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.

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.

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.

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

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.

CDC is collaborating with Vitalant Research Institute, American Red Cross, and Westat Inc. to conduct a nationwide COVID-19 seroprevalence survey of blood donors. De-identified blood samples are tested for antibodies to SARS-CoV-2 to better understand the percentage of people in the United States who have antibodies against SARS-CoV-2 (the virus that causes COVID-19) and to track how this percentage changes over time. Both SARS-CoV-2 infection and COVID-19 vaccines currently used in the United States result in production of anti-spike (anti-S) antibodies but only infection results in production of anti-nucleocapsid (anti-N) antibodies. Infection-induced seroprevalence estimates the proportion of the population with antibody evidence of previous SARS-CoV-2 infection and refers to the percent of the population with anti-nucleocapsid antibodies. Combined infection-Induced and Vaccination-Induced seroprevalence estimates the proportion of the population with antibody evidence of previous SARS-CoV-2 infection, COVID-19 vaccination, or both, and refers to the percent of the population that has anti-spike antibodies, anti-nucleocapsid antibodies, or both. This link connects to a webpage that displays the data from the Nationwide Blood Donor Seroprevalence Survey. It offers an interactive visualization available at https://covid.cdc.gov/covid-data-tracker/#nationwide-blood-donor-seroprevalence-2022

View daily updates and historical trends for US Coronavirus Cases Per Day. from United States. Source: Johns Hopkins Center for Systems Science and Engine…

On September 30, 2020, there were 17 new reported confirmed cases of COVID-19 in Australia. Australia's daily new confirmed coronavirus cases peaked on July 30 with 746 new cases on that day. This was considered to be the second wave of coronavirus infections in Australia, with the first wave peaking at the end of March at 460 cases before dropping to less than 20 cases per day throughout May and most of June.

 A second wave

Australia’s second wave of coronavirus found its epicenter in Melbourne, after over a month of recording low numbers of national daily cases. Despite being primarily focused within a single state, clusters of coronavirus cases in Victoria soon pushed the daily number of recorded cases over that of the first wave, with well over double the number of deaths. As a result, the Victorian Government once again increased lockdown measures to limit movement and social interaction. At the same time the other states and territories closed or restricted movement across borders, with some of the strictest border closures taking place in Western Australian.

 Is Australia entering into a recession?

After narrowly avoiding a recession during the global financial crisis, by September 2020 Australia had recorded two consecutive quarters of economic decline, hailing the country’s first recession since 1991. This did not necessarily come as a surprise for many Australians who had already witnessed a rising unemployment rate throughout the second quarter of 2020 alongside ongoing restrictions on retail and hospitality trading. However, thanks to welfare initiatives like JobKeeper and a government stimulus payment supplementing many household incomes, the economic situation could have been much worse at this point.

Excel spread sheet of the 9550 blood donors that were evaluated in this study broken into columns that shows the date of visit to the blood collection center, the State, the geographic region as east (E), west (W) or Kentucky (KY), the blood type, the age, gender, race and raw S protein ELISA OD value. (XLSX)

Rate of S protein ELISA positivity clustered by regions within the GCMA.

Cannabis sales have surged in ***** U.S. states in the wake of the coronavirus outbreak. On March 16, 2020, sales of recreational marijuana in California increased around *** percent compared to the same day in 2019, while sales in Washington state and Colorado also increased by around 100 percent and ** percent on the same day.

For further information about the coronavirus (COVID-19) pandemic, please visit our dedicated Facts and Figures page.

Assessment of raw S protein OD values in donors with 2 or more donations analyzed over 2 time periods from August 13th to December 8th of 2020.

Protein-Protein, Genetic, and Chemical Interactions for Olia AS (2021):SARS-CoV-2 S2P spike ages through distinct states with altered immunogenicity. curated by BioGRID (https://thebiogrid.org); ABSTRACT: The SARS-CoV-2 spike is the primary target of virus-neutralizing antibodies and critical to the development of effective vaccines against COVID-19. Here, we demonstrate that the prefusion-stabilized two-proline "S2P" spike-widely employed for laboratory work and clinical studies-unfolds when stored at 4 °C, physiological pH, as observed by electron microscopy (EM) and differential scanning calorimetry, but that its trimeric, native-like conformation can be reacquired by low pH treatment. When stored for approximately 1 week, this unfolding does not significantly alter antigenic characteristics; however, longer storage diminishes antibody binding, and month-old spike elicits virtually no neutralization in mice despite inducing high ELISA-binding titers. Cryo-EM structures reveal the folded fraction of spike to decrease with aging; however, its structure remains largely similar, although with varying mobility of the receptor-binding domain. Thus, the SARS-CoV-2 spike is susceptible to unfolding, which affects immunogenicity, highlighting the need to monitor its integrity.

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) virus has infected over 100 million people and caused over 2.5 million deaths worldwide. Yet, the molecular mechanisms underlying the clinical manifestations of COVID-19, as well as what distinguishes them from common seasonal influenza virus and other lung injury states such as Acute Respiratory Distress Syndrome (ARDS) remains poorly understood. To address these challenges, we combined transcriptional profiling of 646 clinical nasopharyngeal swabs and 39 patient autopsy tissues, matched with spatial protein and expression profiling (GeoMx) across 357 tissue sections. These results define both body-wide and tissue-specific (heart, liver, lung, kidney, and lymph nodes) damage wrought by the SARS-CoV-2 infection, which are a function both of viral load (high vs. low) and transcriptional signatures (splicing isoforms, T-cell receptor expression, cell state regression). These findings reveal a massive disruption of cellular and transcriptional pathways from COVID-19 that can inform subsequent studies on the pathophysiology SARS-CoV-2 as well as other viruses. Overall design: The molecular mechanisms and clinical manifestations of COVID-19 are still poorly understood, especially in terms of the differences between COVID-19, influenza virus, Acute Respiratory Distress Syndrome (ARDS), and other viral infections. To address these challenges, we combined transcriptional profiling of 646 clinical nasopharyngeal swabs and 39 patient autopsy tissues, matched with spatial protein and expression profiling (GeoMx) across 357 tissue sections (regions of interest, ROIs) with 373 areas of interest (i.e., samples). Note that 1 or more AOIs can be found in a given ROI. The dataset comprises the GeoMx data samples only. Specifically, there are five groups (Covid-19_High, Covid-19_Low, Non-viral [ARDS], Flu, and Normal). The breakdown of Patients, ROIs, and AOIs are as follows: Covid-19_High, 4 patients and 86 AOIs within 86 ROIs; Covid-19_Low, 4 patients and 94 AOIs within 94 ROIs; Non-viral, 3 patients and 67 AOIs within 63 ROIs; Flu, 2 patients and 46 AOIs within 42 ROIs; Normal, 3 patients and 64 AOIs within 60 ROIs. For each AOI (sample), digital spatial profiling was performed using NanoStiring's Cancer Transcriptome Atlas (CTA) with Covid-19 spike-in genes.

Comparison of age of donors losing S protein positivity versus donors maintaining positivity.

This file contains a list of sequences from GISAID’s EpiFlu Database on which this research is based and their corresponding authors and laboratories. (CSV)

Map between 20-NT ISM and 11-NT compressed ISM.

The ongoing COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in more than 28,000,000 infections and 900,000 deaths worldwide to date. Antibody development efforts mainly revolve around the extensively glycosylated SARS-CoV-2 spike (S) protein, which mediates host cell entry by binding to the angiotensin-converting enzyme 2 (ACE2). Similar to many other viral fusion proteins, the SARS-CoV-2 spike utilizes a glycan shield to thwart the host immune response. Here, we built a full-length model of the glycosylated SARS-CoV-2 S protein, both in the open and closed states, augmenting the available structural and biological data. Multiple microsecond-long, all-atom molecular dynamics simulations were used to provide an atomistic perspective on the roles of glycans and on the protein structure and dynamics. We reveal an essential structural role of N-glycans at sites N165 and N234 in modulating the conformational dynamics of the spike’s receptor binding domain (RBD), which is responsible for ACE2 recognition. This finding is corroborated by biolayer interferometry experiments, which show that deletion of these glycans through N165A and N234A mutations significantly reduces binding to ACE2 as a result of the RBD conformational shift toward the “down” state. Additionally, end-to-end accessibility analyses outline a complete overview of the vulnerabilities of the glycan shield of the SARS-CoV-2 S protein, which may be exploited in the therapeutic efforts targeting this molecular machine. Overall, this work presents hitherto unseen functional and structural insights into the SARS-CoV-2 S protein and its glycan coat, providing a strategy to control the conformational plasticity of the RBD that could be harnessed for vaccine development.

Protein-Protein, Genetic, and Chemical Interactions for Hakansson-McReynolds S (2006):Solution structure of the severe acute respiratory syndrome-coronavirus heptad repeat 2 domain in the prefusion state. curated by BioGRID (https://thebiogrid.org); ABSTRACT: The envelope glycoprotein, termed the spike protein, of severe acute respiratory syndrome coronavirus (SARS-CoV) is known to mediate viral entry. Similar to other class 1 viral fusion proteins, the heptad repeat regions of SARS-CoV spike are thought to undergo conformational changes from a prefusion form to a subsequent post-fusion form that enables fusion of the viral and host membranes. Recently, the structure of a post-fusion form of SARS-CoV spike, which consists of isolated domains of heptad repeats 1 and 2 (HR1 and HR2), has been determined by x-ray crystallography. To date there is no structural information for the prefusion conformations of SARS-CoV HR1 and HR2. In this work we present the NMR structure of the HR2 domain (residues 1141-1193) from SARS-CoV (termed S2-HR2) in the presence of the co-solvent trifluoroethanol. We find that in the absence of HR1, S2-HR2 forms a coiled coil symmetric trimer with a complex molecular mass of 18 kDa. The S2-HR2 structure, which is the first example of the prefusion form of coronavirus envelope, supports the current model of viral membrane fusion and gives insight into the design of structure-based antagonists of SARS.

The trimeric SARS coronavirus (SARS-CoV) surface spike (S) glycoprotein consisting of three S1-S2 heterodimers binds the cellular receptor angiotensin-converting enzyme 2 (ACE2) and mediates fusion of the viral and cellular membranes through a pre- to postfusion conformation transition. Here, we report the structure of the SARS-CoV S glycoprotein in complex with its host cell receptor ACE2 revealed by cryo-electron microscopy (cryo-EM). The complex structure shows that only one receptor-binding domain of the trimeric S glycoprotein binds ACE2 and adopts a protruding “up” conformation. In addition, we studied the structures of the SARS-CoV S glycoprotein and its complexes with ACE2 in different in vitro conditions, which may mimic different conformational states of the S glycoprotein during virus entry. Disassociation of the S1-ACE2 complex from some of the prefusion spikes was observed and characterized. We also characterized the rosette-like structures of the clustered SARS-CoV S2 trimers in the postfusion state observed on electron micrographs. Structural comparisons suggested that the SARS-CoV S glycoprotein retains a prefusion architecture after trypsin cleavage into the S1 and S2 subunits and acidic pH treatment. However, binding to the receptor opens up the receptor-binding domain of S1, which could promote the release of the S1-ACE2 complex and S1 monomers from the prefusion spike and trigger the pre- to postfusion conformational transition.