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.

The COVID-19 dashboard includes data on city/town COVID-19 activity, confirmed and probable cases of COVID-19, confirmed and probable deaths related to COVID-19, and the demographic characteristics of cases and deaths.

As demonstrated by severe acute respiratory syndrome coronavirus 2, coronaviruses pose a significant pandemic threat. Here, we show that coronavirus disease 2019 mRNA vaccination can induce significant levels of cross-reactive antibodies against diverse coronavirus spike proteins. While these antibodies are binding antibodies that likely have little neutralization capacity and while their contribution to cross-protection is unclear, it is possible that they may play a role in protection from progression to severe disease with novel coronaviruses.

Context

Hoping this data will be used to identify new predictions as a new COVID19 data spike was reported at Iran in the city of Tehran. NOTE: The data is mined from WHO.

Content

The data is from the official WHO website that you can also download. I downloaded it here to code it inside Kaggle for easier import of data and developing the code. The data is composed of COVID19 by country, every data that is up to the latest as of December 8, 2020.

Acknowledgements

We wouldn't be here without the help of others. If you owe any attributions or thanks, include them here along with any citations of past research.

Inspiration

Your data will be in front of the world's largest data science community.

The time it takes for the number of COVID-19 deaths to double varies by country. The doubling rate in the United States was 139 days as of December 13, 2020. In comparison, the number of confirmed deaths in Australia doubled from 450 to 908 in the space of 117 days between August 18 and December 13, 2020.

COVID-19: We are all in this together The commitment of civilians to follow basic hygiene measures and maintain social distancing must continue. The wellbeing of populations cannot be jeopardized, and young people must also engage in the response. In Australia, the 20- to 29-year-old age group accounts for the highest number of COVID-19 cases. With lockdown restrictions lifted, many people have returned to their regular routines and jumped back into socializing. However, there are concerns about complacency and suggestions that young adults could be driving spikes in coronavirus cases.

Receive coronavirus warnings on your smartphone It is of paramount importance that countries keep a vigilant eye on the spread of the coronavirus. One way of doing so is to invest in track and trace surveillance systems. Electronic tools are not essential, but many countries are using contact-tracing smartphone apps to make the tracking of cases more efficient. In June 2020, a contact-tracing app was rolled out across Japan, and it received nearly eight million downloads in the first month. A COVID-19 alert app was also launched in Canada at the end of July 2020. The smartphone software is initially being piloted in Ontario, but it will soon be possible for people in other provinces to use the app and report a diagnosis.

The map shows the 7-day incidence of confirmed cases of COVID-19 in the Austrian districts on a daily basis since the data were available (26 February 2020) and puts them in relation to the political targets.

Virus loads and recoveries of cDNA and final SGS in HT-SGS from upper respiratory swab samples.

Coronaviruses (CoVs) [E1] are a diverse group of enveloped, plus-stranded RNAviruses that infect humans and many animal species, in which they can causerespiratory, enteric, hepatic, central nervous system and neurologicaldiseases of varying severity. A CoV contains four structural proteins,including spike (S), envelope (E), membrane (M), and nucleocapsid (N)proteins. Among them, the S protein, which is located on the envelope surfaceof the virion, functions to mediate receptor recognition and membrane fusionand is therefore a key factor determining the virus tropism for a specificspecies. This protein is composed of an N-terminal receptor-binding domain(S1) and a C-terminal trans-membrane fusion domain (S2) .The S2 subunit contains two 4-3 heptad repeats (HRs) of hydrophobic residues,HR1 and HR2, typical of coiled coils, separated by an ~170-aa-long interveningdomain. The S2 subunit is expected to present rearrangement of its HRs to forma stable 6-helix bundle fusion core .HR1 forms a 24-turn alpha-helix, while HR2 adopts a mixed conformation: thecentral part fold into a nine-turn alpha-helix, while the residues on eitherside of the helix adopt an extended conformation. The HR1 region forms a longtrimeric helical coiled-coil structure with peptides from the HR2 regionpacking in an oblique antiparallel manner on the grooves of the HR1 trimer ina mixed extended and helical conformation. Packing of thehelical parts of HR2 on the HR1 trimer grooves and formation of a six-helicalbundle plays an important role in the formation of a stable post-fusionstructure. In contrast to their extended helical conformations in the post-fusion state, the HR1 motifs within S2 form several shorter helices in theirpre-fusion state .The profiles we developed cover the entire CoV S2-HR1 -HR2 regions.

As of March 10, 2023, there have been 1.1 million deaths related to COVID-19 in the United States. There have been 101,159 deaths in the state of California, more than any other state in the country – California is also the state with the highest number of COVID-19 cases.

The vaccine rollout in the U.S. Since the start of the pandemic, the world has eagerly awaited the arrival of a safe and effective COVID-19 vaccine. In the United States, the immunization campaign started in mid-December 2020 following the approval of a vaccine jointly developed by Pfizer and BioNTech. As of March 22, 2023, the number of COVID-19 vaccine doses administered in the U.S. had reached roughly 673 million. The states with the highest number of vaccines administered are California, Texas, and New York.

Vaccines achieved due to work of research groups Chinese authorities initially shared the genetic sequence to the novel coronavirus in January 2020, allowing research groups to start studying how it invades human cells. The surface of the virus is covered with spike proteins, which enable it to bind to human cells. Once attached, the virus can enter the cells and start to make people ill. These spikes were of particular interest to vaccine manufacturers because they hold the key to preventing viral entry.

This dataset reports the daily reported number of the 7-day moving average rates of Deaths involving COVID-19 by vaccination status and by age group. Learn how the Government of Ontario is helping to keep Ontarians safe during the 2019 Novel Coronavirus outbreak. Effective November 14, 2024 this page will no longer be updated. Information about COVID-19 and other respiratory viruses is available on Public Health Ontario’s interactive respiratory virus tool: https://www.publichealthontario.ca/en/Data-and-Analysis/Infectious-Disease/Respiratory-Virus-Tool Data includes: * Date on which the death occurred * Age group * 7-day moving average of the last seven days of the death rate per 100,000 for those not fully vaccinated * 7-day moving average of the last seven days of the death rate per 100,000 for those fully vaccinated * 7-day moving average of the last seven days of the death rate per 100,000 for those vaccinated with at least one booster ##Additional notes As of June 16, all COVID-19 datasets will be updated weekly on Thursdays by 2pm. As of January 12, 2024, data from the date of January 1, 2024 onwards reflect updated population estimates. This update specifically impacts data for the 'not fully vaccinated' category. On November 30, 2023 the count of COVID-19 deaths was updated to include missing historical deaths from January 15, 2020 to March 31, 2023. CCM is a dynamic disease reporting system which allows ongoing update to data previously entered. As a result, data extracted from CCM represents a snapshot at the time of extraction and may differ from previous or subsequent results. Public Health Units continually clean up COVID-19 data, correcting for missing or overcounted cases and deaths. These corrections can result in data spikes and current totals being different from previously reported cases and deaths. Observed trends over time should be interpreted with caution for the most recent period due to reporting and/or data entry lags. The data does not include vaccination data for people who did not provide consent for vaccination records to be entered into the provincial COVaxON system. This includes individual records as well as records from some Indigenous communities where those communities have not consented to including vaccination information in COVaxON. “Not fully vaccinated” category includes people with no vaccine and one dose of double-dose vaccine. “People with one dose of double-dose vaccine” category has a small and constantly changing number. The combination will stabilize the results. Spikes, negative numbers and other data anomalies: Due to ongoing data entry and data quality assurance activities in Case and Contact Management system (CCM) file, Public Health Units continually clean up COVID-19, correcting for missing or overcounted cases and deaths. These corrections can result in data spikes, negative numbers and current totals being different from previously reported case and death counts. Public Health Units report cause of death in the CCM based on information available to them at the time of reporting and in accordance with definitions provided by Public Health Ontario. The medical certificate of death is the official record and the cause of death could be different. Deaths are defined per the outcome field in CCM marked as “Fatal”. Deaths in COVID-19 cases identified as unrelated to COVID-19 are not included in the Deaths involving COVID-19 reported. Rates for the most recent days are subject to reporting lags All data reflects totals from 8 p.m. the previous day. This dataset is subject to change.

As of January 1, 2025, the number of active coronavirus (COVID-19) infections in Italy was approximately 218,000. Among these, 42 infected individuals were being treated in intensive care units. Another 1,332 individuals infected with the coronavirus were hospitalized with symptoms, while approximately 217,000 thousand were in isolation at home. The total number of coronavirus cases in Italy reached over 26.9 million (including active cases, individuals who recovered, and individuals who died) as of the same date. The region mostly hit by the spread of the virus was Lombardy, which counted almost 4.4 million cases.For a global overview, visit Statista's webpage exclusively dedicated to coronavirus, its development, and its impact.

The COVID-19 pandemic has prompted a rapid response in vaccine and drug development targeting SARS-CoV-2. Herein, we modelled a complete membrane-embedded SARS-CoV-2 spike (S) protein and used molecular dynamics (MD) simulations in the presence of benzene probes designed to enhance discovery of cryptic, potentially druggable pockets. This approach recapitulated lipid binding sites previously characterized by cryo-electron microscopy, and uncovered a novel cryptic pocket with promising druggable properties located underneath the 617-628 loop, which was shown to be involved in modulating the stability of cleaved S protein trimers a well as the formation of S protein multimers on the viral surface. A multi-conformational behaviour of this loop in simulations was validated using hydrogen-deuterium exchange mass spectrometry (HDX-MS) experiments, supportive of opening and closing dynamics. The pocket is the site of multiple mutations associated with increased transmissibility and severity of infection found in SARS-CoV-2 variants of concern including D614G. Collectively, this work highlights the utility of the benzene mapping approach in uncovering potential druggable sites on the surface of SARS-CoV-2 targets.

Here, the investigators report that infection with and vaccination against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induces broadly cross-reactive binding antibodies to spikes from a wide range of coronaviruses.

1. Sequence GenBank IDs of all 615,374 nucleotide spike sequences isolated from samples collected between December 2019 and July 2021.
2. Nucleotide alignment of the 16,808 unique spike sequences derived from the above.
3. Baseline Sequence IDs collected up to July 2021
4. B.1.1.7 Sequences IDs collected up to March 2022
5. P.1 Sequences IDs collected up to February 2022
6. AY.4 Sequences IDs collected up to February 2022
7. AY.4.2 Sequences IDs collected up to February 2022
8. BA.1 Sequences IDs collected up to February 2022
9. BA.1.1 Sequences IDs collected up to March 2022
10. BA.2 Sequences IDs collected up to March 2022
11. Biosample accession of deep sequenced patient samples
12. Newick tree for figure 1B - S3 Data
13. Newick tree for figure 2A - S4 Data
14. BA.4 Sequences IDs collected up to April 2023
15. BA.5 Sequences IDs collected up to April 2023

The type I glycoprotein S of Coronavirus, trimers of which constitute the typical viral spikes, is assembled into virions through noncovalent interactions with the M protein. The spike glycoprotein is translated as a large polypeptide that is subsequently cleaved to S1 ([interpro:IPR002551]) and S2 . The cleavage of S can occur at two distinct sites: S2 or S2' . The spike is present in two very different forms: pre-fusion (the form on mature virions) and post-fusion (the form after membrane fusion has been completed). The spike is cleaved sequentially by host proteases at two sites: first at the S1/S2 boundary (i.e. S1/S2 site) and second within S2 (i.e. S2' site). After the cleavages, S1 dissociates from S2, allowing S2 to transition to the post-fusion structure . Both chimeric S proteins appeared to cause cell fusion when expressed individually, suggesting that they were biologically fully active . The spike is a type I membrane glycoprotein that possesses a conserved transmembrane anchor and an unusual cysteine-rich (cys) domain that bridges the putative junction of the anchor and the cytoplasmic tail .SARS-CoV S is largely uncleaved after biosynthesis. It can be later processed by endosomal cathepsin L, trypsin, thermolysin, and elastase, which are shown to induce syncytia formation and virus entry. Other proteases that are of potential biological relevance in potentiating SARS-CoV S include TMPRSS2, TMPRSS11a, and HAT which are localized on the cell surface and are highly expressed in the human airway . The furin-like S2' cleavage site at KR/SF with P1 and P2 basic residues and a P2' hydrophobic Phe downstream of the IFP is identical between the SARS-CoV-2 and SARS-CoV. One or more furin-like enzymes would cleave the S2' site at KR/SF . Deletion of SARS-CoV-2 furin cleavage site suggests that it may not be required for viral entry but may affect replication kinetics and altered sites have been still seen proteolytically cleaved. Several substitutions within the S2' cleavage domain of SARS-COV-2 have been reported, including P812L/S/T, S813I/G, F817L, I818S/V, but further experimental study of their consequences and the replication properties of the altered viruses are required to understand the role of furin cleavage in SARS-CoV-2 infection and virulence .

To evaluate the neutralization and binding activities of sera collected from COVID-19 mRNA vaccine recipients against current SARS-CoV-2 Variants of Concern/Interest.

COVID-19 pandemics has led to genetic diversification of SARS-CoV-2 and the appearance of variants with potential impact in transmissibility and viral escape from acquired immunity. We report a new and highly divergent lineage containing 21 distinctive mutations (10 non-synonymous, eight synonymous, and three substitutions in non-coding regions). The amino acid changes L249S and E484K located at the CTD and RBD of the Spike protein could be of special interest due to their potential biological role in the virus-host relationship. Further studies are required for monitoring the epidemiologic impact of this new lineage.

The dataset contains a total of 40 snapshots of the four trajectories (10 snapshots each system = two per replica x 5 replicas/system):

1. SARS-CoV-2002 spike protein without ACE2
2. SARS-CoV-2 spike protein without ACE2
3. SARS-CoV-2002 spike protein with ACE2
4. SARS-CoV-2 spike protein with ACE2

Molecular dynamics simulation trajectories (320ns each) have been performed using the Amber ff14SB force field running with the Amber18 package at the the NSF-funded (OAC-1826915, OAC-1828163) ELSA high performance computing cluster at The College of New Jersey. Under the following simulation methodology:

All-atom simulations were carried out with Amber18 (ambermd.org), and system components (protein, ions, water) were modeled with the included FF14SB and TIP3P parameter sets. Energy minimization used CPU pmemd, while later simulation stages used GPU pmemd. CoV2 and CoV1 systems with one RBD up (with/without ACE2) were solvated in 12 angstrom water shells. Cysteine residues identified in the initial models as having a disulfide bond (DB) were bonded using tLeap. All simulations used 0.150 M NaCl. Hydrogen mass repartitioning was applied only to the protein to enable a 4 fs timestep (https://pubs.acs.org/doi/abs/10.1021/ct5010406). The SHAKE algorithm was applied to hydrogens, and a real-space cutoff of 8 angstroms was used. Periodic boundary conditions were applied and PME was used for long-range electrostatics. Minimization was by steepest descent (2000 steps) followed by conjugate gradient (3000 steps). Heating used two stages: (1) NVT heating from 0 K to 100 K (50 ps), and (2) NPT heating from 100 K to 300 K (100 ps). Restraints of 10 kcal mol^-1 angstrom^-2 were applied during minimization and heating to C-alpha atoms. During 6 ns of equilibration at 300 K C-alpha restraints were gradually reduced from 10 kcal mol^-1 angstrom^-2 to 0.1 kcal mol^-1 angstrom^-2. Finally, restraints were released and 320 ns unrestrained production simulations were carried out for CoV2 and CoV1 systems. Production simulations began from the final equilibrated snapshots, and five copies of each system were simulated. As unrestrained systems can freely rotate we monitored simulations for any close contacts and found that in one copy of the CoV1 simulation without ACE2 and one RBD up that a few contacts close to 8 angstrom occur near the end of the 320 ns between the RBD and a different subdomain of the spike complex in a periodic image. However this did not influence analyzed structural properties which is verified by comparing results across simulations. The Monte Carlo barostat was used to maintain pressure (1 atm), and the Langevin thermostat was used to maintain 300 K temperature (collision frequency 1 ps^-1), as implemented in Amber18. In aggregate, nearly 7 microseconds of simulation of systems ranging from 396,147 to 879,100 atoms was carried out for this work.
For further details on the trajectories, please contact Joseph Baker (bakerj@tcnj.edu).

Regarding the contact map analysis scripts (contactMaps_Analysis.tar.gz), they contain the following workflow:

contactmap --> source files from contact_map executable
process_nc.sh --> convert raw data from all-atom simulation to numbered PDB files and get the contact maps
frequency.lua --> read a set of PDB files and output the frequency count for each contact
consensus.fasta --> align sequence of Covid19 and SARS from Chimera
consensus.lua --> read data previously generated and compute the frequency per residue, among other things.
consensus.sh --> input information to consensus.lua
consensus.gp --> gnuplot script to plot figures

This dataset and the code is part of tripartite collaboration between:

• The Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland (supported by the National Science Centre, Poland, under grant No. 2017/26/D/NZ1/0046)
• Department of Chemistry, The College of New Jersey, New Jersey, United States (supported by National Science Foundation under grant numbers OAC-1826915 and OAC-1828163).
• Jozef Stefan Institute, Ljubljana, Slovenia (supported by the Slovenian Research Agency (Funding No. P1-0055)).

To describe a sensitive and reliable SARS-CoV-2 S�bearing lentivirus inGluc neutralization assay that is validated by the authentic SARS-CoV-2 plaque-reduction assay

The dataset of spike Covid proteins was obtained from GISAID. Each protein in the dataset is represented as a sequence of amino acids (AAs).