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Archived news – The spreading /transmission/tracking of COVID-19

Covid-19: New variant ‘raises R number by up to 0.7’ (January 1) – The UK’s latest R number has been estimated at between 1.1 and 1.3. It needs to be below 1.0 for the number of cases to start falling.

More COVID Variants Expected on U.S. Shores (December 30) – The strain may be at least 56% and up to 70% more transmissible than the “wild type” virus, although not more severe or more deadly. The British variant has likely been circulating there since September 2020.

Update on new SARS-CoV-2 variant and how COG-UK tracks emerging mutations (December 14) – COG-UK has been supporting genomic surveillance efforts to identify variants of the SARS-CoV-2 virus in the genome sequencing data from the UK.

COVID-19 spread increases when UV levels decrease (December 16) – Natural variations in ultraviolet radiation influence the spread of COVID-19, but the influence is modest compared to preventive measures such as physical distancing, mask wearing, and quarantine.

The Vaccines Are Coming. It’s Time to Call Your Mom (December 7) – The next, crucial step in beating the pandemic? Having conversations with our vaccine-shy loved ones.

40,000-Person Iceland Study Finds Youth Under 15 Half as Likely to Catch and Spread Coronavirus (December 11) – The findings build on the scientific consensus that age matters when it comes to catching and spreading COVID-19. Some studies, however, put the immunological threshold even earlier, at 10 to 12 years old. As children begin to go through puberty, it appears that their risk of contracting and transmitting the virus increases.

The Swiss Cheese Model of Pandemic Defense (December 5) – A NYT article discussing how a several layers combined — social distancing, plus masks, plus hand-washing, plus testing and tracing, plus ventilation, plus government messaging — significantly reduce the overall risk. Vaccination will add one more protective layer.

This scientist’s decades of mRNA research led to both COVID-19 vaccines (December 5) – Kariko’s obsessive 40 years of research into synthetic messenger RNA was long thought to be a boring dead-end. She said she was chronically overlooked, scorned, fired, demoted, repeatedly refused government and corporate grants, and threatened with deportation — among other indignities. She fled Communist-run Hungary at 30 for the US in 1985 with $1,200 hidden inside her 2-year-old daughter’s teddy bear.

Mayo Clinic research confirms critical role of masks in preventing COVID-19 infection (November 24)

NIH expands research to improve COVID-19 testing among underserved and vulnerable populations (November 20) – The National Institutes of Health has awarded nearly $45 million to expand the research network of the Rapid Acceleration of Diagnostics Underserved Populations (RADx-UP) program, adding 20 institutions and seven states and territories. 

Pre-symptomatic detection of COVID-19 from smartwatch data (November 18) – This study analysed physiological and activity data from 32 individuals infected with COVID-19, identified from a cohort of nearly 5,300 participants, and found that 26 of them (81%) had alterations in their heart rate, number of daily steps or time asleep. Of the 25 cases of COVID-19 with detected physiological alterations for which we had symptom information, 22 were detected before (or at) symptom onset, with four cases detected at least nine days earlier.

More than half of in-hospital deaths from COVID-19 among Black, Hispanic patients, study finds (November 17) – Researchers found that Black and Hispanic people made up 58% of all patients hospitalized for COVID-19, yet no racial or ethnic differences in mortality rates among people hospitalized with the disease was found with 53% of inpatients died from the disease.

Machine Learning to Predict Mortality and Critical Events in a Cohort of Patients With COVID-19 in New York City: Model Development and Validation (November 11) – New models assess COVID patients’ risk of adverse clinical events.

Stanford-led team creates a computer model that can predict how COVID-19 spreads in cities (November 10) – The study merges demographic data, epidemiological estimates and anonymous cellphone location information, and appears to confirm that most COVID-19 transmissions occur at “superspreader” sites, like full-service restaurants, fitness centers and cafes, where people remain in close quarters for extended periods. The researchers say their model’s specificity could serve as a tool for officials to help minimize the spread of COVID-19 as they reopen businesses by revealing the tradeoffs between new infections and lost sales if establishments open, say, at 20 percent or 50 percent of capacity.

The Worst Day of the Pandemic Since May (November 10) – The United States is experiencing an unprecedented surge of hospitalizations across the country. Today, states reported that 61,964 people were hospitalized with COVID-19, more than at any other time in the pandemic. For context, there are now 40 percent more people hospitalized with COVID-19 than there were two weeks ago.

The emergence of SARS-CoV-2 in Europe and North America (October 30) – Washington State & Germany did not lead to major outbreaks, rather serial, independent introductions triggered the major outbreaks in the United States and Europe that still hold us in the grip of control measures.

United States Records Its Worst Week Yet for Virus Cases (October 30) – The outlook for the pandemic continues to worsen, and many areas of the United States are experiencing their worst weeks yet. The country reported a record of more than 500,000 new #coronavirus cases in the past week.

Why COVID outbreaks look set to worsen this winter (October 23)

Herd Immunity and Implications for SARS-CoV-2 Control (October 19) – Assuming no population immunity and that all individuals are equally susceptible and equally infectious, the herd immunity threshold for SARS-CoV-2 would be expected to range between 50% and 67% in the absence of any interventions.

CDC expands definition of ‘close contacts,’ after study suggests Covid-19 can be passed in brief interactions (October 21) – Previously, the CDC described a close contact as someone who spent 15 minutes or more within six feet of someone who was infectious. Now, the agency says it’s someone who spent a cumulative 15 minutes or more within six feet of someone who was infectious over 24 hours, even if the time isn’t consecutive, according to an agency spokesperson.

Covid in the U.S.: Latest Map and Case Count (October 16) – Covid-19 cases going up – still the same wave, but now going towards peak 3!

COVID-19 and Excess All-Cause Mortality in the US and 18 Comparison Countries (October 12) – The US has experienced more deaths from coronavirus disease 2019 (COVID-19) than any other country and has one of the highest cumulative per capita death rates. An unanswered question is to what extent high US mortality was driven by the early surge of cases prior to improvements in prevention and patient management vs a poor longer-term response. This study compared US COVID-19 deaths and excess all-cause mortality in 2020 (vs 2015-2019) to that of 18 countries with diverse COVID-19 responses.

Why COVID-19 Isn’t Just A Bad Version Of The Flu (October 6) – Two of the five reasons: SARS-CoV-2 is more than two times as transmissible as flu and Covid-19 is more fatal than flu.

Flu Season Never Came to the Southern Hemisphere (September 30) – Mask wearing and social distancing for COVID-19 may have cut influenza cases south of the equator.

COVID-19 CG: Tracking SARS-CoV-2 mutations by locations and dates of interest (September 28)

Clustering and superspreading potential of SARS-CoV-2 infections in Hong Kong (September 17) – Discusses several superspreader events traced back to severals bars and weddings.

COVID-19: All the wrong moves in all the wrong places (September 15) – As the world continues to be ravaged by Covid-19, three major systemic failures appear to have coalesced to block progress in disease control, containment, and treatment. These failures reflect a “perfect storm” of governmental ineptitude, scientific ignorance/misprioritization, and the abdication of medical training to market-driven forces. This editorial highlight the shortcomings in our collective response to the COVID-19 pandemic and underscore the need for more basic research into this new disease.

COVID-19 herd immunity: where are we? (September 9) – A great article on what it takes to achieve herd immunity, and this in relation to COVID-19.

The emergence of SARS-CoV-2 in Europe and North America (September 10) – It seems SARS-CoV-2 was circulating under the radar in Washington State for weeks, though it is noct clear for how long and where the introduction came from. It is still necessary to resolve where the virus first initiated substantial community outbreaks, and whether the earliest coast-to-coast spread of the virus within the US was from west-to-east or east-to-west.

Two metres or one: what is the evidence for physical distancing in covid-19? (August 25) – Rigid safe distancing rules are an oversimplification based on outdated science and experiences of past viruses.

The pandemic appears to have spared Africa so far. Scientists are struggling to explain why (August 11) – Although Africa reported its millionth official COVID-19 case last week, it seems to have weathered the pandemic relatively well so far, with fewer than one confirmed case for every thousand people and just 23,000 deaths so far. Yet several antibody surveys suggest far more Africans have been infected with the coronavirus—a discrepancy that is puzzling scientists around the continent. “We do not have an answer,” says immunologist Sophie Uyoga at the Kenya Medical Research Institute–Wellcome Trust Research Programme.

Gene study shows how coronavirus swept through cruise ship Diamond Princess (August 5) – A genetic retracing of events shows the outbreak on the Diamond Princess likely stemmed from just one infected person, according to Japanese researchers.

Uber launches service to help with COVID-19 contact tracing: report (July 20)

Genetic detectives begin work to trace spread of COVID-19 in Canada (July 13) – COVID-19 in New York came from Europe, not China or Iran, genetic sequencing discovered.

Bringing COVID-19 exposure notification to the public health community (July 17) – Working in conjunction with Apple, Google and Microsoft, APHL is taking a major step to support public health agencies that want to provide focused, privacy-preserving and user-controlled exposure notifications.

Trump Administration Strips C.D.C. of Control of Coronavirus Data (July 14) – Hospitals have been ordered to bypass the Centers for Disease Control and Prevention and send all patient information to a central database in Washington, raising questions about transparency.

Mounting Evidence Suggests Coronavirus Is Airborne—but Health Advice Has Not Caught Up (July 8) – After months of denying the importance of aerosol transmission of SARS-CoV-2, the World Health Organization is reconsidering its stance​.

Risk factors associated with COVID-19 death in 17 million patients (July 8) – COVID-19-related death was associated with: being male; older age and deprivation; diabetes; severe asthma; and various other medical conditions. Compared with people with white ethnicity, Black and South Asian people were at higher risk even after adjustment for other factors.

Google Searches Reveal Covid-19 Hot Spots Before Governments Do (July 6) – A model built by UCL computer scientist Bill Lampos and team shows that Google searches predict Covid-19 case volumes up to 14 days ahead. Among the most predictive are searches for anosmia.

The Fullest Look Yet at the Racial Inequity of Coronavirus (July 5) – Black and Latino people have been disproportionately affected by the coronavirus in a widespread manner that spans the country, throughout hundreds of counties in urban, suburban and rural areas, and across all age groups.

7.8% of Orleans, Jefferson were infected with coronavirus; nearly half were asymptomatic (July 2) – Researchers from Ochsner Health System selected a sample of 2,640 people from a group of 25,000 volunteers and gave them an antibody test as well as a test used to diagnose active infections. The tests were conducted in mid-May, just ahead of the Phase 1 reopening of the city. 

How the virus won (June 25) – Great infographic depicting the coronavirus outbreak over the last few months in the U.S. and the delayed measures taken by the current administration, while some of the data was clearly highlighting the outbreak was taking shape.

Coronavirus Antibody Tests Have a Mathematical Pitfall (July) – The accuracy of screening tests is highly dependent on the infection rate.

Vaccination as a social contractGoogle and Apple’s rules for virus tracking apps sow division among states (June 10) – The tech companies tried to create a uniform standard, but some states are rejecting their rules and several are spurning the idea altogether.

How to avoid the virus as the world reopens (June 9) – Three key factors determine risk of exposure: proximity to people; duration of exposure; and how confined the environment is. The greatest peril lies where the three overlap.

WHO Leverages Amazon Data Analytics Tools for COVID-19 Response (June 8) – The World Health Organization is tracking and containing COVID-19 with data analytics technologies from Amazon Web Services.

The effect of large-scale anti-contagion policies on the COVID-19 pandemic (June 8) – Study estimates that across these six countries, interventions prevented or delayed on the order of 62 million confrmed cases, corresponding to averting roughly 530 million total infections. These fndings may help inform whether or when these policies should be deployed, intensifed, or lifted, and they can support decision-making in the other 180+ countries where COVID-19 has been reported.

The long journey to herd immunity (June 5) – The sought-after state of herd immunity — in which widespread outbreaks are prevented because enough people in a community are immune to a disease — is complicated by open questions about the effectiveness of a future vaccine and how COVID-19 spreads and why it matters.

Thousands of people will help scientists to track the long-term health effects of the coronavirus crisis (June 2) – Cohort studies that follow populations over years have quickly pivoted to trace the pandemic’s physical, mental and social consequences. Since April 24, 5,000 individuals have been tested.

Intercepting pandemics through genomics (June 2) – There is an urgent need to establish a global,genomic-based biosurveillance platform a development which would be of immense value to biosecurity,biodefense, and the economy. If implemented, this “pandemic interception system” would hugely advance our understanding of the natural world.Intercepting pandemics through genomics. Three major research programs are poised to support this effort: BIOSCAN, the Earth BioGenome Project (EBP), and the Global Virome Project (GVP).

After taming COVID-19, Iceland re-opens with confidence (May 14) – Iceland is weathering the pandemic well – with 1,802 cases of the virus and 10 deaths – and appears better able than most to adjust to the new world that COVID-19 is creating. The number of new COVID-19 cases each day has fallen to around one case every five days. Health officials rushed in to contain the spread, with the government building a team of contact tracers to interview those with a positive diagnosis and track down people they’d been in contact with. As a result, the country has not faced the large-scale and very strict lockdowns seen across Europe. Iceland’s flagship genomics company, deCODE genetics, has carried out over 80 per cent of all tests. “I’m convinced we’ll be able to live with this until there’s a vaccine. I’m more concerned about the economic damage,” said Kari Stefánsson, founder and CEO of deCODE, which has now administered 43,000 tests.

App Shows Promise in Tracking New Coronavirus Cases, Study Finds (May 11) – A study Nature Medicine study found that an app that allows people to check off symptoms they are experiencing was remarkably effective in predicting coronavirus infections among the 2.5 million people who were using it between March 24 and April 21.The study, which tracked people in the US, the UK, and Sweden, found that the loss of taste and smell was the No. 1 predictor of whether a person was going to get sick with Covid-19, the illness caused by the coronavirus, followed by extreme fatigue and acute muscle pain.

Sustained suppression (May 13) – Further COVID-19 outbreaks are unavoidable. To detect and suppress them, governments ought to implement a range of public health measures aided by technology.

Estimating the burden of SARS-CoV-2 in France (May 13) – The results strongly suggest that, without a vaccine, herd immunity on its own will be insufficient to avoid a second wave at the end of the lockdown and efficient control measures need to be maintained.

Risk factors for COVID-19 death revealed in world’s largest analysis of patient records to date (May 7) – Largest study to date, analysing NHS health data from 17.4 million UK adults between 01 February 2020 and 25 April 2020, has given the strongest evidence to date on risk factors associated with COVID-19 death. Among the 17.4 million adults in the sample, there were 5,707 deaths in hospitals attributed to COVID-19. People of Asian and Black ethnic backgrounds are at a higher risk of death and, contrary to prior speculation, this is only partially attributable to pre-existing clinical risk factors or deprivation. Key factors related to COVID-19 death included being male, older age, uncontrolled diabetes and severe asthma.A deprived background was also found to be a major risk factor: this was also only partially attributable to other clinical risk factors. Access the full paper.

Study to determine incidence of novel coronavirus infection in U.S. children begins (May 4) – A study to help determine the rate of novel coronavirus infection in children and their family members in the United States has begun enrolling participants. The study, called Human Epidemiology and Response to SARS-CoV-2 (HEROS), also will help determine what percentage of children infected with SARS-CoV-2.

The subways seeded the massive coronavirus epidemic in New York City (April 2020) – Maps of subway station turnstile entries, superimposed upon zip code-level maps of reported #coronavirus incidence, are strongly consistent with subway-facilitated disease propagation. Local train lines appear to have a higher propensity to transmit infection than express lines.

Spread of SARS-CoV-2 in the Icelandic Population (April 14) – The frequency of the SARS-CoV-2 infection in the overall Icelandic population was stable from March 13 to April 1, a finding that appears to indicate that the containment measures had been working. However, the virus has spread to the extent that unless continued testing and isolation, tracking contacts, and quarantining, they are likely to fail in their efforts to contain the virus.

Not Like the Flu, Not Like Car Crashes, Not Like… (April 13) – COVID-19 has quickly risen to number one as cause of death, surpassing seasonal flu, past pandemics, or car crashes.

NIH seeks volunteers for at-home COVID-19 antibody test as study looks to find undetected cases in U.S. (April 13) – Federal health officials are recruiting up to 10,000 volunteers nationwide as they investigate just how pervasive the novel coronavirus has been in the United States.

How Apple and Google Are Enabling Covid-19 Contact-Tracing (April 10) – The two companies announced a rare joint project to create the groundwork for Bluetooth-based contact-tracing apps that can work across both iOS and Android phones. In mid-May, they plan to release an application programming interface that apps from public health organizations can tap into. The API will let those apps use a phone’s Bluetooth radios—which have a range of about 30 feet—to keep track of whether a smartphone’s owner has come into contact with someone who later turns out to have been infected with Covid-19. Once alerted, that user can then self-isolate or get tested themselves

Mount Sinai seeks citywide engagement with app to track COVID-19 spread in NYC (April 2) – The app – accessed by texting “COVID” to 64722 – enables New York City residents to easily enroll to help the health system monitor coronavirus symptoms across the five boroughs, informing care decisions and pointing the way toward possible cures.

National coronavirus response: A road map to reopening (March 29) – This report, by former FDA commissioner Scott Gottlieb, provides a road map for navigating through the current COVID-19 pandemic in the United States. It outlines specific directions for adapting our public-health approach away from sweeping mitigation strategies as we limit the epidemic spread of COVID-19, such that we can transition to new tools and approaches to prevent further spread of the disease.

Iceland’s testing suggests 50% of COVID-19 cases are asymptomatic (March 26) – Iceland’s population puts it in the unique position of having very high testing capabilities with help from the Icelandic medical research company deCode Genetics, who are offering to perform large scale testing. With 50% testing positive, this would suggest that, on one hand, the virus is not as dangerous as we thought, but on the other hand, it would also suggest that it has spread far more than we are currently aware of.

UK launches whole genome sequence alliance to map spread of coronavirus (March 23) – The COVID-19 Genomics UK Consortium – comprised of the NHS , Public Health Agencies, Wellcome Sanger Institute , and numerous academic institutions – will deliver large scale, rapid sequencing of the cause of the disease and share intelligence with hospitals, regional NHS centres and the government.

Covert coronavirus infections could be seeding new outbreaks (March 20) – Scientists are rushing to estimate the proportion of people with mild or no symptoms who could be spreading the pathogen.

Substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (SARS-CoV2) (March 16) – A modeling of a synthetic outbreak: A high proportion of undocumented infections, many of whom were likely not severely symptomatic, appears to have facilitated the rapid spread of the virus throughout China. The best-fitting model used has a reporting delay of 9 days from initial infectiousness to confirmation; in contrast line-list data for the same 10–23 January period indicates an average 6.6 day delay from initial manifestation of symptoms to confirmation The findings also indicate that a radical increase in the identification and isolation of currently undocumented infections would be needed to fully control SARS-CoV2. These findings underscore the seriousness and the pandemic potential of SARS-CoV2 with populations without symptoms potentially spreading COVID-19.

The effect of travel restrictions on the spread of the 2019 novel coronavirus (COVID-19) outbreak (March 6) – Since travel limitations could be instrumental to national and international agencies for public health response planning, this study shows that by 23 January 2020, the epidemic had already spread to other cities within Mainland China. While the Wuhan travel ban was initially effective at reducing international case importations, the number of cases observed outside Mainland China will resume its growth after 2-3 weeks from cases that originated elsewhere. Furthermore, the modeling study shows that additional travel limitations up to 90% of the traffic have a modest effect unless paired with public health interventions and behavioral changes that achieve a considerable reduction in the disease transmissibility. The model also indicates that even in the presence of the strong travel restrictions in place to and from Mainland China since 23 January 2020, a large number of individuals exposed to the SARS-CoV-2 have been traveling internationally without being detected.

Estimating the clinical severity of COVID-19 from the transmission dynamics in Wuhan, China (February 13) – Discusses death rate estimates for the coronavirus and fatality rate in people who have symptoms of the disease which is about 1.4% (compared to 0.1% for the seasonal flu).