Category Archives: Covid-19

A COVID-19 antibody testing center is seen at Steve's 9th Street Market in Brooklyn on April 25. Here's a quick guide to sorting out the pluses and minuses to each type of test. Michael Nagle/Xinhua News Agency/Getty Images hide caption

A COVID-19 antibody testing center is seen at Steve's 9th Street Market in Brooklyn on April 25. Here's a quick guide to sorting out the pluses and minuses to each type of test.

Testing for the coronavirus has been very much in the news. The first and most urgent focus is on increasing access to tests to diagnose people with current infections. But now other tests are appearing as well. Antibody tests, which can identify people with signs of past infection, are starting to be available. And a third type of test is on the way.

Here's a quick guide to sorting out the pluses and minuses to each type of test.

What it does: Doctors use this test to diagnose people who are currently sick with COVID-19. This is the one we've been hearing so much about.

How it works: This test uses a sample of mucus typically taken from a person's nose or throat. The test may also work on saliva that's under investigation. It looks for the genetic material of the coronavirus. The test uses a technology called PCR (polymerase chain reaction), which greatly amplifies the viral genetic material if it is present. That material is detectable when a person is actively infected.

How accurate is it: Generally speaking, these are the most reliable tests. However, a few days may pass before the virus starts replicating in the throat and nose, so the test won't identify someone who has recently been infected. And swabs can sometimes fail to pick up signs of active infection.

How quick is it: These samples are generally sent to centralized labs for analysis, so it can take several days to get results back. Wait times were longer earlier in the pandemic because of a testing backlog. There are also two rapid PCR tests, which can be run on specialized equipment already widely distributed throughout the U.S. The speediest one, by Abbott Laboratories, can provide a result in 13 minutes, but one study suggests this test can miss more than 10% of cases.

What it does: Antibody tests identify people who have previously been infected with the coronavirus. They do not show whether a person is currently infected. This is primarily a good way to track the spread of the coronavirus through a population.

How it works: This is a blood test. It looks for antibodies to the coronavirus. Your body produces antibodies in response to an infectious agent such as a virus. These antibodies generally arise after four days to more than a week after infection, so they are not used to diagnose current disease.

How accurate is it: There are more than 120 antibody tests on the market. The Food and Drug Administration has allowed them to be marketed without FDA authorization, and quality is a great concern. A few tests have voluntarily submitted to extra FDA approval. Other tests are being validated by individual medical labs or university researchers.

In general, these tests aren't reliable enough for individuals to act based on the results. And researchers say, even if you were certain you had antibodies to the coronavirus, it's still unknown if that protects you from getting sick again. Still, these tests can provide good information about rates of infection in a community, where errors in an individual result have less impact.

How quick is it: These tests generally produce results in a few minutes, based on a drop of blood taken from the finger. Some research labs use a more sophisticated antibody test, called an Elisa (Enzyme-linked immunoassay) that are more accurate but are not as widely available.

What it does: This test identifies people who are currently infected with the coronavirus. It may be used as a quick test to detect active infections. Initially it will not be used to diagnose disease, but it may be used to screen people to identify those who need a more definitive test.

How it works: Antigen tests can identify virus in nose and throat secretions. It does this by looking for proteins on the surface of the virus (as opposed to the diagnostic test, which looks for genetic material that is carried inside the virus). This is the same technology used in your doctor's office for rapid strep testing.

How accurate is it: These tests are not yet on the market, so there is currently no information about their accuracy. Researchers do not expect it to be as accurate as the PCR diagnostic test, but it is possible they could be used to screen patients for infection. Dr. Jordan Laser, a lab director at Northwell Health, notes antigen testing is used for rapid strep tests, which are reliable, and rapid flu tests, which are not.

How quick is it: These tests should provide results in just a few minutes. As a result, they could be used to screen people in hospitals, certain workplaces, or in other instances where it's important to find out quickly whether someone is currently at risk of spreading the disease. But unless these tests are proven to be highly accurate, physicians would still need to follow up a positive result with a PCR test to make a medical diagnosis.

You can contact NPR science correspondent Richard Harris at rharris@npr.org.

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Antibody, Antigen And PCR Tests For COVID-19: Know The Differences : Shots - Health News - NPR

Congress has opened a probe into Carnival Corporation, the operator of the Princess Cruises line of cruise ships, over its handling of COVID-19 outbreaks, according to a report from Bloomberg. Officials are now requesting Carnival turn over documents and communications about its coronavirus response and its plans for future improvement.

The investigation, led by the US House Committee on Transportation and Infrastructure, is specifically looking into how much Carnival executives were aware of the severity of the coronavirus outbreaks on its cruise ships and the lack of action it took during active cruises after being informed of the risks. More than 1,500 confirmed COVID-19 cases can be traced back to the company's cruise ships, and dozens of Carnival customers and crew members have since died from the virus.

The probe cites a damning Bloomberg feature story from writers Austin Carr and Chris Palmeri from last month that delves intricately into how Florida-based Carnival handled news of the COVID-19 outbreaks aboard nine of its ships. The story itself, which everyone should go read, is astonishing, featuring illuminating interviews with crew members and passengers and a lengthy sit-down with Carnival CEO Arnold Donald. It paints the picture of a company that, even in early March as the threat of the novel coronavirus become abundantly clear worldwide, did not take action fast enough to order its passengers into self-isolation and dock its cruise ships. Instead, many ships decided to let customers remain in extremely close contact with one another in swimming pools and in dining areas featuring buffets.

We would hope that the reality of the COVID-19 pandemic will place a renewed emphasis on public health and passenger safety, but frankly that has not been seen up to this point, wrote House member Peter DeFazio (D-OR) in the letter sent to Carnival announcing the investigation. It seems as though Carnival Corporation and its portfolio of nine cruise lines, which represents 109 cruise ships, is still trying to sell this cruise line fantasy and ignoring the public health threat.

Bloomberg reports that many of the customers who received refunds from Carnival were given the option to receive the credit for a future cruise, and Carnival in some cases sweetened the deal by giving out free vouchers as well. While the company suspended its cruises starting in March, some passengers and crew remain stuck on ships around the world. Our goal is the same as the committees goal, Carnival said in a statement to Bloomberg, to protect the health, safety and well-being of our guests and crew, along with compliance and environmental protection.

In addition to the House probe, Australian police last month launched a criminal investigation into how Carnival handled the docking of one of its Princess ships, the Ruby Princess, in Sydney on March 19th. The investigation is looking into whether Carnival officials misled Australian authorities about the COVID-19 outbreak aboard the ship, as Carnival customers at the time made up nearly one-third of all Australian deaths from the virus.

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Congress is investigating cruise ship company Carnival over COVID-19 outbreaks - The Verge

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This undated electron microscope image made available by the U.S. National Institutes of Health in February 2020 shows the novel coronavirus SARS-CoV-2, yellow, emerging from the surface of cells, blue/pink, cultured in the lab. Also known as 2019-nCoV, the virus causes COVID-19. The sample was isolated from a patient in the U.S.

SOUTH SIOUX CITY -- An additional COVID-19 death recorded in Dakota County on Saturday is believed to have been a worker at the Tyson Fresh Meats plant at Dakota City.

The Dakota County Health Department provided no information on the individual, but a source in South Sioux City told the Journal Saturday that the deceased was a woman in her 50s or 60s who worked at the Tyson plant. She suffered breathing problems due to the virus and was pronounced dead shortly after her arrival at a Sioux City hospital Friday night.

This death marks the second in Dakota County attributed to the virus.

Ahmad Mohammad, the imam of the Islamic Center of Siouxland, said in a statement Saturday that the woman's funeral was underway, and that he expects it won't be the last death of a worker at the plant.

"Sadly and unfortunately, I do expect many more deaths of Muslim Somali employees of Tyson Foods Plant in Dakota City in the coming days, because many of these Somali employees of this plant tested positive to COVID-19 and they are sick and are staying home," he wrote.

Mohammad wrote that the woman was near death by the time she was taken to the hospital, and criticized local hospitals for what he described as their unwillingness to accept COVID-19 patients until their illness has reached a critical level.

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COVID-19 death reported in Dakota County Saturday; believed to be Tyson worker - Sioux City Journal

Many people in Britain are likely to suffer from physical and mental problems for several years after the Covid-19 epidemic has subsided. That is the grim message from doctors and psychologists who last week warned that even after lockdown measures had been lifted thousands of individuals would still be suffering.

Some of these problems will be due directly to the impact that the virus has had on those it has infected, especially those who went through life-saving interventions in intensive care units (ICUs) in hospital. In addition there will be a considerable impact on vulnerable people affected by the lockdown and isolation.

As a result, there is a danger our society could become more anxious and risk-averse, say scientists who have called for a range of research programmes to be launched to understand the issues and to allow society to prepare itself for the physiological and psychological problems that lie ahead.

This has been a national trauma like no other that we have experienced, said psychologist Professor Dame Til Wykes, of Kings College London. Consider the terrible flooding we had earlier this year. People watched river levels rise and listened to weather forecasts to find out if they might be inundated the next day or the day after. That was stressful.

But it was nothing compared to this threat which has hung over us for weeks already and is likely to go on for much longer. Spending months looking over your shoulder all the time is going to cause considerable, lasting anxiety for many people. In addition, if you look at other natural disasters, you can usually find help or comfort from people around you. However, it is the people around you that are the threat in this case. So there is no consolation there.

Many who were treated in ICUs for Sars and Mers had post-traumatic stress disorders months, sometimes years, after the event

This point was backed by Rory OConnor, professor of health psychology at Glasgow University. Increased social isolation, loneliness, health anxiety, stress and an economic downturn are a perfect storm to harm peoples mental health, he said.

If we do nothing, we risk seeing an increase in mental health conditions such as anxiety and depression, and a rise in problem behaviours such as alcohol and drug addiction, gambling, cyberbullying or social consequences such as homelessness and relationship breakdown.

These are problems that face society in general. For those struck down by Covid-19 and who have been treated in ICUs, there are likely to be further issues, researchers have warned. These problems have been revealed in studies of those who contracted two other diseases caused by coronaviruses severe acute respiratory syndrome (Sars) and Middle East respiratory syndrome (Mers) and who also required intensive care in hospitals.

Being in an ICU can be a horrible experience, said Wykes. Studies from those who were treated in ICUs for Sars and Mers reveal that many had post-traumatic stress disorders months, sometimes years, after the event, especially if they were put on ventilators. That can induce panic on its own. Later you get flashbacks, extreme anxiety particularly about your family and your partner.

In one study by Hong Kong University researchers of people who had contracted Sars, it was found that those who survived the disease still had, a year later, elevated stress levels and worrying levels of psychological distress. They also showed alarming levels of depression, anxiety and post-traumatic symptoms. There is every reason to expect to see the same sorts of symptoms appearing in those directly affected by Covid-19, added Wykes.

In addition to the psychological impact of the disease, it is also clear that lingering physiological problems are likely to be associated with Covid-19. No one knows exactly what the disease will do in the long term to patients but we do know what impacts other forms of viral pneumonia which Covid-19 can trigger can have on patients, said Professor Ian Hall of Nottingham University.

With these conditions, many patients suffer from significant lung scarring and are affected by a condition known as advanced respiratory distress syndrome which can require months of recovery. There is some initial evidence to suggest that for Covid-19 patients, it may take even longer, he said.

Hall added that there was likely to be impacts on other parts of the body. For example, Covid-19 can cause serious inflammation that affects patients in the early stages of dementia and can leave them increasingly confused and stressed.

Cardiologist Professor Tim Chico at Sheffield University also pointed to studies indicating that people hospitalised with Covid-19 were also at risk from blood clots in multiple locations, including their lungs, veins and brain. Crucially, the risk of blood clots with Covid-19 appears to be even greater than the increased risk of blood clots seen in other severe illnesses, he said. Such an effect would leave patients vulnerable to pulmonary embolisms, strokes and deep vein thrombosis.

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Britons will suffer health problems from Covid-19 for years, warn doctors - The Guardian

UPDATE (12 p.m. PT) Gov. Kate Brown said on Friday a new study with 100,000 randomly selected Oregonians could shed light on how far the coronavirus has spread throughout the state and will help guide the states decisions to reopen theeconomy.

It was one month ago the governor ordered everyone to stay home to help stop the spread ofCOVID-19.

But holy smokes, it feels a lot longer than that, the governor said onFriday.

At a press conference, Brown unveiled new details on how the state plans to expand COVID-19 testing and trace people who have been exposed to the coronavirus. Both measures are crucial to reopening the economy, which the governor said could start happening in some regions of the state as soon as May15.

The governor warned reopening Oregon wouldnt happen all at once and would be slower than what anyonewants.

This is not like a light switch, Brown said, adding it will be more like adimmer.

An OHSU research team will randomly select Oregonians to voluntarily participate in the study. The study will focus on vulnerable populations and will help the state create a better map of where the virus exists in the state and how it affects certainpopulations.

The research team will track the temperatures and other COVID-19 symptoms of the participants. Those invited to participate will receive a letter and would agree to be tracked for up to oneyear.

Brown and her advisers were clear that easing social distancing will come with a cost: More people will become infected with COVID-19 and some of them willdie.

This is not without risk. If we move forward and open up, there will be more cases, Patrick Allen, director of the Oregon Health Authority,said in a briefing before Brownaddressedreporters.

The OHA released a plan Friday that details a new plan for testing and contact-tracing finding and monitoring those who have come into contact with someone who has the disease. Its everything they need to have in place so Oregon can re-open more safely, Allensaid.

These are the foundational pieces that need to be in place to be able to move forward, Allensaid.

Participating is voluntary and people will receive an invite to participate. Brown called it a game-changer. If asked, Brown urged people to heed thecall.

Medical assistant Melanie Zamudio is reflected in the window of a car as she reaches in to take a nasal swab from a driver at a drive-up coronavirus testing site Wednesday, April 29, 2020, in Seattle. The site, open Wednesdays and Saturdays from 10 a.m. to 3 p.m. in the Rainier Beach neighborhood, is available to anyone displaying the virus symptoms, are pregnant, over 60 or have a chronic condition, as well as health care workers and firstresponders.

ElaineThompson/AP

We are all in this together, the governor said.Make no mistake, physical distancing will remain part of our daily lives until we have security of a vaccine or a treatment for the disease, Brownsaid.

One of the keys to Oregons plan for reopening is to increase testing and contacttracing.

Contact tracing is what public health does, Oregon State Epidemiologist Dean Sidelinger said. Weve been identifying individuals who can do this in the short term while we set up a permanent network of contact-tracers who know what works best in theircommunity.

Modeling released May 1, 2020 by the Oregon Health Authority shows the projected COVID-19-related cases and deaths under two scenarios. Under the 70% reductionthe number of severe cases requiring hospitalization would stay the same. Under the 60% reduction they will start to increaseslowly.

Oregon HealthAuthority

The state plans to hire 600 people to do contact tracing. Until the new staff members are trained, theyll redeploy existing staff to fill the gap. The agency also is rewriting its investigativeguidelines.

Were making sure we have the latest tools to do those investigations, hiring new people, and increasing training opportunities, Sidelinger said inthebriefing.

Sidelinger said that shortly after the lockdown began, OHA started looking into what it would take to ease those restrictions, hesaid.

But first, they needed time to get everything together. The initial cases were overwhelming. As social distancing slowed transmission, they started looking into how to implement a reduced version of social distancing, while simultaneously ramping up testing, contact tracing and isolating patients at home and quarantining theircontacts.

This is going to be more difficult now than we thought at the beginning because of asymptomatic transmission. Before they even come down with the disease, it will be spreading, Sidelinger said. Theyre trying to factor that into their assumptions and models, headded.

The state has been able to increase the number of tests in recent weeks to about 9,000 tests per week. Overall, the state has tested about 56,000people.

The number of positive tests has declined from 9% from the start of the pandemic to closer to 4.8%, which is lower than most states, according to the states healthauthority.

The governor praised Oregonians for abiding by her stay home, save lives order. The state estimated by staying home more than 70,000 COVID-19 infections were avoided and more than 1,500 hospitalizationsprevented.

As part of its contact-tracing effort, Oregon will be doing more outreach in the communities that are disproportionately affected by COVID-19. In Oregon,Latino communities have been hard-hit by the disease.

People in farm work situations especially have unique challenges, Allen said. He acknowledged that many immigrants have reason to distrust government officials, and may be in vulnerable financialsituations.

Contact tracers can ask intrusive questions, so its especially important to make sure that the people who do it are trusted by theircommunity.

Theyll also be reaching out to Native American tribes to develop plans together and make more testingavailable.

Oregon can only do contact tracing rapidly and accurately if it has the ability to do more testing. OHAs plan outlines ways to increase testing capacity in more rural parts of the state. The agency plans to employ couriers to make sure tests are where theyre needed, and Sidelinger said the state is working with thestates hospital network to develop a plan to treat all of their internal testing strategies as one cohesiveunit.

Weve been working on improving testing since the beginning of the outbreak, but weve really begun to make progress. Its jumped dramatically, we actually got some breakthroughs on our supply chain, said Sidelinger. A global shortage of the chemicals needed to run the tests had slowed efforts before. The long-awaited test kits for the ABBOTT rapid tests provided by the federal government have arrived, too, so rural hospitals will be able to test some patients onsite.

With more, better-distributed testing, OHA hopes to be able to look for spikes in cases in certain regions of the state. Then, they can respond to that region in particular, find sick individuals and ask them to isolate they should not be near anyone who isnt actively sick. People who have been exposed to the virus will be asked to quarantine to see whether they get sick, so they dont spread the virus into the larger community. Once they develop symptoms, theyll be asked toisolate.

These measures are voluntary, and there is no punishment for not following them. Instead, the plan is to educate individuals on how and why they should quarantine. These individuals will be asked to sign an agreement to stay home, provided a resource packet that includes a way to document symptoms, and possibly a thermometer. Help will be provided to people who cant isolate at home find another option. Theyre also looking to acquire pulse oximeters, which would allow people to monitor their blood oxygen at home, so they could get early warnings before theycrash.

Oregons isolate-and-quarantine strategy will require a lot of support from public health systems, Allen said. Part of the plan involves linking individuals in underserved communities to the services theyneed.

For example, people who are confirmed COVID-19-positive will be asked to isolate themselves. But depending on the individuals living situation, OHA may need to find them alternative housing if they live with other people, or find a place for them to isolate at all if theyre experiencinghomelessness.

Support could also be linking to them to food or services that have medication. If theyve been laid off, we could link them to the Oregon Health Plan, Allen said. Were still kind of working out those details. It will look different in eachcommunity.

Its unclear what order social distancing restrictions will be eased. The government is still working on that plan, and it may look different in less densely-populated counties than it does in urban areas. Large workplaces, for example, wont re-open for a while. Sidelinger said the agency plans to watch what happens in states that have already eased some social distancing restrictions, and learn from what happensthere.

What is clear is that very small changes can have a large impact on the spread of COVID-19 inOregon.

(The story continuesbelow)

Modeling data from Oregon Health Authority released May 1, 2020. It shows how the impact of COVID-19 is projected to differ based on whether current preventive measures (represented by the 70% reduction line) arerelaxed.

Oregon HealthAuthority

State-produced models looked at several different scenarios. Right now, Oregons social-distancing measures seem to be reducing the transmission of the virus by about 70%. The state modeled what the pandemic could look like in Oregon if it continues this level of social distancing, and also looked at what would happen if it eased social distancing guidelines so the transmission was reduced by 60%, 50%, and30%.

The results are stark. If Oregon keeps the current restrictions, the modeling shows about the same amount of transmission as the currentlevels.

If some social distancing is eased, and there is a 60% reduced transmission, over the next six weeks cases will go up and more people will die, but hospitals would not be overwhelmed. By June 4, there would be about 200 more new infections per day. But if Oregon lifts social distancing restrictions just a little bit more, to 50% reduction, by June 4 there would be about 600 new infections eachday.

As with all models, these arent predictions. Theyre designed to estimate the impact that small changes in behavior can have on the spread of disease. Real people are a lot more complicated than computer simulations. Its less important to look at the actual numbers than it is to look at thetrends.

The models also only look forward six weeks, because the farther into the future the models work, the less accurate their numbers willbe

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Gov. Kate Brown Lays Out COVID-19 Testing And Contact Tracing As Keys To Reopening Oregon - OPB News

Tracing infection from mobility data

What sort of measures are required to contain the spread of severe acute respiratory syndromecoronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19)? The rich data from the Open COVID-19 Data Working Group include the dates when people first reported symptoms, not just a positive test date. Using these data and real-time travel data from the internet services company Baidu, Kraemer et al. found that mobility statistics offered a precise record of the spread of SARS-CoV-2 among the cities of China at the start of 2020. The frequency of introductions from Wuhan were predictive of the size of the epidemic sparked in other provinces. However, once the virus had escaped Wuhan, strict local control measures such as social isolation and hygiene, rather than long-distance travel restrictions, played the largest part in controlling SARS-CoV-2 spread.

Science, this issue p. 493

The ongoing coronavirus disease 2019 (COVID-19) outbreak expanded rapidly throughout China. Major behavioral, clinical, and state interventions were undertaken to mitigate the epidemic and prevent the persistence of the virus in human populations in China and worldwide. It remains unclear how these unprecedented interventions, including travel restrictions, affected COVID-19 spread in China. We used real-time mobility data from Wuhan and detailed case data including travel history to elucidate the role of case importation in transmission in cities across China and to ascertain the impact of control measures. Early on, the spatial distribution of COVID-19 cases in China was explained well by human mobility data. After the implementation of control measures, this correlation dropped and growth rates became negative in most locations, although shifts in the demographics of reported cases were still indicative of local chains of transmission outside of Wuhan. This study shows that the drastic control measures implemented in China substantially mitigated the spread of COVID-19.

The outbreak of coronavirus disease 2019 (COVID-19) spread rapidly from its origin in Wuhan, Hubei Province, China (1). A range of interventions were implemented after the detection in late December 2019 of a cluster of pneumonia cases of unknown etiology and identification of the causative virus, severe acute respiratory syndromecoronavirus 2 (SARS-CoV-2), in early January 2020 (2). Interventions include improved rates of diagnostic testing; clinical management; rapid isolation of suspected cases, confirmed cases, and contacts; and, most notably, restrictions on mobility (hereafter called cordon sanitaire) imposed on Wuhan city on 23 January 2020. Travel restrictions were subsequently imposed on 14 other cities across Hubei Province, and partial movement restrictions were enacted in many cities across China. Initial analysis suggests that the Wuhan cordon sanitaire resulted in an average 3-day delay of COVID-19 spread to other cities (3), but the full extent of the effect of the mobility restrictions and other types of interventions on transmission has not been examined quantitatively (46). Questions remain over how these interventions affected the spread of SARS-CoV-2 to locations outside of Wuhan. Here, we used real-time mobility data, crowdsourced line list data of cases with reported travel history, and timelines of reporting changes to identify early shifts in the epidemiological dynamics of the COVID-19 epidemic in China, from an epidemic driven by frequent importations to local transmission.

As of 1 March 2020, 79,986 cases of COVID-19 were confirmed in China (Fig. 1A) (7). Reports of cases in China were mostly restricted to Hubei until 23 January 2020 (81% of all cases), after which most provinces reported rapid increases in cases (Fig. 1A). We built a line list dataset from reported cases in China with information on travel history and demographic characteristics (8). We note that the majority of early cases (before 23 January 2020; see the materials and methods) reported outside of Wuhan had known travel history to Wuhan (57%) and were distributed across China (Fig. 1B), highlighting the importance of Wuhan as a major source of early cases. However, initial testing was focused mainly on travelers from Wuhan, potentially biasing estimates of travel-related infections upward (see the materials and methods). Among cases known to have traveled from Wuhan before 23 January 2020, the time from symptom onset to confirmation was 6.5 days (SD = 4.2 days; fig. S2), providing opportunity for onward transmission at the destination. More active surveillance reduced this interval to 4.8 days (SD = 3.03 days; fig. S2) for those who traveled after 23 January 2020.

(A) Epidemic curve of the COVID-19 outbreak in provinces in China. Bars indicate key dates: implementation of the cordon sanitaire of Wuhan (gray) and the end of the first incubation period after the travel restrictions (red). The black line represents the closure of the Wuhan seafood market on 1 January 2020. The width of each horizontal tube represents the number of reported cases in that province. (B) Map of COVID-19 confirmed cases (n = 554) that had reported travel history from Wuhan before travel restrictions were implemented on 23 January 2020. Colors of the lines indicate date of travel relative to the date of travel restrictions.

To identify accurately a time frame for evaluating early shifts in SARS-CoV-2 transmission in China, we first estimated from case data the average incubation period of COVID-19 infection [i.e., the duration between time of infection and symptom onset (9, 10)]. Because infection events are typically not observed directly, we estimated the incubation period from the span of exposure during which infection likely occurred. Using detailed information on 38 cases for whom both the dates of entry to and exit from Wuhan were known, we estimated the mean incubation period to be 5.1 days (SD = 3.0 days; fig. S1), similar to previous estimates from other data (11, 12). In subsequent analyses, we added an upper estimate of one incubation period (mean + 1 SD = 8 days) to the date of Wuhan shutdown to delineate the date before which cases recorded in other provinces might represent infections acquired in Hubei (i.e., 1 February 2020; Fig. 1A).

To understand whether the volume of travel within China could predict the epidemic outside of Wuhan, we analyzed real-time human mobility data from Baidu Inc., together with epidemiological data from each province (see the materials and methods). We investigated spatiotemporal disease spread to elucidate the relative contribution of Wuhan to transmission elsewhere and to evaluate how the cordon sanitaire may have affected it.

Among cases reported outside of Hubei province in our dataset, we observed 515 cases with known travel history to Wuhan and a symptom onset date before 31 January 2020, compared with only 39 cases after 31 January 2020, illustrating the effect of travel restrictions (Figs. 1B and 2A and fig. S3). We confirmed the expected decline of importation with real-time human mobility data from Baidu Inc. Movements of individuals out of Wuhan increased in the days before the Lunar New Year and the establishment of the cordon sanitaire, before rapidly decreasing to almost no movement (Fig. 2, A and B). The travel ban appears to have prevented travel into and out of Wuhan around the time of the Lunar New Year celebration (Fig. 2A) and likely reduced further dissemination of SARS-CoV-2 from Wuhan.

(A) Human mobility data extracted in real time from Baidu Inc. Travel restrictions from Wuhan and large-scale control measures started on 23 January 2020. Gray and red lines represent fluxes of human movements for 2019 and 2020, respectively. (B) Relative movements from Wuhan to other provinces in China. (C) Timeline of the correlation between daily incidence in Wuhan and incidence in all other provinces, weighted by human mobility.

To test the contribution of the epidemic in Wuhan to seeding epidemics elsewhere in China, we built a nave COVID-19 generalized linear model [GLM (13)] of daily case counts (see the materials and methods). We estimated the epidemic doubling time outside of Hubei to be 4.0 days (range across provinces, 3.6 to 5.0 days) and estimated the epidemic doubling time within Hubei to be 7.2 days, consistent with previous reports (5, 12, 14, 15). Our model predicted daily case counts across all provinces with relatively high accuracy (as measured with a pseudo-R2 from a negative binomial GLM) throughout early February 2020 and when accounting for human mobility (Fig. 2C and tables S1 and S2), consistent with an exploratory analysis (6).

We found that the magnitude of the early epidemic (total number of cases until 10 February 2020) outside of Wuhan was very well predicted by the volume of human movement out of Wuhan alone (R2 = 0.89 from a log-linear regression using cumulative cases; fig. S8). Therefore, cases exported from Wuhan before the cordon sanitaire appear to have contributed to initiating local chains of transmission, both in neighboring provinces (e.g., Henan) and in more distant provinces (e.g., Guangdong and Zhejiang) (Figs. 1A and 2B). Further, the frequency of introductions from Wuhan were also predictive of the size of the early epidemic in other provinces (controlling for population size) and thus the probability of large outbreaks (fig. S8).

After 1 February 2020 (corresponding to one mean + one SD incubation period after the cordon sanitaire and other interventions were implemented), the correlation of daily case counts and human mobility from Wuhan decreased (Fig. 2C), indicating that variability among locations in daily case counts was better explained by factors unrelated to human mobility, such as local public health response. This suggests that whereas travel restrictions may have reduced the flow of case importations from Wuhan, other local mitigation strategies aimed at halting local transmission increased in importance later.

We also estimated the growth rates of the epidemic in all other provinces (see the materials and methods). We found that all provinces outside of Hubei experienced faster growth rates between 9 January and 22 January 2020 (Fig. 3, A and B, and fig. S4b), which was the time before travel restrictions and substantial control measures were implemented (Fig. 3C and fig. S6); this was also apparent from the case counts by province (fig. S6). In the same period, variation in the growth rates is almost entirely explained by human movements from Wuhan (Fig. 3C and fig. S9), consistent with the theory of infectious disease spread in highly coupled metapopulations (16, 17). After the implementation of drastic control measures across the country, growth rates became negative (Fig. 3B), indicating that transmission was successfully mitigated. The correlation of growth rates and human mobility from Wuhan became negative; that is, provinces with larger mobility from Wuhan before the cordon sanitaire (but also larger number of cases overall) had more rapidly declining growth rates of daily case counts. This could be due partly to travel restrictions but also to the fact that control measures may have been more drastic in locations with larger outbreaks driven by local transmission (for more details, see Current role of imported cases in Chinese provinces section).

(A) Daily counts of cases in China. (B) Time series of province-level growth rates of the COVID-19 epidemic in China. Estimates of the growth rate were obtained by performing a time-series analysis using a mixed-effects model of lagged, log linear daily case counts in each province (see the materials and methods). Above the red line are positive growth rates and below are negative rates. Blue indicates dates before the implementation of the cordon sanitaire and green after. (C) Relationship between growth rate and human mobility at different times of the epidemic. Blue indicates before the implementation of the cordon sanitaire and green after.

The travel ban coincided with increased testing capacity across provinces in China. Therefore, an alternative hypothesis is that the observed epidemiological patterns outside of Wuhan were the result of increased testing capacity. We tested this hypothesis by including differences in testing capacity before and after the rollout of large-scale testing in China on 20 January 2020 [the date that COVID-19 became a class B notifiable disease (18, 19)] and determined the impact of this binary variable on the predictability of daily cases (see the materials and methods). We plotted the relative improvement in the prediction of our model (on the basis of normalized residual error) of (i) a model that includes daily mobility from Wuhan and (ii) a model that includes testing availability (for more details, see the materials and methods). Overall, the inclusion of mobility data from Wuhan produced an improvement in the models prediction [delta-Bayesian information criterion > 250 (20)] over a nave model that considers only autochthonous transmission with a doubling time of 2 to 8 days (Fig. 3B). Of the 27 provinces in China reporting cases through 6 February 2020, we found that the largest improvements in prediction for 12 provinces could be achieved using mobility only (fig. S5). In 10 provinces, both testing and mobility improved the models prediction, and in only one province (Hunan) was testing the most important factor improving model prediction (fig. S5). We conclude that laboratory testing during the early phase of the epidemic was critical; however, mobility out of Wuhan remained the main driver of spread before the cordon sanitaire. Large-scale molecular and serological data will be important to investigate further the exact magnitude of the impact of human mobility compared with other factors.

Because case counts outside of Wuhan have decreased (Fig. 3B), we can further investigate the current contribution of imported cases to local epidemics outside of Wuhan by investigating case characteristics. Age and sex distributions can reflect heterogeneities in the risk of infection within affected populations. To investigate meaningful shifts in the epidemiology of the COVID-19 outbreak through time, we examined age and sex data for cases from different periods of the outbreak and from individuals with and without travel from Wuhan. However, details of travel history exist for only a fraction of confirmed cases, and this information was particularly scant for some provinces (e.g., Zhejiang and Guangdong). Therefore, we grouped confirmed cases into four categories: (I) early cases (i.e., reported before 1 February 2020) with travel history, (II) early cases without travel history, (III) later cases (i.e., reported between 1 February and 10 February 2020) with travel history, and (IV) later cases without travel history.

Using crowdsourced case data, we found that cases with travel history (categories I and III) had similar median ages and sex ratios in both the early and later phases of the outbreak (age 41 versus 42 years; 50% interquartile interval: 32.75 versus 30.75 and 54.25 versus 53.5 years, respectively; P value > 0.1, 1.47 versus 1.45 males per female, respectively; Fig. 4D and fig. S7). Early cases with no information on travel history (category II) had a median age and sex ratio similar to those with known travel history (age 42 years; 50% interquartile interval: 30.5 to 49.5, P value > 0.1; 1.80 males per female; Fig. 4D). However, the sex ratio of later cases without reported travel history (category IV) shifted to ~1:1 (57 male versus 62 female, 2 test, P value < 0.01), as expected under a null hypothesis of equal transmission risk [Fig. 4, A, B, and D; see also (21, 22) and the materials and methods], and the median age in this group increased to 46 (50% interquartile interval: 34.25 to 58, t test: P value < 0.01; Fig. 4, A to C, and fig. S7). We hypothesize that many of the cases with no known travel history in the early phase were indeed travelers who contributed to disseminating SARS-CoV-2 outside of Wuhan. The shift toward more equal sex ratios and older ages in nontravelers after 31 January 2020 confirms the finding that epidemics outside of Wuhan were then driven by local transmission dynamics. The case definition changed to include cases without travel history to Wuhan after 23 January 2020 (see the materials and methods).

(A) Age and sex distributions of confirmed cases with known travel history to Wuhan. (B) Age and sex distributions of confirmed cases that had no travel history to Wuhan. (C) Median age for cases reported early (before 1 February) and those reported later (between 1 and 10 February). Full distributions are shown in fig. S7. (D) Change through time in the sex ratio of (i) all reported cases in China with no reported travel history, (ii) cases reported in Beijing without travel history, and (iii) cases known to have traveled from Wuhan.

Containment of respiratory infections is particularly difficult if they are characterized by relatively mild symptoms or transmission before the onset of symptoms (23, 24). Intensive control measures, including travel restrictions, have been implemented to limit the spread of COVID-19 in China. Here, we show that travel restrictions are particularly useful in the early stage of an outbreak when it is confined to a certain area that acts as a major source. However, travel restrictions may be less effective once the outbreak is more widespread. The combination of interventions implemented in China was clearly successful in mitigating spread and reducing local transmission of COVID-19, although in this work it was not possible to definitively determine the impact of each intervention. Much further work is required to determine how to balance optimally the expected positive effect on public health with the negative impact on freedom of movement, the economy, and society at large.

T. J. Hastie, D. Pregibon, Generalized linear models in Statistical Models in S, J. M. Chambers, T. J. Hastie, Eds. (Wadsworth & Brooks/Cole, 1992), pp. 195246.

M. J. Keeling, O. N. Bjrnstad, B. T. Grenfell, Metapopulation dynamics of infectious diseases in Ecology, Genetics and Evolution of Metapopulations, I. Hanski, O. E. Gaggiotti, Eds. (Elsevier, 2004), pp. 415445.

J. H. McDonald, Handbook of Biological Statistics (Sparky House, ed. 3, 2014).

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The effect of human mobility and control measures on the COVID-19 epidemic in China - Science Magazine

US meat production has continued to decline as the coronavirus crisis forces the shutdown of more processing facilities, sparking fears of shortages at grocery stores nationwide.

The US Department of Agricultures weekly report found that from 27 April, beef production was down nearly 25% compared to the same time last year. Pork production was down 15%.

While Sonny Perdue, the agriculture secretary, has said the US has plenty of food for all of [its] citizens, fewer pigs are being slaughtered at processing plants, down by nearly 50% since mid-March.

Meat processing companies have paused operations as some workers have tested positive for Covid-19, the disease caused by the coronavirus.

Last month, Tyson Foods, one of Americas largest meat producers, warned the food supply chain is breaking in a full-page ad in newspapers including the New York Times.

There will be limited supply of products, the Arkansas-based company said, until it can reopen closed facilities.

On Thursday, Tyson temporarily suspended operations at its beef processing plant outside Sioux City, Iowa, after more than 900 workers tested positive for the coronavirus.

The company said it would close through the weekend for deep cleaning. The facility is one of the largest beef plants in the country, employing about 4,300 people.

An analysis from USA Today and the Midwest Center for Investigative Reporting found at least 4,400 workers had tested positive for the virus across 80 plants, causing 28 to close for at least one day.

According to the United Food and Commercial Workers International Unions, at least 20 workers have died.

I wouldnt say the food system is breaking, but at least the meat sector is in real serious, critical condition at the moment, said Jayson Lusk, the head of the Department of Agricultural Economics at Purdue University, told USA Today.

However, there were some signs on Friday that some meat-packing plants could be reopening. A Smithfield Foods pork processing plant in South Dakota where more than 850 workers tested positive will partially reopen on Monday after shuttering for more than two weeks, a union that represents plant workers said late on Friday.

Arkansas-based Tyson Foods said its Logansport, Indiana, pork processing plant where nearly 900 employees tested positive will also resume limited production on Monday.

Donald Trump has attempted to curb the looming shortage, signing an executive order on Tuesday declaring meatpacking plants critical to keep open.

Legal experts, however, said the order is unlikely to curb the decline, as it doesnt compel meat producers to remain in production and doesnt give employers immunity from lawsuits.

Still, Perdue told Bloomberg on Thursday he expected the order to have meat packing plants reopening within days, not weeks.

There will be some less production, some inefficiency based on line speeds, some employees that will not be able to come back to work, he said. We want to assure the workers and the community of their safety.

Fears of meat shortages have had shoppers looking for alternatives to retail grocers. Restaurants and food service vendors have reported shortages as processors shift to selling directly to consumers.

Shoppers are stocking up, but experts warn panic buying will only exacerbate shortages.

[Americans] have often been confronted by higher prices for beef and pork products, or in some circumstances, nearly empty meat cases, the Democratic senators Mike Lee and Amy Klobuchar wrote in a letter to the US justice department and Federal Trade Commission.

The senators called on law enforcement to investigate the meat supply chain.

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US consumers rush to buy meat amid concerns over Covid-19 shortages - The Guardian

Models predicting the potential spread of the COVID-19 pandemic have become a fixture of American life. Yet each model tells a different story about the devastation to come, making it hard to know which one is right. But COVID-19 models arent made to be unquestioned oracles. Theyre not trying to tell us one precise future, but rather the range of possibilities given the facts on the ground.

One of their more sober tasks is predicting the number of Americans who will die due to COVID-19. FiveThirtyEight with the help of the Reich Lab at the University of Massachusetts Amherst has assembled six models published by infectious disease researchers to illustrate possible trajectories of the pandemics death toll. In doing so, we hope to make them more accessible, as well as highlight how the assumptions underlying the models can lead to vastly different estimates. Here are the models U.S. fatality projections for the coming weeks.

See forecasts from

TodayMay 1April 21April 14April 7

Forecasts like these are useful because they help us understand the most likely outcomes as well as best- and worst-case possibilities and they can help policymakers make decisions that can lead us closer to those best-case outcomes.

And looking at multiple models is better than looking at just one because it's difficult to know which model will match reality the closest. Even when models disagree, understanding why they are different can give us valuable insight.

Each model makes different assumptions about properties of the novel coronavirus, such as how infectious it is and the rate at which people die once infected. They also use different types of math behind the scenes to make their projections. And perhaps most importantly, they make different assumptions about the amount of contact we should expect between people in the near future.

Understanding the underlying assumptions that each model is currently using can help us understand why some forecasts are more optimistic or pessimistic than others.

Below are individual forecasts for all 50 states and the District of Columbia.

See forecasts from

Forecasts from

TodayMay 1April 21April 14April 7

Scroll to a state

AllAlabamaAlaskaArizonaArkansasCaliforniaColoradoConnecticutDelawareDistrict of ColumbiaFloridaGeorgiaHawaiiIdahoIllinoisIndianaIowaKansasKentuckyLouisianaMaineMarylandMassachusettsMichiganMinnesotaMississippiMissouriMontanaNebraskaNevadaNew HampshireNew JerseyNew MexicoNew YorkNorth CarolinaNorth DakotaOhioOklahomaOregonPennsylvaniaRhode IslandSouth CarolinaSouth DakotaTennesseeTexasUtahVermontVirginiaWashingtonWest VirginiaWisconsinWyoming

Show models

AllColumbia Univ.IHMELos AlamosMITNortheastern Univ.Univ. of Texas

289deathsas ofMay 1

9deaths

330deaths

64deaths

2,126deaths

821deaths

2,339deaths

159deaths

231deaths

1,314deaths

1,169deaths

16deaths

63deaths

2,457deaths

1,175deaths

170deaths

140deaths

246deaths

1,970deaths

55deaths

1,080deaths

3,716deaths

3,866deaths

370deaths

281deaths

360deaths

16deaths

73deaths

246deaths

81deaths

7,538deaths

131deaths

24,039deaths

419deaths

23deaths

1,003deaths

230deaths

104deaths

2,635deaths

279deaths

256deaths

21deaths

204deaths

840deaths

46deaths

50deaths

581deaths

824deaths

46deaths

327deaths

7deaths

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Where The Latest COVID-19 Models Think We're Headed And Why They Disagree - FiveThirtyEight

Good morning, good afternoon and good evening.

Three months ago, I convened the Emergency Committee under the International Health Regulations, and after receiving their advice, I declared a global health emergency WHOs highest level of alarm.

Yesterday, I reconvened the Emergency Committee to review the evolution of the pandemic and advise me accordingly.

The committee consists of independent, international experts, representing all regions and the full range of relevant expertise.

Id like to thank the Chair of the committee, Professor Didier Houssin, and all the committee members.

Of course, the pandemic remains a public health emergency of international concern.

The committee has made several recommendations for WHO, and for countries.

To outline those recommendations, Id now like to invite Professor Houssin to say a few words.

Professor, you have the floor.

[PROFESSOR HOUSSIN SPOKE]

Thank you, Professor Houssin.

I would like to make a few remarks about the committees advice for WHO.

We appreciate the confidence and trust expressed by the committee in WHO to continue to lead and coordinate the global response to the pandemic, in collaboration with countries and partners.

We are committed to fulfilling that role, and to accelerating our efforts.

WHO will continue supporting all countries with technical and logistical support, especially those that need it most.

We accept the committees advice that WHO works to identify the animal source of the virus through international scientific and collaborative missions, in collaboration with the World Organisation for Animal Health and the Food and Agriculture Organization of the United Nations.

We will continue supporting countries to sustain essential health services, including vaccination, care for women during pregnancy and childbirth, and care for non-communicable diseases, including mental health conditions.

As we have done clearly from the beginning, we will continue to call on countries to implement a comprehensive package of measures to find, isolate, test and treat every case, and trace every contact.

We will continue working with countries and partners to enable essential travel needed for pandemic response, humanitarian relief and cargo operations, and for countries to gradually resume normal passenger travel.

As Professor Houssin explained, the committee has also made recommendations for countries, and we encourage countries to pay careful attention to that advice.

And we encourage countries to follow WHOs advice, which we are constantly reviewing and updating as we learn more about the virus, and as we learn more from countries about best practices for responding to it.

In accordance with the International Health Regulations, I will reconvene the Emergency Committee again in 90 days, or sooner if needed.

====

As you remember, last Friday we joined the European Commission and other partners to launch the ACT Accelerator, to ensure all people enjoy access to all the tools to prevent, detect and treat COVID-19.

This coming Monday, May 4, the Commission will host a pledging conference to generate funds for investment in vaccine research. I hope you have heard the call from the President of the European Commission, President Ursula von der Leyen.

Today we are deepening our relationship with the European Union, by signing a new Memorandum of Understanding with the European Investment Bank, EIB.

This agreement covers five main areas of work.

First, WHO and EIB will collaborate on a new EU Malaria Fund, to address market failures in developing more effective vaccines, drugs and diagnostics for malaria.

Although malaria deaths have fallen by more than half since the year 2000, progress has stalled in recent years, and may even reverse if the COVID-19 pandemic disrupts malaria control programmes.

Last year, WHOs Strategic Advisory Group on Malaria Eradication and the Lancet Commission on Malaria Eradication both concluded that we will need new tools if we are to achieve the dream of eradicating malaria.

Both reports called for increased investment in research and development to deliver new tools.

With WHOs technical expertise and the European Investment Banks financial muscle, we are confident of accelerating the development of those new tools.

Second, our two organizations will work together to foster the development of new innovative antibacterial treatments.

Antibiotic resistance is one the most urgent health challenges of our time.

It threatens to unravel a century of medical progress, and leave us defenceless against infections that were previously easily treated.

Investment in antibiotic development has continued to decline. Some small antibiotic companies went bankrupt in 2019 because of the limited profitability of new antibiotics.

Very few new antibiotics are in the pipeline. Most of them offer little benefit over existing treatments, and very few target the most critical resistant bacteria.

To address this challenge, WHO and the European Investment Bank are working on a fund to invest in the development of new antibiotics for priority pathogens.

WHO and EIB now are in discussions with potential investors and other stakeholders on this initiative.

Third, we will work together to strengthen primary health care and build resilient health systems.

The COVID-19 crisis has illustrated that even the most sophisticated health systems have struggled to cope with a pandemic.

WHO has grave concerns about the potential impact the virus could have as it starts to accelerate in countries with weaker health systems.

With the EIB, we will therefore work urgently to invest in health infrastructure and health workers in 10 countries in Africa and the Middle East, to start with.

Fourth, EIB and WHO are exploring how the European Investment Bank could support the COVID-19 Supply Chain System, to facilitate the distribution of diagnostics, personal protective equipment and other medical supplies to countries that need them most.

And fifth, we will work together to study market failures in other areas of public health, to examine how innovative financing could help overcome investment barriers and increase access to lifesaving products and services.

The EIB has rich experience in innovative financing. I learned from my friend Werner Hoyer today that the EIB were pioneers of so-called green bonds 30 years ago, to generate funds for climate and environmental projects billions of dollars.

We look forward to seeing how that type of innovative financing could deliver real results for global health, when WHO is advocating health for all. As you know, we have been saying that all roads should lead to universal health coverage, and its more important than ever to say exactly the same: all roads should lead to universal health coverage, health for all.

WHO is deeply grateful to the European Investment Bank for its support and collaboration.

Id now like to invite the President of the European Investment Bank, Mr Werner Hoyer, to say a few words.

Vielen dank, my friend, and you have the floor.

Originally posted here:

WHO Director-General's opening remarks at the media briefing on COVID-19 - 1 May 2020 - World Health Organization

State health officials announced nine additional deaths due to COVID-19 and 164 new cases on Friday, putting the death toll at 81 in New Hampshire since the pandemic began.

The latest victims were one female resident of Grafton County, three female residents of Hillsborough County, one male resident of Hillsborough County, one female resident of Merrimack County, two male residents of Rockingham County and one female resident of Rockingham County.

The state Department of Health and Human Services (DHHS) said 26 of the new cases involved residents of Manchester, putting the total number of cases in the Queen City at 481. DHHS said 13 new cases involved residents of Nashua, putting the total number of cases in the Gate City at 206.

There have been a total of 2,310 confirmed cases of COVID-19 reported in the Granite State.

Eight new hospitalized cases were identified for a total of 270, or 12% of the 2,310 confirmed cases.

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Nine new COVID-19 deaths reported in NH Friday - The Union Leader