are critical for assessing global resilience to epidemic and pandemic outbreaks. However, existing preparedness assessments focus primarily on public health systems or specific legislative frameworks, and do not measure other essential capacities that enable and support public health preparedness and response. Methods: We developed an Epidemic Preparedness Index (EPI) to assess national-level preparedness. The EPI is global, covering 188 countries. It consists of five subindices measuring each country’s economic resources, public health communications, infrastructure, public health systems and institutional capacity. To evaluate the construct validity of the EPI, we tested its correlation with proxy measures for preparedness and response capacity, including the timeliness of outbreak detection and reporting, as well as vaccination rates during the 2009 H1N1 influenza pandemic. Results: The most prepared countries were concentrated in Europe and North America, while the least prepared countries clustered in Central and West Africa and Southeast Asia. Better prepared countries were found to report infectious disease outbreaks more quickly and to have vaccinated a larger proportion of their population during the 2009 pandemic. Conclusion: The EPI measures a country’s capacity to detect and respond to infectious disease events. Existing tools, such as the Joint External Evaluation (JEE), have been designed to measure preparedness within a country over time. The EPI complements the JEE by providing a holistic view of preparedness and is constructed to support comparative risk assessment between countries. The index can be updated rapidly to generate global estimates of pandemic preparedness that can inform strategy and resource allocation.
Dec 04, 2017
Pandemics: Risks, Impacts, MitigationIntroduction: Pandemics are large-scale outbreaks of infectious disease that can greatly increase morbidity and mortality over a wide geographic area and cause significant economic, social, and political disruption. Evidence suggests that the likelihood of pandemics has increased over the past century because of increased global travel and integration, urbanization, changes in land use, and greater exploitation of the natural environment (Jones and others 2008; Morse 1995). These trends likely will continue and will intensify. Significant policy attention has focused on the need to identify and limit emerging outbreaks that might lead to pandemics and to expand and sustain investment to build preparedness and health capacity (Smolinsky, Hamburg, and Lederberg 2003). The international community has made progress toward preparing for and mitigating the impacts of pandemics. The 2003 severe acute respiratory syndrome (SARS) pandemic and growing concerns about the threat posed by avian influenza led many countries to devise pandemic plans (U.S. Department of Health and Human Services 2005). Delayed reporting of early SARS cases also led the World Health Assembly to update the International Health Regulations (IHR) to compel all World Health Organization member states to meet specific standards for detecting, reporting on, and responding to outbreaks (WHO 2005).
Jun 30, 2017
Yellow Fever and Dengue Fever Viruses' Serosurvey in Non-human Primates of the Kedougou Forest Galleries in Southeastern SenegalThe potential risk of non-human primates in Senegal to be natural hosts for arboviruses of importance for human has been assessed. A total of 58 wild monkeys, including 14 Erythrocebus patas and 44 Chlorocebus sabaeus, were trapped at three sites within forest galleries and the nearby village of Ngari, in the Kedougou area, Southeastern Senegal. ### Photo credit: publicdomainphotography via Visual hunt / CC BY-SA
Aug 19, 2016
Uncovering Earth’s ViromeViruses are the most abundant biological entities on Earth, but challenges in detecting, isolating, and classifying unknown viruses have prevented exhaustive surveys of the global virome. Here we analysed over 5 Tb of metagenomic sequence data from 3,042 geographically diverse samples to assess the global distribution, phylogenetic diversity, and host specificity of viruses. We discovered over 125,000 partial DNA viral genomes, including the largest phage yet identified, and increased the number of known viral genes by 16-fold. Half of the predicted partial viral genomes were clustered into genetically distinct groups, most of which included genes unrelated to those in known viruses. Using CRISPR spacers and transfer RNA matches to link viral groups to microbial host(s), we doubled the number of microbial phyla known to be infected by viruses, and identified viruses that can infect organisms from different phyla. Analysis of viral distribution across diverse ecosystems revealed strong habitat-type specificity for the vast majority of viruses, but also identified some cosmopolitan groups. Our results highlight an extensive global viral diversity and provide detailed insight into viral habitat distribution and host–virus interactions. doi:10.1038/nature1909
Aug 02, 2016
The Importance of Data in Salmonella Risk Mitigation: Development of a Cloud-based Technical Platform for Food Safety Management in Poultry ProductionFoodborne disease outbreaks represent an ever-present risk to human health and the poultry industry, with notable Salmonella outbreaks occurring in recent years. Outbreaks result in adverse health effects to the consumer, as well as negative brand impact and financial losses to companies. Following a multistate outbreak of Salmonella Heidelberg, a poultry producer worked with a biotechnology firm to collect, integrate, and analyze data across its operations.
Jun 17, 2016
Zika Virus in the Americas: Early Epidemiological and Genetic FindingsBrazil has experienced an unprecedented epidemic of Zika virus (ZIKV), with ~30,000 cases reported to date. ZIKV was first detected in Brazil in May 2015 and cases of microcephaly potentially associated with ZIKV infection were identified in November 2015. Using next generation sequencing we generated seven Brazilian ZIKV genomes, sampled from four self-limited cases, one blood donor, one fatal adult case, and one newborn with microcephaly and congenital malformations. Phylogenetic and molecular clock analyses show a single introduction of ZIKV into the Americas, estimated to have occurred between May-Dec 2013, more than 12 months prior to the detection of ZIKV in Brazil. The estimated date of origin coincides with an increase in air passengers to Brazil from ZIKV endemic areas, and with reported outbreaks in Pacific Islands. ZIKV genomes from Brazil are phylogenetically interspersed with those from other South American and Caribbean countries. Mapping mutations onto existing structural models revealed the context of viral amino acid changes present in the outbreak lineage; however no shared amino acid changes were found among the three currently available virus genomes from microcephaly cases. Municipality-level incidence data indicate that reports of suspected microcephaly in Brazil best correlate with ZIKV incidence around week 17 of pregnancy, although this does not demonstrate causation. Our genetic description and analysis of ZIKV isolates in Brazil provide a baseline for future studies of the evolution and molecular epidemiology in the Americas of this emerging virus.
Oct 01, 2015
The Vietnam Initiative on Zoonotic Infections (VIZIONS): A Strategic Approach to Studying Emerging Zoonotic Infectious DiseasesThe effect of newly emerging or re-emerging infectious diseases of zoonotic origin in human populations can be potentially catastrophic, and large-scale investigations of such diseases are highly challenging. The monitoring of emergence events is subject to ascertainment bias, whether at the level of species discovery, emerging disease events, or disease outbreaks in human populations. Disease surveillance is generally performed post hoc, driven by a response to recent events and by the availability of detection and identification technologies.
Sep 22, 2015