Among the ten major virus outbreaks in the last 50 years, Marburg ranked first in terms of the fatality rate with 80 percent. In comparison, the recent novel coronavirus, originating from the Chinese city of Wuhan, had an estimated fatality rate of 2.2 percent as of January 31, 2020.

Alarming COVID-19 fatality rate in Mexico More than 812,000 people worldwide had died from COVID-19 as of August 24, 2020. Three of the most populous countries in the world have reported particularly large numbers of coronavirus-related deaths: Mexico, Brazil, and the United States. Out of those three nations, Mexico has the highest COVID-19 death rate, with around one in ten confirmed cases resulting in death. The high fatality rate in Mexico indicates that cases may be much higher than reported because testing capacity has been severely stretched.

Post-lockdown complacency a real danger In March 2020, each infected person was estimated to transmit the COVID-19 virus to between 1.5 and 3.5 other people, which was a higher infection rate than the seasonal flu. The coronavirus is primarily spread through respiratory droplets, and transmission commonly occurs when people are in close contact. As lockdowns ease around the world, people are being urged not to become complacent; continue to wear face coverings and practice social distancing, which can help to prevent further infections.

Based on a comparison of coronavirus deaths in 210 countries relative to their population, Peru had the most losses to COVID-19 up until July 13, 2022. As of the same date, the virus had infected over 557.8 million people worldwide, and the number of deaths had totaled more than 6.3 million. Note, however, that COVID-19 test rates can vary per country. Additionally, big differences show up between countries when combining the number of deaths against confirmed COVID-19 cases. The source seemingly does not differentiate between "the Wuhan strain" (2019-nCOV) of COVID-19, "the Kent mutation" (B.1.1.7) that appeared in the UK in late 2020, the 2021 Delta variant (B.1.617.2) from India or the Omicron variant (B.1.1.529) from South Africa.

The difficulties of death figures

This table aims to provide a complete picture on the topic, but it very much relies on data that has become more difficult to compare. As the coronavirus pandemic developed across the world, countries already used different methods to count fatalities, and they sometimes changed them during the course of the pandemic. On April 16, for example, the Chinese city of Wuhan added a 50 percent increase in their death figures to account for community deaths. These deaths occurred outside of hospitals and went unaccounted for so far. The state of New York did something similar two days before, revising their figures with 3,700 new deaths as they started to include “assumed” coronavirus victims. The United Kingdom started counting deaths in care homes and private households on April 29, adjusting their number with about 5,000 new deaths (which were corrected lowered again by the same amount on August 18). This makes an already difficult comparison even more difficult. Belgium, for example, counts suspected coronavirus deaths in their figures, whereas other countries have not done that (yet). This means two things. First, it could have a big impact on both current as well as future figures. On April 16 already, UK health experts stated that if their numbers were corrected for community deaths like in Wuhan, the UK number would change from 205 to “above 300”. This is exactly what happened two weeks later. Second, it is difficult to pinpoint exactly which countries already have “revised” numbers (like Belgium, Wuhan or New York) and which ones do not. One work-around could be to look at (freely accessible) timelines that track the reported daily increase of deaths in certain countries. Several of these are available on our platform, such as for Belgium, Italy and Sweden. A sudden large increase might be an indicator that the domestic sources changed their methodology.

Where are these numbers coming from?

The numbers shown here were collected by Johns Hopkins University, a source that manually checks the data with domestic health authorities. For the majority of countries, this is from national authorities. In some cases, like China, the United States, Canada or Australia, city reports or other various state authorities were consulted. In this statistic, these separately reported numbers were put together. For more information or other freely accessible content, please visit our dedicated Facts and Figures page.

The New York Times is releasing a series of data files with cumulative counts of coronavirus cases in the United States, at the state and county level, over time. We are compiling this time series data from state and local governments and health departments in an attempt to provide a complete record of the ongoing outbreak.

Since late January, The Times has tracked cases of coronavirus in real time as they were identified after testing. Because of the widespread shortage of testing, however, the data is necessarily limited in the picture it presents of the outbreak.

We have used this data to power our maps and reporting tracking the outbreak, and it is now being made available to the public in response to requests from researchers, scientists and government officials who would like access to the data to better understand the outbreak.

The data begins with the first reported coronavirus case in Washington State on Jan. 21, 2020. We will publish regular updates to the data in this repository.

This dataset provides values for CORONAVIRUS DEATH reported in several countries. The data includes current values, previous releases, historical highs and record lows, release frequency, reported unit and currency.

The World Health Organization reported 6932591 Coronavirus Deaths since the epidemic began. In addition, countries reported 766440796 Coronavirus Cases. This dataset provides - World Coronavirus Deaths- actual values, historical data, forecast, chart, statistics, economic calendar and news.

As of May 2, 2023, the outbreak of the coronavirus disease (COVID-19) had spread to almost every country in the world, and more than 6.86 million people had died after contracting the respiratory virus. Over 1.16 million of these deaths occurred in the United States.

Waves of infections Almost every country and territory worldwide have been affected by the COVID-19 disease. At the end of 2021 the virus was once again circulating at very high rates, even in countries with relatively high vaccination rates such as the United States and Germany. As rates of new infections increased, some countries in Europe, like Germany and Austria, tightened restrictions once again, specifically targeting those who were not yet vaccinated. However, by spring 2022, rates of new infections had decreased in many countries and restrictions were once again lifted.

What are the symptoms of the virus? It can take up to 14 days for symptoms of the illness to start being noticed. The most commonly reported symptoms are a fever and a dry cough, leading to shortness of breath. The early symptoms are similar to other common viruses such as the common cold and flu. These illnesses spread more during cold months, but there is no conclusive evidence to suggest that temperature impacts the spread of the SARS-CoV-2 virus. Medical advice should be sought if you are experiencing any of these symptoms.

BackgroundInfluenza and respiratory syncytial virus (RSV) associated mortality has not been well-established in tropical Africa.MethodsWe used the negative binomial regression method and the rate-difference method (i.e. deaths during low and high influenza/RSV activity months), to estimate excess mortality attributable to influenza and RSV using verbal autopsy data collected through a health and demographic surveillance system in Western Kenya, 2007–2013. Excess mortality rates were calculated for a) all-cause mortality, b) respiratory deaths (including pneumonia), c) HIV-related deaths, and d) pulmonary tuberculosis (TB) related deaths.ResultsUsing the negative binomial regression method, the mean annual all-cause excess mortality rate associated with influenza and RSV was 14.1 (95% confidence interval [CI] 0.0–93.3) and 17.1 (95% CI 0.0–111.5) per 100,000 person-years (PY) respectively; and 10.5 (95% CI 0.0–28.5) and 7.3 (95% CI 0.0–27.3) per 100,000 PY for respiratory deaths, respectively. Highest mortality rates associated with influenza were among ≥50 years, particularly among persons with TB (41.6[95% CI 0.0–122.7]); and with RSV were among

Among COVID-19 patients in the United States from February 12 to March 16, 2020, estimated case-fatality rates were highest for adults aged 85 years and older. Younger people appeared to have milder symptoms, and there were no deaths reported among persons aged 19 years and under.

Tracking the virus in the United States The outbreak of a previously unknown viral pneumonia was first reported in China toward the end of December 2019. The first U.S. case of COVID-19 was recorded in mid-January 2020, confirmed in a patient who had returned to the United States from China. The virus quickly started to spread, and the first community-acquired case was confirmed one month later in California. Overall, there had been approximately 4.5 million coronavirus cases in the country by the start of August 2020.

U.S. health care system stretched California, Florida, and Texas are among the states with the most coronavirus cases. Even the best-resourced hospitals in the United States have struggled to cope with the crisis, and certain areas of the country were dealt further blows by new waves of infections in July 2020. Attention is rightly focused on fighting the pandemic, but as health workers are redirected to care for COVID-19 patients, the United States must not lose sight of other important health care issues.

BackgroundIn a given population the age pattern of mortality is an important determinant of total number of deaths, age structure, and through effects on age structure, the number of births and thereby growth. Good mortality models exist for most populations except those experiencing generalized HIV epidemics and some developing country populations. The large number of deaths concentrated at very young and adult ages in HIV-affected populations produce a unique ‘humped’ age pattern of mortality that is not reproduced by any existing mortality models. Both burden of disease reporting and population projection methods require age-specific mortality rates to estimate numbers of deaths and produce plausible age structures. For countries with generalized HIV epidemics these estimates should take into account the future trajectory of HIV prevalence and its effects on age-specific mortality. In this paper we present a parsimonious model of age-specific mortality for countries with generalized HIV/AIDS epidemics.Methods and FindingsThe model represents a vector of age-specific mortality rates as the weighted sum of three independent age-varying components. We derive the age-varying components from a Singular Value Decomposition of the matrix of age-specific mortality rate schedules. The weights are modeled as a function of HIV prevalence and one of three possible sets of inputs: life expectancy at birth, a measure of child mortality, or child mortality with a measure of adult mortality. We calibrate the model with 320 five-year life tables for each sex from the World Population Prospects 2010 revision that come from the 40 countries of the world that have and are experiencing a generalized HIV epidemic. Cross validation shows that the model is able to outperform several existing model life table systems.ConclusionsWe present a flexible, parsimonious model of age-specific mortality for countries with generalized HIV epidemics. Combined with the outputs of existing epidemiological and demographic models, this model makes it possible to project future age-specific mortality profiles and number of deaths for countries with generalized HIV epidemics.

PurposeCardiovascular disease (CVD) is the leading cause of death in the United States, and sepsis significantly contributes to hospitalization and mortality. This study aims to assess the trends of sepsis-associated CVD mortality rates and variations in mortality based on demographics and regions in the US.MethodsThe Centers for Disease Control and Prevention Wide-ranging Online Data for Epidemiologic Research (CDC WONDER) database was used to identify CVD and sepsis-related deaths from 1999 to 2022. Data on gender, race and ethnicity, age groups, region, and state classification were statistically analyzed to obtain crude and age-adjusted mortality rates (AAMR). The Joinpoint Regression Program was used to determine trends in mortality within the study period.ResultsDuring the study period, there were a total of 1,842,641 deaths with both CVD and sepsis listed as a cause of death. Sepsis-associated CVD mortality decreased between 1999 and 2013, from AAMR of 65.7 in 1999 to 58.8 in 2013 (APC −1.06*%, 95% CI: −2.12% to −0.26%), then rose to 74.3 in 2022 (APC 3.23*%, 95% CI: 2.18%–5.40%). Throughout the study period, mortality rates were highest in men, NH Black adults, and elderly adults (65+ years old). The Northeast region, which had the highest mortality rate in the initial part of the study period, was the only region to see a decline in mortality, while the Northwest, Midwest, and Southern regions experienced significant increases in mortality rates.ConclusionSepsis-associated CVD mortality has increased in the US over the past decade, and both this general trend and the demographic disparities have worsened since the onset of the COVID-19 pandemic.

Due to its high mortality rate and continued re-emergence, Ebolavirus disease (EVD) continues to pose a serious threat to global health. A group of viruses within the genus Ebolavirus causes this severe hemorrhagic disease in humans: Ebola virus (EBOV; species Zaire ebolavirus), Sudan virus (SUDV; species Sudan ebolavirus), Bundibugyo virus, and Taï Forest virus. EBOV and SUDV are associated with the highest case fatality rates. While the host response to EBOV has been comprehensively examined, limited data exists for SUDV infection. For medical countermeasure testing, well-characterized SUDV nonhuman primate (NHP) models are thus needed. Here, we describe a natural history study in which rhesus (N = 11) and cynomolgus macaques (N = 14) were intramuscularly exposed to a 1000 plaque-forming unit dose of SUDV (Gulu variant). Time-course analyses of various hematological, pathological, serological, coagulation, and transcriptomic findings are reported. SUDV infection was uniformly lethal in cynomolgus macaques (100% mortality), whereas a single rhesus macaque subject (91% mortality) survived to the study endpoint (median time-to-death of ∼8.0 and ∼8.5 days in cynomolgus and rhesus macaques, respectively). Infected macaques exhibited hallmark features of human EVD. The early stage was typified by viremia, granulocytosis, lymphopenia, albuminemia, thrombocytopenia, and decreased expression of HLA-class transcripts. At mid-to-late disease, animals developed fever and petechial rashes, and expressed high levels of pro-inflammatory mediators, pro-thrombotic factors, and markers indicative of liver and kidney injury. End-stage disease was characterized by shock and multi-organ failure. In summary, macaques recapitulate human SUDV disease, supporting these models for use in the development of vaccines and therapeutics.

The leading causes of death in Massachusetts are cancer, heart disease, unintentional injury, stroke, and chronic lower respiratory disease. These mortality rates tend to be higher for people of color; and Black residents have a higher premature mortality rate overall and Asian residents have a higher rate of mortality due to stroke.

Context - Covid data falsification discussion:

An active discussion about the mortality data in Moscow has erupted in the days. The Moscow Times newspaper drew attention to a significant increase in official mortality rates in April 2020: "Moscow recorded 20% more fatalities in April 2020 compared to its average April mortality total over the past decade, according to newly published preliminary data from Moscow’s civil registry office. The data comes as Russia sees the fastest growth in coronavirus infections in Europe, while its mortality rate remains much lower than in many countries. Moscow, the epicenter of Russia’s coronavirus outbreak, has continued to see daily spikes in new cases despite being under lockdown since March 30. According to the official data, 11,846 people died in Russia’s capital in April of this year, roughly a 20% increase from the 10-year average for April deaths, which is 9,866. The numbers suggest that the city’s statistics of coronavirus deaths may be higher in reality than official numbers indicate. Russia boasts a relatively low coronavirus mortality rate of 0.9%, which experts believe is linked to the way coronavirus-related deaths are counted."

After this publication have been realesed The Moscow Department of Health has denied the statement of the inaccuracy of counting.:

First, Moscow is a region that openly publishes mortality data on its websites. Moscow on an initiative basis published data for April before the federal structures did it. Secondly, the comparison of mortality rates in the monthly dynamics is incorrect and is not a clear evidence of any trends. In April 2020, indeed, according to the Civil Registry Office in Moscow, 11,846 death certificates were issued. So, the increase compared to April 2019 amounted to 1841 people, and compared to the same month of 2018 - 985 people, i.e. 2 times less. Thirdly, the diagnosis of coronavirus-infected deaths in Moscow is established after a mandatory autopsy is performed in strict accordance with the Provisional Guidelines of the Russian Ministry of Health.Of the total number of deaths in April 2020, 639 are people whose cause of death is coronavirus infection and its complications, most often pneumonia.It should be emphasized that the pathological autopsy of the dead with suspected CoV-19 in Russia and Moscow is carried out in 100% of cases, unlike most other countries.It is impossible to name the cause of death of COVID-19 in other cases. For example, over 60% of deaths occurred from obvious alternative causes, such as vascular accidents (myocardial infarction and stroke), stage 4 malignant diseases (essentially palliative patients), leukemia, systemic diseases with the development of organ failure (e.g. amyloidosis and terminal renal insufficiency) and other non-curable deadly diseases. Fourth, any seasonal increase in the incidence of SARS, not to mention the pandemic caused by the spread of the new coronavirus, is always accompanied by an increase in mortality. This is due to the appearance of the dead directly from an infectious disease, but to an even greater extent from other diseases, the exacerbation of which and the decompensation of the condition of patients suffering from these diseases also leads to death. In these cases, the infectious onset is a catalyst for the rapid progression of chronic diseases and the manifestation of new diseases. Fifthly, a similar situation with statistics is observed in other countries - mortality from COVID-19 is lower than the overall increase in mortality. According to the official sites of cities:In New York, mortality from coronavirus in April amounted to 11,861 people. At the same time, the total increase in mortality compared to the same period in 2019 is 15709.In London, in April, 3,589 people died with a diagnosis of coronavirus, while the total increase was 5531 Sixth, even if all the additional mortality for April in Moscow is attributed to coronavirus, the mortality from COVID will be slightly more than 3%, which is lower than the official mortality in New York and London (10% and 23%, respectively). Moreover, if you make such a recount in these cities, the mortality rate in them will be 13% and 32%, respectively. Seventh, Moscow is open for discussion and is ready to share experience with both Russian and foreign experts.

Content

I think community members would be interested in studying the data on mortality in the Russian capital themselves and conducting a competent statistical check.

This may be of particular interest in connection with that he [US announced a grant of $ 250 thousand to "expose the disinformation of health care" in Russia](https://www....

Updates

• Notice of data discontinuation: Since the start of the pandemic, AP has reported case and death counts from data provided by Johns Hopkins University. Johns Hopkins University has announced that they will stop their daily data collection efforts after March 10. As Johns Hopkins stops providing data, the AP will also stop collecting daily numbers for COVID cases and deaths. The HHS and CDC now collect and visualize key metrics for the pandemic. AP advises using those resources when reporting on the pandemic going forward.

  • CDC Weekly case and death counts (national and state level)
  • CDC County level cases and deaths
  • HHS New hospital admissions
  • CDC NowCast COVID variant proportions (national and regional level)

• April 9, 2020

  • The population estimate data for New York County, NY has been updated to include all five New York City counties (Kings County, Queens County, Bronx County, Richmond County and New York County). This has been done to match the Johns Hopkins COVID-19 data, which aggregates counts for the five New York City counties to New York County.

• April 20, 2020

  • Johns Hopkins death totals in the US now include confirmed and probable deaths in accordance with CDC guidelines as of April 14. One significant result of this change was an increase of more than 3,700 deaths in the New York City count. This change will likely result in increases for death counts elsewhere as well. The AP does not alter the Johns Hopkins source data, so probable deaths are included in this dataset as well.

• April 29, 2020

  • The AP is now providing timeseries data for counts of COVID-19 cases and deaths. The raw counts are provided here unaltered, along with a population column with Census ACS-5 estimates and calculated daily case and death rates per 100,000 people. Please read the updated caveats section for more information.

• September 1st, 2020

  • Johns Hopkins is now providing counts for the five New York City counties individually.

• February 12, 2021

  • The Ohio Department of Health recently announced that as many as 4,000 COVID-19 deaths may have been underreported through the state’s reporting system, and that the "daily reported death counts will be high for a two to three-day period."
  • Because deaths data will be anomalous for consecutive days, we have chosen to freeze Ohio's rolling average for daily deaths at the last valid measure until Johns Hopkins is able to back-distribute the data. The raw daily death counts, as reported by Johns Hopkins and including the backlogged death data, will still be present in the new_deaths column.

• February 16, 2021

  - Johns Hopkins has reconciled Ohio's historical deaths data with the state.

  Overview

The AP is using data collected by the Johns Hopkins University Center for Systems Science and Engineering as our source for outbreak caseloads and death counts for the United States and globally.

The Hopkins data is available at the county level in the United States. The AP has paired this data with population figures and county rural/urban designations, and has calculated caseload and death rates per 100,000 people. Be aware that caseloads may reflect the availability of tests -- and the ability to turn around test results quickly -- rather than actual disease spread or true infection rates.

This data is from the Hopkins dashboard that is updated regularly throughout the day. Like all organizations dealing with data, Hopkins is constantly refining and cleaning up their feed, so there may be brief moments where data does not appear correctly. At this link, you’ll find the Hopkins daily data reports, and a clean version of their feed.

The AP is updating this dataset hourly at 45 minutes past the hour.

To learn more about AP's data journalism capabilities for publishers, corporations and financial institutions, go here or email kromano@ap.org.

Queries

Use AP's queries to filter the data or to join to other datasets we've made available to help cover the coronavirus pandemic

• Filter cases by state here

• Rank states by their status as current hotspots. Calculates the 7-day rolling average of new cases per capita in each state: https://data.world/associatedpress/johns-hopkins-coronavirus-case-tracker/workspace/query?queryid=481e82a4-1b2f-41c2-9ea1-d91aa4b3b1ac

• Find recent hotspots within your state by running a query to calculate the 7-day rolling average of new cases by capita in each county: https://data.world/associatedpress/johns-hopkins-coronavirus-case-tracker/workspace/query?queryid=b566f1db-3231-40fe-8099-311909b7b687&showTemplatePreview=true

• Join county-level case data to an earlier dataset released by AP on local hospital capacity here. To find out more about the hospital capacity dataset, see the full details.

• Pull the 100 counties with the highest per-capita confirmed cases here

• Rank all the counties by the highest per-capita rate of new cases in the past 7 days here. Be aware that because this ranks per-capita caseloads, very small counties may rise to the very top, so take into account raw caseload figures as well.

Interactive

The AP has designed an interactive map to track COVID-19 cases reported by Johns Hopkins.

@(https://datawrapper.dwcdn.net/nRyaf/15/)

Interactive Embed Code

<iframe title="USA counties (2018) choropleth map Mapping COVID-19 cases by county" aria-describedby="" id="datawrapper-chart-nRyaf" src="https://datawrapper.dwcdn.net/nRyaf/10/" scrolling="no" frameborder="0" style="width: 0; min-width: 100% !important;" height="400"></iframe><script type="text/javascript">(function() {'use strict';window.addEventListener('message', function(event) {if (typeof event.data['datawrapper-height'] !== 'undefined') {for (var chartId in event.data['datawrapper-height']) {var iframe = document.getElementById('datawrapper-chart-' + chartId) || document.querySelector("iframe[src*='" + chartId + "']");if (!iframe) {continue;}iframe.style.height = event.data['datawrapper-height'][chartId] + 'px';}}});})();</script>

Caveats

• This data represents the number of cases and deaths reported by each state and has been collected by Johns Hopkins from a number of sources cited on their website.
• In some cases, deaths or cases of people who've crossed state lines -- either to receive treatment or because they became sick and couldn't return home while traveling -- are reported in a state they aren't currently in, because of state reporting rules.
• In some states, there are a number of cases not assigned to a specific county -- for those cases, the county name is "unassigned to a single county"
• This data should be credited to Johns Hopkins University's COVID-19 tracking project. The AP is simply making it available here for ease of use for reporters and members.
• Caseloads may reflect the availability of tests -- and the ability to turn around test results quickly -- rather than actual disease spread or true infection rates.
• Population estimates at the county level are drawn from 2014-18 5-year estimates from the American Community Survey.
• The Urban/Rural classification scheme is from the Center for Disease Control and Preventions's National Center for Health Statistics. It puts each county into one of six categories -- from Large Central Metro to Non-Core -- according to population and other characteristics. More details about the classifications can be found here.

Johns Hopkins timeseries data - Johns Hopkins pulls data regularly to update their dashboard. Once a day, around 8pm EDT, Johns Hopkins adds the counts for all areas they cover to the timeseries file. These counts are snapshots of the latest cumulative counts provided by the source on that day. This can lead to inconsistencies if a source updates their historical data for accuracy, either increasing or decreasing the latest cumulative count. - Johns Hopkins periodically edits their historical timeseries data for accuracy. They provide a file documenting all errors in their timeseries files that they have identified and fixed here

Attribution

This data should be credited to Johns Hopkins University COVID-19 tracking project

Every year the CDC releases the country’s most detailed report on death in the United States under the National Vital Statistics Systems. This mortality dataset is a record of every death in the country for 2005 through 2015, including detailed information about causes of death and the demographic background of the deceased.

It's been said that "statistics are human beings with the tears wiped off." This is especially true with this dataset. Each death record represents somebody's loved one, often connected with a lifetime of memories and sometimes tragically too short.

Putting the sensitive nature of the topic aside, analyzing mortality data is essential to understanding the complex circumstances of death across the country. The US Government uses this data to determine life expectancy and understand how death in the U.S. differs from the rest of the world. Whether you’re looking for macro trends or analyzing unique circumstances, we challenge you to use this dataset to find your own answers to one of life’s great mysteries.

Overview

This dataset is a collection of CSV files each containing one year's worth of data and paired JSON files containing the code mappings, plus an ICD 10 code set. The CSVs were reformatted from their original fixed-width file formats using information extracted from the CDC's PDF manuals using this script. Please note that this process may have introduced errors as the text extracted from the pdf is not a perfect match. If you have any questions or find errors in the preparation process, please leave a note in the forums. We hope to publish additional years of data using this method soon.

A more detailed overview of the data can be found here. You'll find that the fields are consistent within this time window, but some of data codes change every few years. For example, the 113_cause_recode entry 069 only covers ICD codes (I10,I12) in 2005, but by 2015 it covers (I10,I12,I15). When I post data from years prior to 2005, expect some of the fields themselves to change as well.

All data comes from the CDC’s National Vital Statistics Systems, with the exception of the Icd10Code, which are sourced from the World Health Organization.

Project ideas

• The CDC's mortality data was the basis of a widely publicized paper, by Anne Case and Nobel prize winner Angus Deaton, arguing that middle-aged whites are dying at elevated rates. One of the criticisms against the paper is that it failed to properly account for the exact ages within the broad bins available through the CDC's WONDER tool. What do these results look like with exact/not-binned age data?
• Similarly, how sensitive are the mortality trends being discussed in the news to the choice of bin-widths?
• As noted above, the data preparation process could have introduced errors. Can you find any discrepancies compared to the aggregate metrics on WONDER? If so, please let me know in the forums!
• WONDER is cited in numerous economics, sociology, and public health research papers. Can you find any papers whose conclusions would be altered if they used the exact data available here rather than binned data from Wonder?

Differences from the first version of the dataset

• This version of the dataset was prepared in a completely different many. This has allowed us to provide a much larger volume of data and ensure that codes are available for every field.
• We've replaced the batch of sql files with a single JSON per year. Kaggle's platform currently offer's better support for JSON files, and this keeps the number of files manageable.
• A tutorial kernel providing a quick introduction to the new format is available here.
• Lastly, I apologize if the transition has interrupted anyone's work! If need be, you can still download v1.

BackgroundFoodborne diseases are important worldwide, resulting in considerable morbidity and mortality. To our knowledge, we present the first global and regional estimates of the disease burden of the most important foodborne bacterial, protozoal, and viral diseases.Methods and FindingsWe synthesized data on the number of foodborne illnesses, sequelae, deaths, and Disability Adjusted Life Years (DALYs), for all diseases with sufficient data to support global and regional estimates, by age and region. The data sources included varied by pathogen and included systematic reviews, cohort studies, surveillance studies and other burden of disease assessments. We sought relevant data circa 2010, and included sources from 1990–2012. The number of studies per pathogen ranged from as few as 5 studies for bacterial intoxications through to 494 studies for diarrheal pathogens. To estimate mortality for Mycobacterium bovis infections and morbidity and mortality for invasive non-typhoidal Salmonella enterica infections, we excluded cases attributed to HIV infection. We excluded stillbirths in our estimates. We estimate that the 22 diseases included in our study resulted in two billion (95% uncertainty interval [UI] 1.5–2.9 billion) cases, over one million (95% UI 0.89–1.4 million) deaths, and 78.7 million (95% UI 65.0–97.7 million) DALYs in 2010. To estimate the burden due to contaminated food, we then applied proportions of infections that were estimated to be foodborne from a global expert elicitation. Waterborne transmission of disease was not included. We estimate that 29% (95% UI 23–36%) of cases caused by diseases in our study, or 582 million (95% UI 401–922 million), were transmitted by contaminated food, resulting in 25.2 million (95% UI 17.5–37.0 million) DALYs. Norovirus was the leading cause of foodborne illness causing 125 million (95% UI 70–251 million) cases, while Campylobacter spp. caused 96 million (95% UI 52–177 million) foodborne illnesses. Of all foodborne diseases, diarrheal and invasive infections due to non-typhoidal S. enterica infections resulted in the highest burden, causing 4.07 million (95% UI 2.49–6.27 million) DALYs. Regionally, DALYs per 100,000 population were highest in the African region followed by the South East Asian region. Considerable burden of foodborne disease is borne by children less than five years of age. Major limitations of our study include data gaps, particularly in middle- and high-mortality countries, and uncertainty around the proportion of diseases that were foodborne.ConclusionsFoodborne diseases result in a large disease burden, particularly in children. Although it is known that diarrheal diseases are a major burden in children, we have demonstrated for the first time the importance of contaminated food as a cause. There is a need to focus food safety interventions on preventing foodborne diseases, particularly in low- and middle-income settings.

Nipah Virus Testing Market Outlook

The Nipah Virus Testing Market is projected to experience significant growth, with the market size valued at approximately USD 250 million in 2023 and expected to reach around USD 750 million by 2032, growing at a CAGR of 12.7%. The global market for Nipah virus testing is driven by the urgent need for effective diagnostic methods due to the recurrent outbreaks of the virus, the high fatality rate associated with Nipah virus infections, and the increasing awareness and preparedness for potential pandemics.

One of the primary growth factors for the Nipah virus testing market is the increased frequency and severity of Nipah virus outbreaks. Countries in Southeast Asia, particularly Bangladesh and India, have reported multiple outbreaks over the years, emphasizing the need for rapid and accurate diagnostics. This demand is further fueled by the high mortality rate associated with Nipah virus infections, which ranges from 40% to 75%, making it imperative to develop reliable testing methods to contain the spread of the virus effectively.

Another significant growth factor is the advancements in diagnostic technologies that have made testing more accessible and accurate. Innovations such as Real-Time Polymerase Chain Reaction (RT-PCR) and Enzyme-Linked Immunosorbent Assay (ELISA) have revolutionized the detection of Nipah virus, allowing for quicker and more precise identification of the virus in infected individuals. These advanced diagnostics not only contribute to better patient outcomes but also help in implementing timely public health interventions to prevent widespread transmission.

Moreover, increasing investments in healthcare infrastructure and research are also contributing to the market growth. Governments and private organizations are investing heavily in the development of diagnostic laboratories and research institutes dedicated to studying and combating emerging infectious diseases. Such investments are crucial in enhancing the capabilities of healthcare systems to respond swiftly to Nipah virus outbreaks, thereby driving the demand for Nipah virus testing solutions.

Regionally, the Asia Pacific region is expected to dominate the Nipah virus testing market due to the higher incidence of Nipah virus outbreaks in this region. Countries like India, Bangladesh, and Malaysia are investing significantly in healthcare infrastructure and diagnostic capabilities to tackle the Nipah virus effectively. In contrast, regions like North America and Europe are witnessing growth in the market due to increased awareness and preparedness for potential outbreaks, further supported by robust healthcare systems and substantial research funding.

Arbovirus Testing is becoming increasingly relevant in the context of global health as the prevalence of arboviruses, such as dengue, Zika, and chikungunya, continues to rise. These viruses, transmitted by arthropods like mosquitoes, pose significant public health challenges, particularly in tropical and subtropical regions. The development of efficient and accurate arbovirus testing methods is crucial for timely diagnosis and management of these infections. Advances in molecular diagnostics, including RT-PCR and serological assays, have enhanced the ability to detect arboviruses quickly and accurately, thereby aiding in the implementation of effective control measures. As the threat of arboviruses grows, the demand for comprehensive testing solutions is expected to increase, paralleling the trends observed in the Nipah virus testing market.

Test Type Analysis

The test type segment in the Nipah virus testing market includes Real-Time Polymerase Chain Reaction (RT-PCR), Enzyme-Linked Immunosorbent Assay (ELISA), Virus Isolation, and other diagnostic methods. Real-Time Polymerase Chain Reaction (RT-PCR) is currently the leading test type due to its high sensitivity and specificity. RT-PCR allows for the rapid detection of Nipah virus RNA in clinical samples, making it an invaluable tool in the timely diagnosis and management of Nipah virus infections. This methodÂ’s ability to detect even low levels of viral RNA contributes to its widespread adoption in diagnostic laboratories.

Enzyme-Linked Immunosorbent Assay (ELISA) is another prominent test type used in Nipah virus testing. ELISA tests are crucial for detecting antibodies against the Nipah virus in patient samples, providing valuable information about the immune response to the infection. T

Yellow fever virus (Flavivirus genus) is an arthropod-borne pathogen, which can infect humans, causing a severe viscerotropic disease with a high mortality rate. Adapted viral strains allow the reproduction of yellow fever disease in hamsters with features similar to the human disease. Here, we used the Infectious Subgenomic Amplicons reverse genetics method to produce an equivalent to the hamster-virulent strain, Yellow Fever Ap7, by introducing a set of four synonymous and six nonsynonymous mutations into a single subgenomic amplicon, derived from the sequence of the Asibi strain. The resulting strain, Yellow Fever Ap7M, induced a disease similar to that described for Ap7 in terms of symptoms, weight evolution, viral loads in the liver and lethality. Using the same methodology, we produced mutant strains derived from either Ap7M or Asibi viruses and investigated the role of each of Ap7M nonsynonymous mutations in its in vivo phenotype. This allowed identifying key components of the virulence mechanism in hamsters. In Ap7M virus, the reversion of either E/Q27H or E/D155A mutations led to an important reduction of both virulence and in vivo replicative fitness. In addition, the introduction of the single D155A Ap7M mutation within the E protein of the Asibi virus was sufficient to drastically modify its phenotype in hamsters toward both a greater replication efficiency and virulence. Finally, inspection of the Asibi strain E protein structure combined to in vivo testing revealed the importance of an exposed α-helix in domain I, containing residues 154 and 155, for Ap7M virulence in hamsters.

Summary of filovirus sequelae and persistence in animal models.

Data from influenza A virus (IAV) infected ferrets (Mustela putorius furo) provides invaluable information towards the study of novel and emerging viruses that pose a threat to human health. This gold standard animal model can recapitulate many clinical signs of infection present in IAV-infected humans, support virus replication of human and zoonotic strains without prior adaptation, and permit evaluation of virus transmissibility by multiple modes. While ferrets have been employed in risk assessment settings for >20 years, results from this work are typically reported in discrete stand-alone publications, making aggregation of raw data from this work over time nearly impossible. Here, we describe a dataset of 746 ferrets inoculated with 129 unique IAV, conducted by a single research group (NCIRD/ID/IPB/Pathogenesis Laboratory Team) under a uniform experimental protocol. This collection of morbidity, mortality, and viral titer data represents the largest publicly available dataset to date of in vivo-generated IAV infection outcomes on a per-individual ferret level.

Published Data Descriptor for more information: Kieran TJ, Sun X, Creager HM, Tumpey TM, Maine TR, Belser JA. 2024. An aggregated dataset of serial morbidity and titer measurements from influenza A virus-infected ferrets. Sci Data 11, 510. https://doi.org/10.1038/s41597-024-03256-6

Additional publications using and describing data: Kieran TJ, Sun X, Maines TR, Beauchemin CAA, Belser JA. 2024. Exploring associations between viral titer measurements and disease outcomes in ferrets inoculated with 125 contemporary influenza A viruses. J Virol. 98:e01661-23. https://doi.org/10.1128/jvi.01661-23

Belser JA, Kieran TJ, Mitchell ZA, Sun X, Mayfield K, Tumpey TM, Spengler JR, Maines TR. 2024. Key considerations to improve the normalization, interpretation and reproducibility of morbidity data in mammalian models of viral disease. Dis Model Mech; 17 (3): dmm050511. https://doi.org/10.1242/dmm.050511

Kieran TJ, Sun X, Maines TR, Belser JA. 2024. Machine learning approaches for influenza A virus risk assessment identifies predictive correlates using ferret model in vivo data. Communications Biology 7, 927. https://doi.org/10.1038/s42003-024-06629-0

Additional publications supporting responsible use and interpretation of data by others: Kieran TJ, Maine TR, Belser JA. 2025. Eleven quick tips to unlock the power of in vivo data science. PLoS Comput Biol, 21(4):e1012947. https://doi.org/10.1371/journal.pcbi.1012947

Kieran TJ, Maine TR, Belser JA. 2025. Data alchemy, from lab to insight: Transforming in vivo experiments into data science gold. PLoS Pathog, 20(8):e1012460. https://doi.org/10.1371/journal.ppat.1012460

Change / Update Log: Nov 7, 2024: Corrected typographical errors in Origin column for A/Ohio/13/2017 and A/Hawaii/28/2020

July 1, 2025: Added 3 viruses (A/Texas/36/1991, A/Texas/37/2024, A/Michigan/90/2024, total n=18 new rows)