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.

On March 10, 2023, the Johns Hopkins Coronavirus Resource Center ceased its collecting and reporting of global COVID-19 data. For updated cases, deaths, and vaccine data please visit: World Health Organization (WHO)For more information, visit the Johns Hopkins Coronavirus Resource Center.COVID-19 Trends MethodologyOur goal is to analyze and present daily updates in the form of recent trends within countries, states, or counties during the COVID-19 global pandemic. The data we are analyzing is taken directly from the Johns Hopkins University Coronavirus COVID-19 Global Cases Dashboard, though we expect to be one day behind the dashboard’s live feeds to allow for quality assurance of the data.DOI: https://doi.org/10.6084/m9.figshare.125529863/7/2022 - Adjusted the rate of active cases calculation in the U.S. to reflect the rates of serious and severe cases due nearly completely dominant Omicron variant.6/24/2020 - Expanded Case Rates discussion to include fix on 6/23 for calculating active cases.6/22/2020 - Added Executive Summary and Subsequent Outbreaks sectionsRevisions on 6/10/2020 based on updated CDC reporting. This affects the estimate of active cases by revising the average duration of cases with hospital stays downward from 30 days to 25 days. The result shifted 76 U.S. counties out of Epidemic to Spreading trend and no change for national level trends.Methodology update on 6/2/2020: This sets the length of the tail of new cases to 6 to a maximum of 14 days, rather than 21 days as determined by the last 1/3 of cases. This was done to align trends and criteria for them with U.S. CDC guidance. The impact is areas transition into Controlled trend sooner for not bearing the burden of new case 15-21 days earlier.Correction on 6/1/2020Discussion of our assertion of an abundance of caution in assigning trends in rural counties added 5/7/2020. Revisions added on 4/30/2020 are highlighted.Revisions added on 4/23/2020 are highlighted.Executive SummaryCOVID-19 Trends is a methodology for characterizing the current trend for places during the COVID-19 global pandemic. Each day we assign one of five trends: Emergent, Spreading, Epidemic, Controlled, or End Stage to geographic areas to geographic areas based on the number of new cases, the number of active cases, the total population, and an algorithm (described below) that contextualize the most recent fourteen days with the overall COVID-19 case history. Currently we analyze the countries of the world and the U.S. Counties. The purpose is to give policymakers, citizens, and analysts a fact-based data driven sense for the direction each place is currently going. When a place has the initial cases, they are assigned Emergent, and if that place controls the rate of new cases, they can move directly to Controlled, and even to End Stage in a short time. However, if the reporting or measures to curtail spread are not adequate and significant numbers of new cases continue, they are assigned to Spreading, and in cases where the spread is clearly uncontrolled, Epidemic trend.We analyze the data reported by Johns Hopkins University to produce the trends, and we report the rates of cases, spikes of new cases, the number of days since the last reported case, and number of deaths. We also make adjustments to the assignments based on population so rural areas are not assigned trends based solely on case rates, which can be quite high relative to local populations.Two key factors are not consistently known or available and should be taken into consideration with the assigned trend. First is the amount of resources, e.g., hospital beds, physicians, etc.that are currently available in each area. Second is the number of recoveries, which are often not tested or reported. On the latter, we provide a probable number of active cases based on CDC guidance for the typical duration of mild to severe cases.Reasons for undertaking this work in March of 2020:The popular online maps and dashboards show counts of confirmed cases, deaths, and recoveries by country or administrative sub-region. Comparing the counts of one country to another can only provide a basis for comparison during the initial stages of the outbreak when counts were low and the number of local outbreaks in each country was low. By late March 2020, countries with small populations were being left out of the mainstream news because it was not easy to recognize they had high per capita rates of cases (Switzerland, Luxembourg, Iceland, etc.). Additionally, comparing countries that have had confirmed COVID-19 cases for high numbers of days to countries where the outbreak occurred recently is also a poor basis for comparison.The graphs of confirmed cases and daily increases in cases were fit into a standard size rectangle, though the Y-axis for one country had a maximum value of 50, and for another country 100,000, which potentially misled people interpreting the slope of the curve. Such misleading circumstances affected comparing large population countries to small population counties or countries with low numbers of cases to China which had a large count of cases in the early part of the outbreak. These challenges for interpreting and comparing these graphs represent work each reader must do based on their experience and ability. Thus, we felt it would be a service to attempt to automate the thought process experts would use when visually analyzing these graphs, particularly the most recent tail of the graph, and provide readers with an a resulting synthesis to characterize the state of the pandemic in that country, state, or county.The lack of reliable data for confirmed recoveries and therefore active cases. Merely subtracting deaths from total cases to arrive at this figure progressively loses accuracy after two weeks. The reason is 81% of cases recover after experiencing mild symptoms in 10 to 14 days. Severe cases are 14% and last 15-30 days (based on average days with symptoms of 11 when admitted to hospital plus 12 days median stay, and plus of one week to include a full range of severely affected people who recover). Critical cases are 5% and last 31-56 days. Sources:U.S. CDC. April 3, 2020 Interim Clinical Guidance for Management of Patients with Confirmed Coronavirus Disease (COVID-19). Accessed online. Initial older guidance was also obtained online. Additionally, many people who recover may not be tested, and many who are, may not be tracked due to privacy laws. Thus, the formula used to compute an estimate of active cases is: Active Cases = 100% of new cases in past 14 days + 19% from past 15-25 days + 5% from past 26-49 days - total deaths. On 3/17/2022, the U.S. calculation was adjusted to: Active Cases = 100% of new cases in past 14 days + 6% from past 15-25 days + 3% from past 26-49 days - total deaths. Sources: https://www.cdc.gov/mmwr/volumes/71/wr/mm7104e4.htm https://covid.cdc.gov/covid-data-tracker/#variant-proportions If a new variant arrives and appears to cause higher rates of serious cases, we will roll back this adjustment. We’ve never been inside a pandemic with the ability to learn of new cases as they are confirmed anywhere in the world. After reviewing epidemiological and pandemic scientific literature, three needs arose. We need to specify which portions of the pandemic lifecycle this map cover. The World Health Organization (WHO) specifies six phases. The source data for this map begins just after the beginning of Phase 5: human to human spread and encompasses Phase 6: pandemic phase. Phase six is only characterized in terms of pre- and post-peak. However, these two phases are after-the-fact analyses and cannot ascertained during the event. Instead, we describe (below) a series of five trends for Phase 6 of the COVID-19 pandemic.Choosing terms to describe the five trends was informed by the scientific literature, particularly the use of epidemic, which signifies uncontrolled spread. The five trends are: Emergent, Spreading, Epidemic, Controlled, and End Stage. Not every locale will experience all five, but all will experience at least three: emergent, controlled, and end stage.This layer presents the current trends for the COVID-19 pandemic by country (or appropriate level). There are five trends:Emergent: Early stages of outbreak. Spreading: Early stages and depending on an administrative area’s capacity, this may represent a manageable rate of spread. Epidemic: Uncontrolled spread. Controlled: Very low levels of new casesEnd Stage: No New cases These trends can be applied at several levels of administration: Local: Ex., City, District or County – a.k.a. Admin level 2State: Ex., State or Province – a.k.a. Admin level 1National: Country – a.k.a. Admin level 0Recommend that at least 100,000 persons be represented by a unit; granted this may not be possible, and then the case rate per 100,000 will become more important.Key Concepts and Basis for Methodology: 10 Total Cases minimum threshold: Empirically, there must be enough cases to constitute an outbreak. Ideally, this would be 5.0 per 100,000, but not every area has a population of 100,000 or more. Ten, or fewer, cases are also relatively less difficult to track and trace to sources. 21 Days of Cases minimum threshold: Empirically based on COVID-19 and would need to be adjusted for any other event. 21 days is also the minimum threshold for analyzing the “tail” of the new cases curve, providing seven cases as the basis for a likely trend (note that 21 days in the tail is preferred). This is the minimum needed to encompass the onset and duration of a normal case (5-7 days plus 10-14 days). Specifically, a median of 5.1 days incubation time, and 11.2 days for 97.5% of cases to incubate. This is also driven by pressure to understand trends and could easily be adjusted to 28 days. Source

🇦🇹 오스트리아

Parallel to the dataset CORD-19 of scholarly articles, we provide the literature graph LG-covid19-HOTP composed of not only articles (graph nodes) that are relevant to the study of coronavirus, but also in and out citation links (directed graph edges) to base navigation and search among the articles. The article records are related and connected, not isolated. The graph has been updated weekly since March 26, 2020. The current graph includes 42,279 hot-off-the-press (HOTP) articles since January 2020. It contains 485,097 articles and 4,259,944 links. The link-to-node ratio is remarkably higher than some other existing literature graphs. In addition to the dataset we provide more functionalities at lg-covid-19-hotp.cs.duke.edu such as new articles, weekly meta-data analysis in terms of publication growth over time, ranking by citation, and statistical near-neighbor embedding maps by similarity in co-citation, and similarity in co-reference. Since April 11, we have enabled a novel functionality - self-navigated surf-search over the maps. At the site we also take courtesy input of COVID-19 articles that are missing from the current collection.

COVID-19 Trends MethodologyOur goal is to analyze and present daily updates in the form of recent trends within countries, states, or counties during the COVID-19 global pandemic. The data we are analyzing is taken directly from the Johns Hopkins University Coronavirus COVID-19 Global Cases Dashboard, though we expect to be one day behind the dashboard’s live feeds to allow for quality assurance of the data.Reasons for undertaking this work:The popular online maps and dashboards show counts of confirmed cases, deaths, and recoveries by country or administrative sub-region. Comparing the counts of one country to another can only provide a basis for comparison during the initial stages of the outbreak when counts were low and the number of local outbreaks in each country was low. By late March 2020, countries with small populations were being left out of the mainstream news because it was not easy to recognize they had high per capita rates of cases (Switzerland, Luxembourg, Iceland, etc.). Additionally, comparing countries that have had confirmed COVID-19 cases for high numbers of days to countries where the outbreak occurred recently is also a poor basis for comparison.The graphs of confirmed cases and daily increases in cases were fit into a standard size rectangle, though the Y-axis for one country had a maximum value of 50, and for another country 100,000, which potentially misled people interpreting the slope of the curve. Such misleading circumstances affected comparing large population countries to small population counties or countries with low numbers of cases to China which had a large count of cases in the early part of the outbreak. These challenges for interpreting and comparing these graphs represent work each reader must do based on their experience and ability. Thus, we felt it would be a service to attempt to automate the thought process experts would use when visually analyzing these graphs, particularly the most recent tail of the graph, and provide readers with an a resulting synthesis to characterize the state of the pandemic in that country, state, or county.The lack of reliable data for confirmed recoveries and therefore active cases. Merely subtracting deaths from total cases to arrive at this figure progressively loses accuracy after two weeks. The reason is 81% of cases recover after experiencing mild symptoms in 10 to 14 days. Severe cases are 14% and last 15-30 days (based on average days with symptoms of 11 when admitted to hospital plus 12 days median stay, and plus of one week to include a full range of severely affected people who recover). Critical cases are 5% and last 31-56 days. Sources:U.S. CDC. April 3, 2020 Interim Clinical Guidance for Management of Patients with Confirmed Coronavirus Disease (COVID-19). Accessed online. Initial older guidance was also obtained online. Additionally, many people who recover may not be tested, and many who are, may not be tracked due to privacy laws. Thus, the formula used to compute an estimate of active cases is: Active Cases = 100% of new cases in past 14 days + 19% from past 15-30 days + 5% from past 31-56 days - total deaths.We’ve never been inside a pandemic with the ability to learn of new cases as they are confirmed anywhere in the world. After reviewing epidemiological and pandemic scientific literature, three needs arose. We need to specify which portions of the pandemic lifecycle this map cover. The World Health Organization (WHO) specifies six phases. The source data for this map begins just after the beginning of Phase 5: human to human spread and encompasses Phase 6: pandemic phase. Phase six is only characterized in terms of pre- and post-peak. However, these two phases are after-the-fact analyses and cannot ascertained during the event. Instead, we describe (below) a series of five trends for Phase 6 of the COVID-19 pandemic.Choosing terms to describe the five trends was informed by the scientific literature, particularly the use of epidemic, which signifies uncontrolled spread. The five trends are: Emergent, Spreading, Epidemic, Controlled, and End Stage. Not every locale will experience all five, but all will experience at least three: emergent, controlled, and end stage.This layer presents the current trends for the COVID-19 pandemic by country (or appropriate level). There are five trends:Emergent: Early stages of outbreak. Spreading: Early stages and depending on an administrative area’s capacity, this may represent a manageable rate of spread. Epidemic: Uncontrolled spread. Controlled: Very low levels of new casesEnd Stage: No New cases These trends can be applied at several levels of administration: Local: Ex., City, District or County – a.k.a. Admin level 2State: Ex., State or Province – a.k.a. Admin level 1National: Country – a.k.a. Admin level 0Recommend that at least 100,000 persons be represented by a unit; granted this may not be possible, and then the case rate per 100,000 will become more important.Key Concepts and Basis for Methodology: 10 Total Cases minimum threshold: Empirically, there must be enough cases to constitute an outbreak. Ideally, this would be 5.0 per 100,000, but not every area has a population of 100,000 or more. Ten, or fewer, cases are also relatively less difficult to track and trace to sources. 21 Days of Cases minimum threshold: Empirically based on COVID-19 and would need to be adjusted for any other event. 21 days is also the minimum threshold for analyzing the “tail” of the new cases curve, providing seven cases as the basis for a likely trend (note that 21 days in the tail is preferred). This is the minimum needed to encompass the onset and duration of a normal case (5-7 days plus 10-14 days). Specifically, a median of 5.1 days incubation time, and 11.2 days for 97.5% of cases to incubate. This is also driven by pressure to understand trends and could easily be adjusted to 28 days. Source used as basis:Stephen A. Lauer, MS, PhD *; Kyra H. Grantz, BA *; Qifang Bi, MHS; Forrest K. Jones, MPH; Qulu Zheng, MHS; Hannah R. Meredith, PhD; Andrew S. Azman, PhD; Nicholas G. Reich, PhD; Justin Lessler, PhD. 2020. The Incubation Period of Coronavirus Disease 2019 (COVID-19) From Publicly Reported Confirmed Cases: Estimation and Application. Annals of Internal Medicine DOI: 10.7326/M20-0504.New Cases per Day (NCD) = Measures the daily spread of COVID-19. This is the basis for all rates. 100 News Cases in a day as a spike threshold: Empirically, this is based on COVID-19’s rate of spread, or r0 of ~2.5, which indicates each case will infect between two and three other people. There is a point at which each administrative area’s capacity will not have the resources to trace and account for all contacts of each patient. Thus, this is an indicator of uncontrolled or epidemic trend. Spiking activity in combination with the rate of new cases is the basis for determining whether an area has a spreading or epidemic trend (see below). Source used as basis:World Health Organization (WHO). 16-24 Feb 2020. Report of the WHO-China Joint Mission on Coronavirus Disease 2019 (COVID-19). Obtained online.Mean of Recent Tail of NCD = Empirical, and a COVID-19-specific basis for establishing a recent trend. The recent mean of NCD is taken from the most recent one third of case days. A minimum of 21 days of cases is required for analysis but cannot be considered reliable. Thus, a preference of 63 days of cases ensures much higher reliability. This analysis is not explanatory and thus, merely represents a likely trend. The tail is analyzed for the following:Most recent 2 days: In terms of likelihood, this does not mean much, but can indicate a reason for hope and a basis to share positive change that is not yet a trend. There are two worthwhile indicators:Last 2 days count of new cases is less than any in either the past five or 6-21 days. Past 2 days has only one or fewer new cases – this is an extremely positive outcome if the rate of testing has continued at the same rate as the previous 5 days or 6 to 21 days. Most recent 5 days: In terms of likelihood, this is more meaningful, as it does represent at short-term trend. There are five worthwhile indicators:Past five days is greater than past 2 days and past 6-21 days indicates the potential of the past 2 days being an aberration. Past five days is greater than past 6-21 days and less than past 2 days indicates slight positive trend, but likely still within peak trend timeframe.Past five days is less than the past 6-21 days. This means a downward trend. This would be an important trend for any administrative area in an epidemic trend that the rate of spread is slowing.If less than the past 2 days, but not the last 6-21 days, this is still positive, but is not indicating a passage out of the peak timeframe of the daily new cases curve.Past 5 days has only one or two new cases – this is an extremely positive outcome if the rate of testing has continued at the same rate as the previous 6 to 21 days. Most recent 6-21 days: Represents the full tail of the curve and provides context for the past 2- and 5-day trends.If this is greater than both the 2- and 5-day trends, then a short-term downward trend has begun. Mean of Recent Tail NCD in the context of the Mean of All NCD, and raw counts of cases:Mean of Recent NCD is less than 0.5 cases per 100,000 = high level of controlMean of Recent NCD is less than 1.0 and fewer than 30 cases indicate continued emergent trend.3. Mean of Recent NCD is less than 1.0 and greater than 30 cases indicate a change from emergent to spreading trend.Mean of All NCD less than 2.0 per 100,000, and areas that have been in epidemic trends have Mean of Recent NCD of less than 5.0 per 100,000 is a significant indicator of changing trends from epidemic to spreading, now going in the direction of controlled trend.Similarly, in the context of Mean of All NCD greater than 2.0

COVID-19 Trends MethodologyOur goal is to analyze and present daily updates in the form of recent trends within countries, states, or counties during the COVID-19 global pandemic. The data we are analyzing is taken directly from the Johns Hopkins University Coronavirus COVID-19 Global Cases Dashboard, though we expect to be one day behind the dashboard’s live feeds to allow for quality assurance of the data.Revisions added on 4/23/2020 are highlighted.Revisions added on 4/30/2020 are highlighted.Discussion of our assertion of an abundance of caution in assigning trends in rural counties added 5/7/2020. Correction on 6/1/2020Methodology update on 6/2/2020: This sets the length of the tail of new cases to 6 to a maximum of 14 days, rather than 21 days as determined by the last 1/3 of cases. This was done to align trends and criteria for them with U.S. CDC guidance. The impact is areas transition into Controlled trend sooner for not bearing the burden of new case 15-21 days earlier.Reasons for undertaking this work:The popular online maps and dashboards show counts of confirmed cases, deaths, and recoveries by country or administrative sub-region. Comparing the counts of one country to another can only provide a basis for comparison during the initial stages of the outbreak when counts were low and the number of local outbreaks in each country was low. By late March 2020, countries with small populations were being left out of the mainstream news because it was not easy to recognize they had high per capita rates of cases (Switzerland, Luxembourg, Iceland, etc.). Additionally, comparing countries that have had confirmed COVID-19 cases for high numbers of days to countries where the outbreak occurred recently is also a poor basis for comparison.The graphs of confirmed cases and daily increases in cases were fit into a standard size rectangle, though the Y-axis for one country had a maximum value of 50, and for another country 100,000, which potentially misled people interpreting the slope of the curve. Such misleading circumstances affected comparing large population countries to small population counties or countries with low numbers of cases to China which had a large count of cases in the early part of the outbreak. These challenges for interpreting and comparing these graphs represent work each reader must do based on their experience and ability. Thus, we felt it would be a service to attempt to automate the thought process experts would use when visually analyzing these graphs, particularly the most recent tail of the graph, and provide readers with an a resulting synthesis to characterize the state of the pandemic in that country, state, or county.The lack of reliable data for confirmed recoveries and therefore active cases. Merely subtracting deaths from total cases to arrive at this figure progressively loses accuracy after two weeks. The reason is 81% of cases recover after experiencing mild symptoms in 10 to 14 days. Severe cases are 14% and last 15-30 days (based on average days with symptoms of 11 when admitted to hospital plus 12 days median stay, and plus of one week to include a full range of severely affected people who recover). Critical cases are 5% and last 31-56 days. Sources:U.S. CDC. April 3, 2020 Interim Clinical Guidance for Management of Patients with Confirmed Coronavirus Disease (COVID-19). Accessed online. Initial older guidance was also obtained online. Additionally, many people who recover may not be tested, and many who are, may not be tracked due to privacy laws. Thus, the formula used to compute an estimate of active cases is: Active Cases = 100% of new cases in past 14 days + 19% from past 15-30 days + 5% from past 31-56 days - total deaths.We’ve never been inside a pandemic with the ability to learn of new cases as they are confirmed anywhere in the world. After reviewing epidemiological and pandemic scientific literature, three needs arose. We need to specify which portions of the pandemic lifecycle this map cover. The World Health Organization (WHO) specifies six phases. The source data for this map begins just after the beginning of Phase 5: human to human spread and encompasses Phase 6: pandemic phase. Phase six is only characterized in terms of pre- and post-peak. However, these two phases are after-the-fact analyses and cannot ascertained during the event. Instead, we describe (below) a series of five trends for Phase 6 of the COVID-19 pandemic.Choosing terms to describe the five trends was informed by the scientific literature, particularly the use of epidemic, which signifies uncontrolled spread. The five trends are: Emergent, Spreading, Epidemic, Controlled, and End Stage. Not every locale will experience all five, but all will experience at least three: emergent, controlled, and end stage.This layer presents the current trends for the COVID-19 pandemic by country (or appropriate level). There are five trends:Emergent: Early stages of outbreak. Spreading: Early stages and depending on an administrative area’s capacity, this may represent a manageable rate of spread. Epidemic: Uncontrolled spread. Controlled: Very low levels of new casesEnd Stage: No New cases These trends can be applied at several levels of administration: Local: Ex., City, District or County – a.k.a. Admin level 2State: Ex., State or Province – a.k.a. Admin level 1National: Country – a.k.a. Admin level 0Recommend that at least 100,000 persons be represented by a unit; granted this may not be possible, and then the case rate per 100,000 will become more important.Key Concepts and Basis for Methodology: 10 Total Cases minimum threshold: Empirically, there must be enough cases to constitute an outbreak. Ideally, this would be 5.0 per 100,000, but not every area has a population of 100,000 or more. Ten, or fewer, cases are also relatively less difficult to track and trace to sources. 21 Days of Cases minimum threshold: Empirically based on COVID-19 and would need to be adjusted for any other event. 21 days is also the minimum threshold for analyzing the “tail” of the new cases curve, providing seven cases as the basis for a likely trend (note that 21 days in the tail is preferred). This is the minimum needed to encompass the onset and duration of a normal case (5-7 days plus 10-14 days). Specifically, a median of 5.1 days incubation time, and 11.2 days for 97.5% of cases to incubate. This is also driven by pressure to understand trends and could easily be adjusted to 28 days. Source used as basis:Stephen A. Lauer, MS, PhD *; Kyra H. Grantz, BA *; Qifang Bi, MHS; Forrest K. Jones, MPH; Qulu Zheng, MHS; Hannah R. Meredith, PhD; Andrew S. Azman, PhD; Nicholas G. Reich, PhD; Justin Lessler, PhD. 2020. The Incubation Period of Coronavirus Disease 2019 (COVID-19) From Publicly Reported Confirmed Cases: Estimation and Application. Annals of Internal Medicine DOI: 10.7326/M20-0504.New Cases per Day (NCD) = Measures the daily spread of COVID-19. This is the basis for all rates. Back-casting revisions: In the Johns Hopkins’ data, the structure is to provide the cumulative number of cases per day, which presumes an ever-increasing sequence of numbers, e.g., 0,0,1,1,2,5,7,7,7, etc. However, revisions do occur and would look like, 0,0,1,1,2,5,7,7,6. To accommodate this, we revised the lists to eliminate decreases, which make this list look like, 0,0,1,1,2,5,6,6,6.Reporting Interval: In the early weeks, Johns Hopkins' data provided reporting every day regardless of change. In late April, this changed allowing for days to be skipped if no new data was available. The day was still included, but the value of total cases was set to Null. The processing therefore was updated to include tracking of the spacing between intervals with valid values.100 News Cases in a day as a spike threshold: Empirically, this is based on COVID-19’s rate of spread, or r0 of ~2.5, which indicates each case will infect between two and three other people. There is a point at which each administrative area’s capacity will not have the resources to trace and account for all contacts of each patient. Thus, this is an indicator of uncontrolled or epidemic trend. Spiking activity in combination with the rate of new cases is the basis for determining whether an area has a spreading or epidemic trend (see below). Source used as basis:World Health Organization (WHO). 16-24 Feb 2020. Report of the WHO-China Joint Mission on Coronavirus Disease 2019 (COVID-19). Obtained online.Mean of Recent Tail of NCD = Empirical, and a COVID-19-specific basis for establishing a recent trend. The recent mean of NCD is taken from the most recent fourteen days. A minimum of 21 days of cases is required for analysis but cannot be considered reliable. Thus, a preference of 42 days of cases ensures much higher reliability. This analysis is not explanatory and thus, merely represents a likely trend. The tail is analyzed for the following:Most recent 2 days: In terms of likelihood, this does not mean much, but can indicate a reason for hope and a basis to share positive change that is not yet a trend. There are two worthwhile indicators:Last 2 days count of new cases is less than any in either the past five or 14 days. Past 2 days has only one or fewer new cases – this is an extremely positive outcome if the rate of testing has continued at the same rate as the previous 5 days or 14 days. Most recent 5 days: In terms of likelihood, this is more meaningful, as it does represent at short-term trend. There are five worthwhile indicators:Past five days is greater than past 2 days and past 14 days indicates the potential of the past 2 days being an aberration. Past five days is greater than past 14 days and less than past 2 days indicates slight positive trend, but likely still within peak trend time frame.Past five days is less than the past 14 days. This means a downward trend. This would be an

KG-COVID-19 graph containing all sources EXCEPT ChEMBL antivirals The follow commit was used to produce this KG on Sep 18, 2020 commit 9fd270e1b141487ee422d138cd74add87118f669 (HEAD -> no_chembl_merge, origin/master, origin/HEAD, fix_internal_tabs_scibite_data) Merge: bf8a47a b545edc Author: Justin Reese justaddcoffee+github@gmail.com Date: Thu Sep 17 12:29:17 2020 -0700

As of November 11, 2022, almost 96.8 million confirmed cases of COVID-19 had been reported by the World Health Organization (WHO) for the United States. The pandemic has impacted all 50 states, with vast numbers of cases recorded in California, Texas, and Florida.

The coronavirus in the U.S. The coronavirus hit the United States in mid-March 2020, and cases started to soar at an alarming rate. The country has performed a high number of COVID-19 tests, which is a necessary step to manage the outbreak, but new coronavirus cases in the U.S. have spiked several times since the pandemic began, most notably at the end of 2022. However, restrictions in many states have been eased as new cases have declined.

The origin of the coronavirus In December 2019, officials in Wuhan, China, were the first to report cases of pneumonia with an unknown cause. A new human coronavirus – SARS-CoV-2 – has since been discovered, and COVID-19 is the infectious disease it causes. All available evidence to date suggests that COVID-19 is a zoonotic disease, which means it can spread from animals to humans. The WHO says transmission is likely to have happened through an animal that is handled by humans. Researchers do not support the theory that the virus was developed in a laboratory.

Dataset general description:

• This dataset reports 4195 recurrent neural network models, their settings, and their generated prediction csv files, graphs, and metadata files, for predicting COVID-19's daily infections in Brazil by training on limited raw data (30 time-steps and 40 time-steps alternatives). The used code is developed by the author and located in the following online data repository link: http://dx.doi.org/10.17632/yp4d95pk7n.1

Dataset content:

• Models, Graphs, and csv predictions files: 1. Deterministic mode (DM): includes 1194 generated models files (30 time-steps), and their generated 2835 graphs and 2835 predictions files. Similarly, this mode includes 1976 generated model files (40 time-steps), and their generated 7301 graphs and 7301 predictions files. 2. Non-deterministic mode (NDM): includes 20 generated model files (30 time-steps), and their generated 53 graphs and 53 predictions files. 3. Technical validation mode (TVM): includes 1001 generated model files (30 time-steps), and their generated 3619 graphs and 3619 predictions files for 358 models, which are a sample of 1001 models. Also, 1 model in control group for India. 4. 1 graph and 1 prediction files for each of DM and NDM, reporting evaluation till 2020-07-11.

• Settings and metadata for the above 3 categories: 1. Used settings in json files for reproducibility. 2. Metadata about training and prediction setup and accuracy in csv files.

Raw data source that was used to train the models:

• The used raw data for training the models is from: COVID-19 Data Repository by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University): https://github.com/CSSEGISandData/COVID-19

• The models were trained on these versions of the raw data: 1. Link till 2020-06-29 (accessed 2020-07-08): https://github.com/CSSEGISandData/COVID-19/raw/78d91b2dbc2a26eb2b2101fa499c6798aa22fca8/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_global.csv 2. Link till 2020-06-13 (accessed 2020-07-08): https://github.com/CSSEGISandData/COVID-19/raw/02ea750a263f6d8b8945fdd3253b35d3fd9b1bee/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_global.csv

License: This prediction Dataset is licensed under CC BY NC 3.0.

Notice and disclaimer: 1- This prediction Dataset is for scientific and research purposes only. 2- The generation of this Dataset complies with the terms of use of the publicly available raw data from the COVID-19 Data Repository by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University: https://github.com/CSSEGISandData/COVID-19 and therefore, the author of the prediction Dataset disclaims any and all responsibility and warranties regarding the contents of used raw data, including but not limited to: the correctness, completeness, and any issues linked to third-party rights.

This RDF dataset provides two main knowledge graphs produced by processing the scholarly articles of the COVID-19 Open Research Dataset (CORD-19), a resource of articles about COVID-19 and the coronavirus family of viruses.

The CORD-19 Named Entities Knowledge Graph describes named entities identified and disambiguated by NCBO BioPortal annotator, Entity-fishing and DBpedia Spotlight. The CORD-19 Argumentative Knowledge Graph describes argumentative components and PICO elements extracted from the articles by the Argumentative Clinical Trial Analysis platform (ACTA).

Homepage: https://github.com/Wimmics/CovidOnTheWeb

License: see the LICENCE file in the archive.

Context

I have been following the Covid stats since January when I realized that if the world does nothing, it would turn into a global pandemic.

Content

I started by downloading the data daily from kaggle: https://www.kaggle.com/sudalairajkumar/novel-corona-virus-2019-dataset/data#2019_nCoV_data.csv Then when he stopped updating the data daily, I switched over to the raw data directly from John Hopkins github data repository: https://github.com/CSSEGISandData/COVID-19

Acknowledgements

Thank you to the Computer Science division of John Hopkins University for sharing their data (Please cite our Lancet Article for any use of this data in a publication: https://doi.org/10.1016/S1473-3099(20)30120-1)

Inspiration

I cannot wait for this pandemic to be over with and hopefully we will eradicate the common cold and Influenza with it.

Telegram graph data of COVID-19 related channels Dataset of 128.148 Telegram channels/groups connected by 320.194.154 forwarded messages. Only vertices and edges are present with a limited amount of metadata. No message content is included. We include one files for the graph "graph.gt.gz" which includes the weighted directed graph. The weights can be found as edge properties. The file are in the gt format.

This dashboard provides a visual of the Coronavirus Disease 2019 (COVID-19) surveillance in San Bernardino County.

The legend items for both graphs (i.e., Positives, Negatives, Total) can be turned on/off by clicking on the legend item. Use the scrollbar on the top of each graph to zoom in/out of the graph items. Selecting certain dates on either graph will also dynamically change the data to the right of the dashboard.

Estimates of excess deaths can provide information about the burden of mortality potentially related to the COVID-19 pandemic, including deaths that are directly or indirectly attributed to COVID-19. Excess deaths are typically defined as the difference between the observed numbers of deaths in specific time periods and expected numbers of deaths in the same time periods. This visualization provides weekly estimates of excess deaths by the jurisdiction in which the death occurred. Weekly counts of deaths are compared with historical trends to determine whether the number of deaths is significantly higher than expected.Counts of deaths from all causes of death, including COVID-19, are presented. As some deaths due to COVID-19 may be assigned to other causes of deaths (for example, if COVID-19 was not diagnosed or not mentioned on the death certificate), tracking all-cause mortality can provide information about whether an excess number of deaths is observed, even when COVID-19 mortality may be undercounted. Additionally, deaths from all causes excluding COVID-19 were also estimated. Comparing these two sets of estimates — excess deaths with and without COVID-19 — can provide insight about how many excess deaths are identified as due to COVID-19, and how many excess deaths are reported as due to other causes of death. These deaths could represent misclassified COVID-19 deaths, or potentially could be indirectly related to the COVID-19 pandemic (e.g., deaths from other causes occurring in the context of health care shortages or overburdened health care systems).Estimates of excess deaths can be calculated in a variety of ways, and will vary depending on the methodology and assumptions about how many deaths are expected to occur. Estimates of excess deaths presented in this webpage were calculated using Farrington surveillance algorithms (1). A range of values for the number of excess deaths was calculated as the difference between the observed count and one of two thresholds (either the average expected count or the upper bound of the 95% prediction interval), by week and jurisdiction.Provisional death counts are weighted to account for incomplete data. However, data for the most recent week(s) are still likely to be incomplete. Weights are based on completeness of provisional data in prior years, but the timeliness of data may have changed in 2020 relative to prior years, so the resulting weighted estimates may be too high in some jurisdictions and too low in others. As more information about the accuracy of the weighted estimates is obtained, further refinements to the weights may be made, which will impact the estimates. Any changes to the methods or weighting algorithm will be noted in the Technical Notes when they occur. More detail about the methods, weighting, data, and limitations can be found in the Technical Notes.This visualization includes several different estimates:Number of excess deaths: A range of estimates for the number of excess deaths was calculated as the difference between the observed count and one of two thresholds (either the average expected count or the upper bound threshold), by week and jurisdiction. Negative values, where the observed count fell below the threshold, were set to zero.Percent excess: The percent excess was defined as the number of excess deaths divided by the threshold.Total number of excess deaths: The total number of excess deaths in each jurisdiction was calculated by summing the excess deaths in each week, from February 1, 2020 to present. Similarly, the total number of excess deaths for the US overall was computed as a sum of jurisdiction-specific numbers of excess deaths (with negative values set to zero), and not directly estimated using the Farrington surveillance algorithms.Select a dashboard from the menu, then click on “Update Dashboard” to navigate through the different graphics.The first dashboard shows the weekly predicted counts of deaths from all causes, and the threshold for the expected number of deaths. Select a jurisdiction from the drop-down menu to show data for that jurisdiction.The second dashboard shows the weekly predicted counts of deaths from all causes and the weekly count of deaths from all causes excluding COVID-19. Select a jurisdiction from the drop-down menu to show data for that jurisdiction.The th

The purpose of this code is to produce a line graph visualization of COVID-19 data. This Jupyter notebook was built and run on Google Colab. This code will serve mostly as a guide and will need to be adapted where necessary to be run locally. The separate COVID-19 datasets uploaded to this Dataverse can be used with this code. This upload is made up of the IPYNB and PDF files of the code.

This publication corresponds to the Common Data Model (CDM) specification of the Baseline Use Case proposed in T.5.2 (WP5) in the BY-COVID project on “SARS-CoV-2 Vaccine(s) effectiveness in preventing SARS-CoV-2 infection.” Research Question: “How effective have the SARS-CoV-2 vaccination programmes been in preventing SARS-CoV-2 infections?” Intervention (exposure): COVID-19 vaccine(s) Outcome: SARS-CoV-2 infection Subgroup analysis: Vaccination schedule (type of vaccine) Study Design: An observational retrospective longitudinal study to assess the effectiveness of the SARS-CoV-2 vaccine in preventing SARS-CoV-2 infections using routinely collected social, health and care data from several countries. A causal model was established using Directed Acyclic Graphs (DAGs) to map domain knowledge, theories and assumptions about the causal relationship between exposure and outcome. The DAG developed for the research question of interest is shown below. Cohort definition: All people eligible to be vaccinated (from 5 to 115 years old, included) or with, at least, one dose of a SARS-CoV-2 vaccine (any of the available brands) having or not a previous SARS-CoV-2 infection. Inclusion criteria: All people vaccinated with at least one dose of the COVID-19 vaccine (any available brands) in an area of residence. Any person eligible to be vaccinated (from 5 to 115 years old, included) with a positive diagnosis (irrespective of the type of test) for SARS-CoV-2 infection (COVID-19) during the period of study. Exclusion criteria: People not eligible for the vaccine (from 0 to 4 years old, included) Study period: From the date of the first documented SARS-CoV-2 infection in each country to the most recent date in which data is available at the time of analysis. Roughly from 01-03-2020 to 30-06-2022, depending on the country. Files included in this publication: Causal model (responding to the research question) SARS-CoV-2 vaccine effectiveness causal model v.1.0.0 (HTML) - Interactive report showcasing the structural causal model (DAG) to answer the research question SARS-CoV-2 vaccine effectiveness causal model v.1.0.0 (QMD) - Quarto RMarkdown script to produce the structural causal model Common data model specification (following the causal model) SARS-CoV-2 vaccine effectiveness data model specification (XLXS) - Human-readable version (Excel) SARS-CoV-2 vaccine effectiveness data model specification dataspice (HTML) - Human-readable version (interactive report) SARS-CoV-2 vaccine effectiveness data model specification dataspice (JSON) - Machine-readable version Synthetic dataset (complying with the common data model specifications) SARS-CoV-2 vaccine effectiveness synthetic dataset (CSV) [UTF-8, pipe | separated, N~650,000 registries] SARS-CoV-2 vaccine effectiveness synthetic dataset EDA (HTML) - Interactive report of the exploratory data analysis (EDA) of the synthetic dataset SARS-CoV-2 vaccine effectiveness synthetic dataset EDA (JSON) - Machine-readable version of the exploratory data analysis (EDA) of the synthetic dataset SARS-CoV-2 vaccine effectiveness synthetic dataset generation script (IPYNB) - Jupyter notebook with Python scripting and commenting to generate the synthetic dataset #### Baseline Use Case: SARS-CoV-2 vaccine effectiveness assessment - Common Data Model Specification v.1.1.0 change log #### Updated Causal model to eliminate the consideration of 'vaccination_schedule_cd' as a mediator Adjusted the study period to be consistent with the Study Protocol Updated 'sex_cd' as a required variable Added 'chronic_liver_disease_bl' as a comorbidity at the individual level Updated 'socecon_lvl_cd' at the area level as a recommended variable Added crosswalks for the definition of 'chronic_liver_disease_bl' in a separate sheet Updated the 'vaccination_schedule_cd' reference to the 'Vaccine' node in the updated DAG Updated the description of the 'confirmed_case_dt' and 'previous_infection_dt' variables to clarify the definition and the need for a single registry per person The scripts (software) accompanying the data model specification are offered "as-is" without warranty and disclaiming liability for damages resulting from using it. The software is released under the CC-BY-4.0 licence, which permits you to use the content for almost any purpose (but does not grant you any trademark permissions), so long as you note the license and give credit.

IBM is providing free access to its COVID-19 Knowledge Graph integrating COVID-19 data from various sources: CORD-19 (https://www.semanticscholar.org/cord19) for literature, Clinicaltrials.gov (https://clinicaltrials.gov/) and WHO ICTRP (https://www.who.int/ictrp/search) for trials, DrugBank (https://www.drugbank.ca/) and GenBank (https://www.ncbi.nlm.nih.gov/genbank) for database data. Prepared search reports at the Reports Page are available on open access. However, to access the COVID-19 Knowledge Graph, it is necessary to request access.

This dataset contains 653 996 tweets related to the Coronavirus topic and highlighted by hashtags such as: #COVID-19, #COVID19, #COVID, #Coronavirus, #NCoV and #Corona. The tweets' crawling period started on the 27^th of February and ended on the 25^th of March 2020, which is spread over four weeks.

The tweets were generated by 390 458 users from 133 different countries and were written in 61 languages. English being the most used language with almost 400k tweets, followed by Spanish with around 80k tweets.

The data is stored in as a CSV file, where each line represents a tweet. The CSV file provides information on the following fields:

• Author: the user who posted the tweet
• Recipient: contains the name of the user in case of a reply, otherwise it would have the same value as the previous field
• Tweet: the full content of the tweet
• Hashtags: the list of hashtags present in the tweet
• Language: the language of the tweet
• Relationship: gives information on the type of the tweet, whether it is a retweet, a reply, a tweet with a mention, etc.
• Location: the country of the author of the tweet, which is unfortunately not always available
• Date: the publication date of the tweet
• Source: the device or platform used to send the tweet

The dataset can as well be used to construct a social graph since it includes the relations "Replies to", "Retweet", "MentionsInRetweet" and "Mentions".

COVID-19 has challenged health systems to learn how to learn. This paper describes the context, methods and challenges for learning to improve COVID-19 care at one academic health center. Challenges to learning include: (1) choosing a right clinical target; (2) designing methods for accurate predictions by borrowing strength from prior patients' experiences; (3) communicating the methodology to clinicians so they understand and trust it; (4) communicating the predictions to the patient at the moment of clinical decision; and (5) continuously evaluating and revising the methods so they adapt to changing patients and clinical demands. To illustrate these challenges, this paper contrasts two statistical modeling approaches - prospective longitudinal models in common use and retrospective analogues complementary in the COVID-19 context - for predicting future biomarker trajectories and major clinical events. The methods are applied to and validated on a cohort of 1,678 patients who were hospitalized with COVID-19 during the early months of the pandemic. We emphasize graphical tools to promote physician learning and inform clinical decision making.

This is a daily updated dataset of COVID-19 deaths around the world. The dataset contains data of 45 countries. This data was collected from

• The New York Times
• The Economist

us-counties.csv contains data of the daily number of new cases and deaths, the seven-day rolling average and the seven-day rolling average per 100,000 residents of US at county level. The average reported is the seven day trailing average i.e. average of the day reported and six days prior.

all_weekly_excess_deaths.csv collates detailed weekly breakdowns from official sources around the world.

Image credits: Unsplash - schluditsch

Let's pray for the ones who lost their lives fighting the battle and for the ones who risk their lives against this virus 🙏