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.

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

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

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

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

This dataset 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.

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 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 .

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.

SARS-Cov-2 proteins: a comparison with ACE2 protein

This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 Spike S2 fragment in its postfusion form (PDB id: 6M1V). Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020.

The files 6M1V_SIRAHcg_rawdata_0-5us.tar, and 6M1V_SIRAHcg_rawdata_5-10us.tar, contain all the raw information required to visualize (on VMD 1.9.3), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at www.sirahff.com.

Additionally, the file 6M1V_SIRAHcg_10us_prot.tar contains only the protein coordinates, while 6LU7_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at the trajectory:

1- Untar the file 6M1V_SIRAHcg_10us_prot_skip10ns.tar

2- Open the trajectory on VMD 1.9.3 using the command line:

vmd 6M1V_SIRAHcg_prot.prmtop 6M1V_SIRAHcg_prot.ncrst 6M1V_SIRAHcg_10us_prot_skip10ns.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

This dataset is part of the SIRAH-CoV2 initiative.

For further details, please contact Florencia Klein (fklein@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).

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.

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 and S2 [interpro:IPR002552] . 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 .

This contribution explores in a new statistical perspective the antibody responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 141 coronavirus disease 2019 (COVID-19) patients exhibiting a broad range of clinical manifestations. This cohort accurately reflects the characteristics of the first wave of the SARS-CoV-2 pandemic in Italy. We determined the IgM, IgA, and IgG levels towards SARS-CoV-2 S1, S2, and NP antigens, evaluating their neutralizing activity and relationship with clinical signatures. Moreover, we longitudinally followed 72 patients up to 9 months postsymptoms onset to study the persistence of the levels of antibodies. Our results showed that the majority of COVID-19 patients developed an early virus-specific antibody response. The magnitude and the neutralizing properties of the response were heterogeneous regardless of the severity of the disease. Antibody levels dropped over time, even though spike reactive IgG and IgA were still detectable up to 9 months. Early baseline antibody levels were key drivers of the subsequent antibody production and the long-lasting protection against SARS-CoV-2. Importantly, we identified anti-S1 IgA as a good surrogate marker to predict the clinical course of COVID-19. Characterizing the antibody response after SARS-CoV-2 infection is relevant for the early clinical management of patients as soon as they are diagnosed and for implementing the current vaccination strategies.

Additional file 1:.

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.

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.

Prevalence-related outcome measures by developmental period and age bracket in US States experiencing spikes in COVID-19 cases.

This dataset contains an updated trajectory of a four microseconds-long coarse-grained molecular dynamics simulation of the hexameric complex between SARS-CoV2 Spike´s RBD, ACE2, and B0AT1 (PDB id: 6M17). It substitutes the previous one on the same system, which was performed in the absence of disulfide bridges.

Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020. Zinc ions were parameterized as reported in Klein et al. 2020.

The files 6M17_SIRAHcg_rawdata_0-1.tar, 6M17_SIRAHcg_rawdata_1-2.tar, 6M17_SIRAHcg_rawdata_2-3.tar, and 6M17_SIRAHcg_rawdata_3-4.tar contain all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at www.sirahff.com.

Additionally, the file 6M17_SIRAHcg_4us_prot.tar contains only the protein coordinates, while 6M17_SIRAHcg_4us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at the trajectory:

1- Untar the file 6M17_SIRAHcg_4us_prot_skip10ns.tar

2- Open the trajectory on VMD 1.9.3 using the command line:

vmd 6M17_SIRAHcg_prot.prmtop 6M17_SIRAHcg_prot.ncrst 6M17_SIRAHcg_4usprot_skip.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

This dataset is part of the SIRAH-CoV2 initiative.

For further details, please contact Florencia Klein (fklein@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).

The dataset contains coronavirus spike sequences for different hosts, including humans, bats, camels, swines, birds, and weasels.

The coronavirus disease 2019 (COVID-19) pandemic is caused by a novel coronavirus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The spike protein (S) of SARS-CoV-2 is a major target for diagnosis and vaccine development because of its essential role in viral infection and host immunity. Currently, time-dependent responses of humoral immune system against various S protein epitopes are poorly understood. In this study, enzyme-linked immunosorbent assay (ELISA), peptide microarray, and antibody binding epitope mapping (AbMap) techniques were used to systematically analyze the dynamic changes of humoral immune responses against the S protein in a small cohort of moderate COVID-19 patients who were hospitalized for approximately two months after symptom onset. Recombinant truncated S proteins, target S peptides, and random peptides were used as antigens in the analyses. The assays demonstrated the dynamic IgM- and IgG recognition and reactivity against various S protein epitopes with patient-dependent patterns. Comprehensive analysis of epitope distribution along the spike gene sequence and spatial structure of the homotrimer S protein demonstrated that most IgM- and IgG-reactive peptides were clustered into similar genomic regions and were located at accessible domains. Seven S peptides were generally recognized by IgG antibodies derived from serum samples of all COVID-19 patients. The dynamic immune recognition signals from these seven S peptides were comparable to those of the entire S protein or truncated S1 protein. This suggested that the humoral immune system recognized few conserved S protein epitopes in most COVID-19 patients during the entire duration of humoral immune response after symptom onset. Furthermore, in this cohort, individual patients demonstrated stable immune recognition to certain S protein epitopes throughout their hospitalization period. Therefore, the dynamic characteristics of humoral immune responses to S protein have provided valuable information for accurate diagnosis and immunotherapy of COVID-19 patients.

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