This repository within the ACTIV TRACE initiative houses a comprehensive collection of datasets related to SARS-CoV-2. The processing of SARS-CoV-2 Sequence Read Archive (SRA) files has been optimized to identify genetic variations in viral samples. This information is then presented in the Variant Call Format (VCF). Each VCF file corresponds to the SRA parent-run's accession ID. Additionally, the data is available in the parquet format, making it easier to search and filter using the Amazon Athena Service. The SARS-CoV-2 Variant Calling Pipeline is designed to handle new data every six hours, with updates to the AWS ODP bucket occurring daily.

As of May 2, 2023, there were roughly 687 million global cases of COVID-19. Around 660 million people had recovered from the disease, while there had been almost 6.87 million deaths. The United States, India, and Brazil have been among the countries hardest hit by the pandemic.

The various types of human coronavirus The SARS-CoV-2 virus is the seventh known coronavirus to infect humans. Its emergence makes it the third in recent years to cause widespread infectious disease following the viruses responsible for SARS and MERS. A continual problem is that viruses naturally mutate as they attempt to survive. Notable new variants of SARS-CoV-2 were first identified in the UK, South Africa, and Brazil. Variants are of particular interest because they are associated with increased transmission.

Vaccination campaigns Common human coronaviruses typically cause mild symptoms such as a cough or a cold, but the novel coronavirus SARS-CoV-2 has led to more severe respiratory illnesses and deaths worldwide. Several COVID-19 vaccines have now been approved and are being used around the world.

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 the first reported coronavirus case in Washington State on Jan. 21, 2020, 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.

Main differences between COVID-19, SARS, and MERS.

This dataset is a zip file of policy documents from Jan 1st - Mar 31st 2020 relating to the COVID-19 pandemic. The documents are in PDF format and have an accompanying JSON file explaining their provenance: where they were collected from, their publication date, original location etc.You can read more about it here:https://blog.overton.io/?p=73

This pathway, SARS-CoV-2 infection of human cells (COVID-19), was initially generated via electronic inference from the manually curated and reviewed Reactome SARS-CoV-1 (Human SARS coronavirus) infection pathway. The inference process created SARS-CoV-2 events corresponding to each event in the SARS-CoV-1 pathway and populated those events with SARS-CoV-2 protein-containing physical entities based on orthology to SARS-CoV-1 proteins (https://reactome.org/documentation/inferred-events). All of these computationally created events and entities have been reviewed by Reactome curators and modified as appropriate where recently published experimental data indicate the existences of differences between the molecular details of the SARS-CoV-1 and SARS-CoV-2 infection pathways.

SARS‑CoV‑2 infection begins with the binding of viral S (spike) protein to cell surface angiotensin converting enzyme 2 (ACE2) and endocytosis of the bound virion. Within the endocytic vesicle, host proteases mediate cleavage of S protein into S1 and S2 fragments, leading to S2‑mediated fusion of the viral and host endosome membranes and release of the viral capsid into the host cell cytosol. The capsid is uncoated to free the viral genomic RNA, whose cap‑dependent translation produces polyprotein pp1a and, by means of a 1‑base frameshift, polyprotein pp1ab. Autoproteolytic cleavage of pp1a and pp1ab generates 15 or 16 nonstructural proteins (nsps) with various functions. Importantly, the RNA dependent RNA polymerase (RdRP) activity is encoded in nsp12. Nsp3, 4, and 6 induce rearrangement of the cellular endoplasmic reticulum membrane to form cytosolic double membrane vesicles (DMVs) where the viral replication transcription complex is assembled and anchored. With viral genomic RNA as a template, viral replicase‑transcriptase synthesizes a full length negative sense antigenome, which in turn serves as a template for the synthesis of new genomic RNA. The replicase‑transcriptase can also switch template during discontinuous transcription of the genome at transcription regulated sequences to produce a nested set of negative‑sense subgenomic (sg) RNAs, which are used as templates for the synthesis of positive‑sense sgRNAs that are translated to generate viral proteins. Finally, viral particle assembly occurs in the ER Golgi intermediate compartment (ERGIC). Viral M protein provides the scaffold for virion morphogenesis (Hartenian et al. 2020; Fung & Liu 2019; Masters 2006).

This Reactome module also describes molecular mechanisms by which SARS-CoV-2 modulates innate and adaptive immune responses, autophagy, host translation, intracellular signaling and regulatory pathways, and PDZ-mediated cell-cell junctions, mostly annotated from studies of cells infected with SARS-CoV-2.

A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a subtype of Betacoronavirus pandemicum. url:https://www.who.int/emergencies/diseases/novel-coronavirus-2019

This dataset includes CSV files that contain IDs and sentiment scores of the tweets related to the COVID-19 pandemic. The tweets have been collected by an on-going project deployed at https://live.rlamsal.com.np. The model monitors the real-time Twitter feed for coronavirus-related tweets using 90+ different keywords and hashtags that are commonly used while referencing the pandemic. This dataset has been wholly re-designed on March 20, 2020, to comply with the content redistribution policy set by Twitter.The paper associated with this dataset is available here: Design and analysis of a large-scale COVID-19 tweets dataset-------------------------------------Related datasets:(a) Tweets Originating from India During COVID-19 Lockdowns(b) Coronavirus (COVID-19) Tweets Sentiment Trend (Global)-------------------------------------Below is the quick overview of this dataset.— Dataset name: COV19Tweets Dataset— Number of tweets : 857,809,018 tweets— Coverage : Global— Language : English (EN)— Dataset usage terms : By using this dataset, you agree to (i) use the content of this dataset and the data generated from the content of this dataset for non-commercial research only, (ii) remain in compliance with Twitter's Developer Policy and (iii) cite the following paper:Lamsal, R. Design and analysis of a large-scale COVID-19 tweets dataset. Applied Intelligence (2020). https://doi.org/10.1007/s10489-020-02029-z— Geo-tagged Version: Coronavirus (COVID-19) Geo-tagged Tweets Dataset (GeoCOV19Tweets Dataset)— Dataset updates : Everyday— Active keywords and hashtags (archive: keywords.tsv) : "corona", "#corona", "coronavirus", "#coronavirus", "covid", "#covid", "covid19", "#covid19", "covid-19", "#covid-19", "sarscov2", "#sarscov2", "sars cov2", "sars cov 2", "covid_19", "#covid_19", "#ncov", "ncov", "#ncov2019", "ncov2019", "2019-ncov", "#2019-ncov", "pandemic", "#pandemic" "#2019ncov", "2019ncov", "quarantine", "#quarantine", "flatten the curve", "flattening the curve", "#flatteningthecurve", "#flattenthecurve", "hand sanitizer", "#handsanitizer", "#lockdown", "lockdown", "social distancing", "#socialdistancing", "work from home", "#workfromhome", "working from home", "#workingfromhome", "ppe", "n95", "#ppe", "#n95", "#covidiots", "covidiots", "herd immunity", "#herdimmunity", "pneumonia", "#pneumonia", "chinese virus", "#chinesevirus", "wuhan virus", "#wuhanvirus", "kung flu", "#kungflu", "wearamask", "#wearamask", "wear a mask", "vaccine", "vaccines", "#vaccine", "#vaccines", "corona vaccine", "corona vaccines", "#coronavaccine", "#coronavaccines", "face shield", "#faceshield", "face shields", "#faceshields", "health worker", "#healthworker", "health workers", "#healthworkers", "#stayhomestaysafe", "#coronaupdate", "#frontlineheroes", "#coronawarriors", "#homeschool", "#homeschooling", "#hometasking", "#masks4all", "#wfh", "wash ur hands", "wash your hands", "#washurhands", "#washyourhands", "#stayathome", "#stayhome", "#selfisolating", "self isolating"Dataset Files (the local time mentioned below is GMT+5:45)corona_tweets_01.csv + corona_tweets_02.csv + corona_tweets_03.csv: 2,475,980 tweets (March 20, 2020 01:37 AM - March 21, 2020 09:25 AM)corona_tweets_04.csv: 1,233,340 tweets (March 21, 2020 09:27 AM - March 22, 2020 07:46 AM)corona_tweets_05.csv: 1,782,157 tweets (March 22, 2020 07:50 AM - March 23, 2020 09:08 AM)corona_tweets_06.csv: 1,771,295 tweets (March 23, 2020 09:11 AM - March 24, 2020 11:35 AM)corona_tweets_07.csv: 1,479,651 tweets (March 24, 2020 11:42 AM - March 25, 2020 11:43 AM)corona_tweets_08.csv: 1,272,592 tweets (March 25, 2020 11:47 AM - March 26, 2020 12:46 PM)corona_tweets_09.csv: 1,091,429 tweets (March 26, 2020 12:51 PM - March 27, 2020 11:53 AM)corona_tweets_10.csv: 1,172,013 tweets (March 27, 2020 11:56 AM - March 28, 2020 01:59 PM)corona_tweets_11.csv: 1,141,210 tweets (March 28, 2020 02:03 PM - March 29, 2020 04:01 PM)corona_tweets_12.csv: 793,417 tweets (March 30, 2020 02:01 PM - March 31, 2020 10:16 AM)corona_tweets_13.csv: 1,029,294 tweets (March 31, 2020 10:20 AM - April 01, 2020 10:59 AM)corona_tweets_14.csv: 920,076 tweets (April 01, 2020 11:02 AM - April 02, 2020 12:19 PM)corona_tweets_15.csv: 826,271 tweets (April 02, 2020 12:21 PM - April 03, 2020 02:38 PM)corona_tweets_16.csv: 612,512 tweets (April 03, 2020 02:40 PM - April 04, 2020 11:54 AM)corona_tweets_17.csv: 685,560 tweets (April 04, 2020 11:56 AM - April 05, 2020 12:54 PM)corona_tweets_18.csv: 717,301 tweets (April 05, 2020 12:56 PM - April 06, 2020 10:57 AM)corona_tweets_19.csv: 722,921 tweets (April 06, 2020 10:58 AM - April 07, 2020 12:28 PM)corona_tweets_20.csv: 554,012 tweets (April 07, 2020 12:29 PM - April 08, 2020 12:34 PM)corona_tweets_21.csv: 589,679 tweets (April 08, 2020 12:37 PM - April 09, 2020 12:18 PM)corona_tweets_22.csv: 517,718 tweets (April 09, 2020 12:20 PM - April 10, 2020 09:20 AM)corona_tweets_23.csv: 601,199 tweets (April 10, 2020 09:22 AM - April 11, 2020 10:22 AM)corona_tweets_24.csv: 497,655 tweets (April 11, 2020 10:24 AM - April 12, 2020 10:53 AM)corona_tweets_25.csv: 477,182 tweets (April 12, 2020 10:57 AM - April 13, 2020 11:43 AM)corona_tweets_26.csv: 288,277 tweets (April 13, 2020 11:46 AM - April 14, 2020 12:49 AM)corona_tweets_27.csv: 515,739 tweets (April 14, 2020 11:09 AM - April 15, 2020 12:38 PM)corona_tweets_28.csv: 427,088 tweets (April 15, 2020 12:40 PM - April 16, 2020 10:03 AM)corona_tweets_29.csv: 433,368 tweets (April 16, 2020 10:04 AM - April 17, 2020 10:38 AM)corona_tweets_30.csv: 392,847 tweets (April 17, 2020 10:40 AM - April 18, 2020 10:17 AM)> With the addition of some more coronavirus specific keywords, the number of tweets captured day has increased significantly, therefore, the CSV files hereafter will be zipped. Lets save some bandwidth.corona_tweets_31.csv: 2,671,818 tweets (April 18, 2020 10:19 AM - April 19, 2020 09:34 AM)corona_tweets_32.csv: 2,393,006 tweets (April 19, 2020 09:43 AM - April 20, 2020 10:45 AM)corona_tweets_33.csv: 2,227,579 tweets (April 20, 2020 10:56 AM - April 21, 2020 10:47 AM)corona_tweets_34.csv: 2,211,689 tweets (April 21, 2020 10:54 AM - April 22, 2020 10:33 AM)corona_tweets_35.csv: 2,265,189 tweets (April 22, 2020 10:45 AM - April 23, 2020 10:49 AM)corona_tweets_36.csv: 2,201,138 tweets (April 23, 2020 11:08 AM - April 24, 2020 10:39 AM)corona_tweets_37.csv: 2,338,713 tweets (April 24, 2020 10:51 AM - April 25, 2020 11:50 AM)corona_tweets_38.csv: 1,981,835 tweets (April 25, 2020 12:20 PM - April 26, 2020 09:13 AM)corona_tweets_39.csv: 2,348,827 tweets (April 26, 2020 09:16 AM - April 27, 2020 10:21 AM)corona_tweets_40.csv: 2,212,216 tweets (April 27, 2020 10:33 AM - April 28, 2020 10:09 AM)corona_tweets_41.csv: 2,118,853 tweets (April 28, 2020 10:20 AM - April 29, 2020 08:48 AM)corona_tweets_42.csv: 2,390,703 tweets (April 29, 2020 09:09 AM - April 30, 2020 10:33 AM)corona_tweets_43.csv: 2,184,439 tweets (April 30, 2020 10:53 AM - May 01, 2020 10:18 AM)corona_tweets_44.csv: 2,223,013 tweets (May 01, 2020 10:23 AM - May 02, 2020 09:54 AM)corona_tweets_45.csv: 2,216,553 tweets (May 02, 2020 10:18 AM - May 03, 2020 09:57 AM)corona_tweets_46.csv: 2,266,373 tweets (May 03, 2020 10:09 AM - May 04, 2020 10:17 AM)corona_tweets_47.csv: 2,227,489 tweets (May 04, 2020 10:32 AM - May 05, 2020 10:17 AM)corona_tweets_48.csv: 2,218,774 tweets (May 05, 2020 10:38 AM - May 06, 2020 10:26 AM)corona_tweets_49.csv: 2,164,251 tweets (May 06, 2020 10:35 AM - May 07, 2020 09:33 AM)corona_tweets_50.csv: 2,203,686 tweets (May 07, 2020 09:55 AM - May 08, 2020 09:35 AM)corona_tweets_51.csv: 2,250,019 tweets (May 08, 2020 09:39 AM - May 09, 2020 09:49 AM)corona_tweets_52.csv: 2,273,705 tweets (May 09, 2020 09:55 AM - May 10, 2020 10:11 AM)corona_tweets_53.csv: 2,208,264 tweets (May 10, 2020 10:23 AM - May 11, 2020 09:57 AM)corona_tweets_54.csv: 2,216,845 tweets (May 11, 2020 10:08 AM - May 12, 2020 09:52 AM)corona_tweets_55.csv: 2,264,472 tweets (May 12, 2020 09:59 AM - May 13, 2020 10:14 AM)corona_tweets_56.csv: 2,339,709 tweets (May 13, 2020 10:24 AM - May 14, 2020 11:21 AM)corona_tweets_57.csv: 2,096,878 tweets (May 14, 2020 11:38 AM - May 15, 2020 09:58 AM)corona_tweets_58.csv: 2,214,205 tweets (May 15, 2020 10:13 AM - May 16, 2020 09:43 AM)> The server and the databases have been optimized; therefore, there is a significant rise in the number of tweets captured per day.corona_tweets_59.csv: 3,389,090 tweets (May 16, 2020 09:58 AM - May 17, 2020 10:34 AM)corona_tweets_60.csv: 3,530,933 tweets (May 17, 2020 10:36 AM - May 18, 2020 10:07 AM)corona_tweets_61.csv: 3,899,631 tweets (May 18, 2020 10:08 AM - May 19, 2020 10:07 AM)corona_tweets_62.csv: 3,767,009 tweets (May 19, 2020 10:08 AM - May 20, 2020 10:06 AM)corona_tweets_63.csv: 3,790,455 tweets (May 20, 2020 10:06 AM - May 21, 2020 10:15 AM)corona_tweets_64.csv: 3,582,020 tweets (May 21, 2020 10:16 AM - May 22, 2020 10:13 AM)corona_tweets_65.csv: 3,461,470 tweets (May 22, 2020 10:14 AM - May 23, 2020 10:08 AM)corona_tweets_66.csv: 3,477,564 tweets (May 23, 2020 10:08 AM - May 24, 2020 10:02 AM)corona_tweets_67.csv: 3,656,446 tweets (May 24, 2020 10:02 AM - May 25, 2020 10:10 AM)corona_tweets_68.csv: 3,474,952 tweets (May 25, 2020 10:11 AM - May 26, 2020 10:22 AM)corona_tweets_69.csv: 3,422,960 tweets (May 26, 2020 10:22 AM - May 27, 2020 10:16 AM)corona_tweets_70.csv: 3,480,999 tweets (May 27, 2020 10:17 AM - May 28, 2020 10:35 AM)corona_tweets_71.csv: 3,446,008 tweets (May 28, 2020 10:36 AM - May 29, 2020 10:07 AM)corona_tweets_72.csv: 3,492,841 tweets (May 29, 2020 10:07 AM - May 30, 2020 10:14 AM)corona_tweets_73.csv: 3,098,817 tweets (May 30, 2020 10:15 AM - May 31, 2020 10:13 AM)corona_tweets_74.csv: 3,234,848 tweets (May 31, 2020 10:13 AM - June 01, 2020 10:14 AM)corona_tweets_75.csv: 3,206,132 tweets (June 01, 2020 10:15 AM - June 02, 2020 10:07 AM)corona_tweets_76.csv: 3,206,417 tweets (June 02, 2020 10:08 AM - June 03, 2020 10:26 AM)corona_tweets_77.csv: 3,256,225 tweets (June 03, 2020

ABSTRACT Background : The Covid-19 pandemic associated with the SARS-CoV-2 has caused very high death tolls in many countries, while it has had less prevalence in other countries of Africa and Asia. Climate and geographic conditions, as well as other epidemiologic and demographic conditions, were a matter of debate on whether or not they could have an effect on the prevalence of Covid-19. Objective : In the present work, we sought a possible relevance of the geographic location of a given country on its Covid-19 prevalence. On the other hand, we sought a possible relation between the history of epidemiologic and demographic conditions of the populations and the prevalence of Covid-19 across four continents (America, Europe, Africa, and Asia). We also searched for a possible impact of pre-pandemic alcohol consumption in each country on the two year death tolls across the four continents. Methods : We have sought the death toll caused by Covid-19 in 39 countries and obtained the registered deaths from specialized web pages. For every country in the study, we have analysed the correlation of the Covid-19 death numbers with its geographic latitude, and its associated climate conditions, such as the mean annual temperature, the average annual sunshine hours, and the average annual UV index. We also analyzed the correlation of the Covid-19 death numbers with epidemiologic conditions such as cancer score and Alzheimer score, and with demographic parameters such as birth rate, mortality rate, fertility rate, and the percentage of people aged 65 and above. In regard to consumption habits, we searched for a possible relation between alcohol intake levels per capita and the Covid-19 death numbers in each country. Correlation factors and determination factors, as well as analyses by simple linear regression and polynomial regression, were calculated or obtained by Microsoft Exell software (2016). Results : In the present study, higher numbers of deaths related to Covid-19 pandemic were registered in many countries in Europe and America compared to other countries in Africa and Asia. The analysis by polynomial regression generated an inverted bell-shaped curve and a significant correlation between the Covid-19 death numbers and the geographic latitude of each country in our study. Higher death numbers were registered in the higher geographic latitudes of both hemispheres, while lower scores of deaths were registered in countries located around the equator line. In a bell shaped curve, the latitude levels were negatively correlated to the average annual levels (last 10 years) of temperatures, sunshine hours, and UV index of each country, with the highest scores of each climate parameter being registered around the equator line, while lower levels of temperature, sunshine hours, and UV index were registered in higher latitude countries. In addition, the linear regression analysis showed that the Covid-19 death numbers registered in the 39 countries of our study were negatively correlated with the three climate factors of our study, with the temperature as the main negatively correlated factor with Covid-19 deaths. On the other hand, cancer and Alzheimer's disease scores, as well as advanced age and alcohol intake, were positively correlated to Covid-19 deaths, and inverted bell-shaped curves were obtained when expressing the above parameters against a country’s latitude. Instead, the (birth rate/mortality rate) ratio and fertility rate were negatively correlated to Covid-19 deaths, and their values gave bell-shaped curves when expressed against a country’s latitude. Conclusion : The results of the present study prove that the climate parameters and history of epidemiologic and demographic conditions as well as nutrition habits are very correlated with Covid-19 prevalence. The results of the present study prove that low levels of temperature, sunshine hours, and UV index, as well as negative epidemiologic and demographic conditions and high scores of alcohol intake may worsen Covid-19 prevalence in many countries of the northern hemisphere, and this phenomenon could explain their high Covid-19 death tolls. Keywords : Covid-19, Coronavirus, SARS-CoV-2, climate, temperature, sunshine hours, UV index, cancer, Alzheimer disease, alcohol.

This dataset represents preliminary estimates of cumulative U.S. COVID-19 disease burden for the 2024-2025 period, including illnesses, outpatient visits, hospitalizations, and deaths. The weekly COVID-19-associated burden estimates are preliminary and based on continuously collected surveillance data from patients hospitalized with laboratory-confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. The data come from the Coronavirus Disease 2019 (COVID-19)-Associated Hospitalization Surveillance Network (COVID-NET), a surveillance platform that captures data from hospitals that serve about 10% of the U.S. population. Each week CDC estimates a range (i.e., lower estimate and an upper estimate) of COVID-19 -associated burden that have occurred since October 1, 2024.

Note: Data are preliminary and subject to change as more data become available. Rates for recent COVID-19-associated hospital admissions are subject to reporting delays; as new data are received each week, previous rates are updated accordingly.

References

1. Reed C, Chaves SS, Daily Kirley P, et al. Estimating influenza disease burden from population-based surveillance data in the United States. PLoS One. 2015;10(3):e0118369. https://doi.org/10.1371/journal.pone.0118369 
2. Rolfes, MA, Foppa, IM, Garg, S, et al. Annual estimates of the burden of seasonal influenza in the United States: A tool for strengthening influenza surveillance and preparedness. Influenza Other Respi Viruses. 2018; 12: 132– 137. https://doi.org/10.1111/irv.12486
3. Tokars JI, Rolfes MA, Foppa IM, Reed C. An evaluation and update of methods for estimating the number of influenza cases averted by vaccination in the United States. Vaccine. 2018;36(48):7331-7337. doi:10.1016/j.vaccine.2018.10.026 
4. Collier SA, Deng L, Adam EA, Benedict KM, Beshearse EM, Blackstock AJ, Bruce BB, Derado G, Edens C, Fullerton KE, Gargano JW, Geissler AL, Hall AJ, Havelaar AH, Hill VR, Hoekstra RM, Reddy SC, Scallan E, Stokes EK, Yoder JS, Beach MJ. Estimate of Burden and Direct Healthcare Cost of Infectious Waterborne Disease in the United States. Emerg Infect Dis. 2021 Jan;27(1):140-149. doi: 10.3201/eid2701.190676. PMID: 33350905; PMCID: PMC7774540.
5. Reed C, Kim IK, Singleton JA,  et al. Estimated influenza illnesses and hospitalizations averted by vaccination–United States, 2013-14 influenza season. MMWR Morb Mortal Wkly Rep. 2014 Dec 12;63(49):1151-4. https://www.cdc.gov/mmwr/preview/mmwrhtml/mm6349a2.htm 
6. Reed C, Angulo FJ, Swerdlow DL, et al. Estimates of the Prevalence of Pandemic (H1N1) 2009, United States, April–July 2009. Emerg Infect Dis. 2009;15(12):2004-2007. https://dx.doi.org/10.3201/eid1512.091413  
7. Devine O, Pham H, Gunnels B, et al. Extrapolating Sentinel Surveillance Information to Estimate National COVID-19 Hospital Admission Rates: A Bayesian Modeling Approach. Influenza and Other Respiratory Viruses. https://onlinelibrary.wiley.com/doi/10.1111/irv.70026. Volume18, Issue10. October 2024.
8. https://www.cdc.gov/covid/php/covid-net/index.html">COVID-NET | COVID-19 | CDC 
9. https://www.cdc.gov/covid/hcp/clinical-care/systematic-review-process.html 
10. https://academic.oup.com/pnasnexus/article/1/3/pgac079/6604394?login=false">Excess natural-cause deaths in California by cause and setting: March 2020 through February 2021 | PNAS Nexus | Oxford Academic (oup.com)
11. Kruschke, J. K. 2011. Doing Bayesian data analysis: a tutorial with R and BUGS. Elsevier, Amsterdam, Section 3.3.5.

On 27 February 2020, the first case of COVID-19 disease was confirmed in The Netherlands by RIVM (National Institute for Public Health and the Environment). In the weeks after, thousands of people were diagnosed with the infectious disease. Data on COVID-19 case counts are important for research and applications on various topics like epidemiology and statistics.

This dataset contains reported case counts derived from official sources like RIVM (National Institute for Public Health and the Environment), LCPS (National Coordination Center for Patient Distribution), and NICE (National Intensive Care Evaluation). Data from these sources are collected, standardized, and published in various formats on a daily basis.

The README document in this repository provides an overview of the available datasets, their file location(s), and codebooks. Copies of the original data are stored in the folder named 'raw_data'. Scripts to process the raw data into standardized files can be found in the folder workflows.

The aim of the special survey of the GESIS panel on the outbreak of the corona virus SARS-CoV-2 in Germany was to collect timely data on the effects of the corona crisis on people´s daily lives. The study focused on questions of risk perception, risk minimization measures, evaluation of political measures and their compliance, trust in politics and institutions, changed employment situation, childcare obligations, and media consumption. Due to the need for timely data collection, only the GESIS panel sub-sample of online respondents was invited (about three quarters of the sample). Since, due to time constraints, respondents could only participate in the online survey but not by mail, the results cannot be easily transferred to the overall population. Further longitudinal surveys on Covid-19 with the entire sample of the GESIS panel are planned for 2020.

Topics: Risk perception: Probability of events related to corona infection in the next two months (self, infection of a person from close social surrondings, hospital treatment, quarantine measures regardless of whether infected or not, infecting other people)

Risk minimization: risk minimization measures taken in the last seven days (avoided certain (busy) places, kept minimum distance to other people, adapted school or work situation, quarantine due to symptoms or without symptoms, washed hands more often, used disinfectant, stocks increased, reduced social interactions, worn face mask, other, none of these measures).

Evaluation of the effectiveness of various policy measures to combat the further spread of corona virus (closure of day-care centres, kindergartens and schools, closure of sports facilities, closure of bars, cafés and restaurants, closure of all shops except supermarkets and pharmacies, ban on visiting hospitals, nursing homes and old people´s homes, curfew for persons aged 70 and over or people with health problems or for anyone not working in the health sector or other critical professions (except for basic purchases and urgent medical care).

Curfew compliance or refusal: Willingness to obey a curfew vs. refusal; reasons for the compliance with curfew (social duty, fear of punishment, protection against infection, fear of infecting others (loved ones, infecting others in general, a risk group); reasons for refusal of curfew (restrictions too drastic or not justified, other obligations, does not stop the spread, not affected by the outbreak, boring at home, will not be punished).

Evaluation of the effectiveness of various government measures (medical care, restrictions on social life such as closure of public facilities and businesses, reduction of economic damage, communication with the population).

Trust in politics and institutions with regard to dealing with the coronavirus (physician, local health authority, local and municipal administration, Robert Koch Institute (RKI), Federal Government, German Chancellor, Ministry of Health, World Health Organization (WHO), scientists).

Changed employment situation: employment status at the beginning of March; change in occupational situation since the spread of coronavirus: dependent employees: number of hours reduced, number of hours increased, more home office, leave of absence with/ without continued wage payment , fired, no change; self-employed: working hours reduced, working hours increased, more home office, revenue decreased, revenue increased, company temporarily closed by the authorities, company temporarily voluntarily closed, financial hardship, company permanently closed or insolvent, no change.

Childcare: children under 12 in the household; organisation of childcare during the closure of day-care centres, kindergartens and schools (staying at home, partner stays at home, older siblings take care, grandparents are watching, etc.)

Media consumption on Corona: information sources used for Corona (e.g. nationwide public or private television or radio, local public or private television or radio, national newspapers or local newspapers, Facebook, other social media, personal conversations with friends and family, other, do not inform myself on the subject); frequency of Facebook usage; information about Corona obtained from regional Facebook page or regional Facebook group.

Demography: sex; age (categorized); education (categorized); intention to vote and choice of party (Sunday question); Left-right self-assessment; marital status; size of household.

Additionally coded: Respondent ID;...

COVID-19, coronavirus disease 2019; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2. (XLSX)

The dataset shows the 7-day median of the RNA copies of the specified virus per day and 100’000 people in the wastewater treatment plant (ARA) Basel as well as the 7-day median of the corresponding case numbers. The data set is usually updated on Tuesdays with the data until the previous Sunday. ProRheno AG (operator of ARA Basel) takes a 24h sample of the raw waste water, which is examined for RNA of the specified viruses by the Cantonal Laboratory Basel-Stadt (KL BS). The measurement methodology has not been changed since the beginning of the monitoring: see publication https://smw.ch/index.php/smw/article/view/3226. The plausibility of the values is continuously checked against internal quality parameters. The study area comprises the catchment area of the ARA Basel, which consists mainly of the canton of Basel-Stadt as well as the municipalities of Allschwil, Binningen, Birsfelden, Bottmingen, Oberwil and Schönenbuch (all Canton Baselland). Until the end of June 2023, the measured values of the KL BS were also presented on the wastewater dashboard of the BAG Covid-19 Switzerland | Coronavirus | Dashboard (https://www.covid19.admin.ch/de/epidemiologic/waste-water?wasteWaterFacility=270101). As of July 2023, the measured values of the EAWAG SARS-CoV2 in wastewater – Eawag (https://www.eawag.ch/de/abteilung/sww/projekte/sars-cov2-im-abwasser/) will be published on this page, which also examines the raw wastewater of ARA Basel. The examination methods used by KL BS and EAWAG are very similar but not identical.Case figures correspond to the number of confirmed and reported cases of infections in the catchment area of ARA Basel.Interpretation of curvesThe monitoring of viruses in wastewater is primarily about identifying trends (in particular, of course, the increase of a circulating virus). It is not possible to derive a certain number of cases or the severity of an infection. A comparison of the curve rash (height of peaks) at different times is hardly possible, because different virus variants lead to different amounts of virus per case. Different virus variants can also affect the symptoms, so that, for example, infections in humans run without a trace, but nevertheless viruses are released into the wastewater.

The pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) led to the death of millions of people worldwide and thousands more infected individuals developed sequelae due to the disease of the new coronavirus of 2019 (COVID-19). The development of several studies has contributed to the knowledge about the evolution of SARS-CoV2 infection and the disease to more severe forms. Despite this information being debated in the scientific literature, many mechanisms still need to be better understood in order to control the spread of the virus and treat clinical cases of COVID-19. In this article, we carried out an extensive literature review in order to bring together, in a single article, the biological, social, genetic, diagnostic, therapeutic, immunization, and even socioeconomic aspects that impact the SAR-CoV-2 pandemic. This information gathered in this article will enable a broad and consistent reading of the main aspects related to the current pandemic.

Note: Reporting of new COVID-19 Case Surveillance data will be discontinued July 1, 2024, to align with the process of removing SARS-CoV-2 infections (COVID-19 cases) from the list of nationally notifiable diseases. Although these data will continue to be publicly available, the dataset will no longer be updated.

Authorizations to collect certain public health data expired at the end of the U.S. public health emergency declaration on May 11, 2023. The following jurisdictions discontinued COVID-19 case notifications to CDC: Iowa (11/8/21), Kansas (5/12/23), Kentucky (1/1/24), Louisiana (10/31/23), New Hampshire (5/23/23), and Oklahoma (5/2/23). Please note that these jurisdictions will not routinely send new case data after the dates indicated. As of 7/13/23, case notifications from Oregon will only include pediatric cases resulting in death.

This case surveillance public use dataset has 12 elements for all COVID-19 cases shared with CDC and includes demographics, any exposure history, disease severity indicators and outcomes, presence of any underlying medical conditions and risk behaviors, and no geographic data.

CDC has three COVID-19 case surveillance datasets:

• COVID-19 Case Surveillance Public Use Data with Geography: Public use, patient-level dataset with clinical data (including symptoms), demographics, and county and state of residence. (19 data elements)
• COVID-19 Case Surveillance Public Use Data: Public use, patient-level dataset with clinical and symptom data and demographics, with no geographic data. (12 data elements)
• COVID-19 Case Surveillance Restricted Access Detailed Data: Restricted access, patient-level dataset with clinical and symptom data, demographics, and state and county of residence. Access requires a registration process and a data use agreement. (33 data elements)

• Data elements can be found on the COVID-19 case report form located at www.cdc.gov/coronavirus/2019-ncov/downloads/pui-form.pdf.
• Data are considered provisional by CDC and are subject to change until the data are reconciled and verified with the state and territorial data providers.
• Some data cells are suppressed to protect individual privacy.
• The datasets will include all cases with the earliest date available in each record (date received by CDC or date related to illness/specimen collection) at least 14 days prior to the creation of the current datasets. This 14-day lag allows case reporting to be stabilized and ensures that time-dependent outcome data are accurately captured.
• Datasets are updated monthly.
• Datasets are created using CDC’s Policy on Public Health Research and Nonresearch Data Management and Access and include protections designed to protect individual privacy.
• For more information about data collection and reporting, please see https://www.cdc.gov/coronavirus/2019-ncov/covid-data/about-us-cases-deaths.html.
• For more information about the COVID-19 case surveillance data, please see https://www.cdc.gov/coronavirus/2019-ncov/covid-data/faq-surveillance.html
  

Overview

The COVID-19 case surveillance database includes individual-level data reported to U.S. states and autonomous reporting entities, including New York City and the District of Columbia (D.C.), as well as U.S. territories and affiliates. On April 5, 2020, COVID-19 was added to the Nationally Notifiable Condition List and classified as “immediately notifiable, urgent (within 24 hours)” by a Council of State and Territorial Epidemiologists (CSTE) Interim Position Statement (Interim-20-ID-01). CSTE updated the position statement on August 5, 2020, to clarify the interpretation of antigen detection tests and serologic test results within the case classification (Interim-20-ID-02). The statement also recommended that all states and territories enact laws to make COVID-19 reportable in their jurisdiction, and that jurisdictions conducting surveillance should submit case notifications to CDC. COVID-19 case surveillance data are collected by jurisdictions and reported voluntarily to CDC.

For more information: NNDSS Supports the COVID-19 Response | CDC.

The deidentified data in the “COVID-19 Case Surveillance Public Use Data” include demographic characteristics, any exposure history, disease severity indicators and outcomes, clinical data, laboratory diagnostic test results, and presence of any underlying medical conditions and risk behaviors. All data elements can be found on the COVID-19 case report form located at www.cdc.gov/coronavirus/2019-ncov/downloads/pui-form.pdf.

COVID-19 Case Reports

COVID-19 case reports have been routinely submitted using nationally standardized case reporting forms. On April 5, 2020, CSTE released an Interim Position Statement with national surveillance case definitions for COVID-19 included. Current versions of these case definitions are available here: https://ndc.services.cdc.gov/case-definitions/coronavirus-disease-2019-2021/.

All cases reported on or after were requested to be shared by public health departments to CDC using the standardized case definitions for laboratory-confirmed or probable cases. On May 5, 2020, the standardized case reporting form was revised. Case reporting using this new form is ongoing among U.S. states and territories.

Data are Considered Provisional

• The COVID-19 case surveillance data are dynamic; case reports can be modified at any time by the jurisdictions sharing COVID-19 data with CDC. CDC may update prior cases shared with CDC based on any updated information from jurisdictions. For instance, as new information is gathered about previously reported cases, health departments provide updated data to CDC. As more information and data become available, analyses might find changes in surveillance data and trends during a previously reported time window. Data may also be shared late with CDC due to the volume of COVID-19 cases.
• Annual finalized data: To create the final NNDSS data used in the annual tables, CDC works carefully with the reporting jurisdictions to reconcile the data received during the year until each state or territorial epidemiologist confirms that the data from their area are correct.
• Access Addressing Gaps in Public Health Reporting of Race and Ethnicity for COVID-19, a report from the Council of State and Territorial Epidemiologists, to better understand the challenges in completing race and ethnicity data for COVID-19 and recommendations for improvement.

Data Limitations

To learn more about the limitations in using case surveillance data, visit FAQ: COVID-19 Data and Surveillance.

Data Quality Assurance Procedures

CDC’s Case Surveillance Section routinely performs data quality assurance procedures (i.e., ongoing corrections and logic checks to address data errors). To date, the following data cleaning steps have been implemented:

• Questions that have been left unanswered (blank) on the case report form are reclassified to a Missing value, if applicable to the question. For example, in the question “Was the individual hospitalized?” where the possible answer choices include “Yes,” “No,” or “Unknown,” the blank value is recoded to Missing because the case report form did not include a response to the question.
• Logic checks are performed for date data. If an illogical date has been provided, CDC reviews the data with the reporting jurisdiction. For example, if a symptom onset date in the future is reported to CDC, this value is set to null until the reporting jurisdiction updates the date appropriately.
• Additional data quality processing to recode free text data is ongoing. Data on symptoms, race and ethnicity, and healthcare worker status have been prioritized.

Data Suppression

To prevent release of data that could be used to identify people, data cells are suppressed for low frequency (<5) records and indirect identifiers (e.g., date of first positive specimen). Suppression includes rare combinations of demographic characteristics (sex, age group, race/ethnicity). Suppressed values are re-coded to the NA answer option; records with data suppression are never removed.

For questions, please contact Ask SRRG (eocevent394@cdc.gov).

Additional COVID-19 Data

COVID-19 data are available to the public as summary or aggregate count files, including total counts of cases and deaths by state and by county. These

The COVID Tracking Project was a volunteer organization launched from The Atlantic and dedicated to collecting and publishing the data required to understand the COVID-19 outbreak in the United States. Our dataset was in use by national and local news organizations across the United States and by research projects and agencies worldwide.

Every day, we collected data on COVID-19 testing and patient outcomes from all 50 states, 5 territories, and the District of Columbia by visiting official public health websites for those jurisdictions and entering reported values in a spreadsheet. The files in this dataset represent the entirety of our COVID-19 testing and outcomes data collection from March 7, 2020 to March 7, 2021. This dataset includes official values reported by each state on each day of antigen, antibody, and PCR test result totals; the total number of probable and confirmed cases of COVID-19; the number of people currently hospitalized, in intensive care, and on a ventilator; the total number of confirmed and probable COVID-19 deaths; and more.

This dataset has been temporarily removed as of April 3, 2023. This dataset is still being maintained internally and will be restored after internal processes undergo a transition. Similar data are available from CDPH: https://calcat.covid19.ca.gov/cacovidmodels/.

This dataset displays SARS-CoV-2 lineages identified through whole genome sequencing (WGS) in Marin County by date the sample was collected. There is a minimum 7-day (and up to 21-day) lag in reporting. Not all positive samples in Marin County are sequenced, thus these data may not fully represent the variants circulating in the community. Summarized data can be found in the "Prevalence of Variants of SARS-CoV-2 in Marin County" chart at https://coronavirus.marinhhs.org/surveillance.

More information about variants of SARS-CoV-2 can be found via the CDC at https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-info.html

Splitgraph serves as an HTTP API that lets you run SQL queries directly on this data to power Web applications. For example:

See the Splitgraph documentation for more information.

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.