Fast spread of COVID-19 in Europe and the US and its implications: even modest public health goals require comprehensive intervention
Ruian Ke, PhD, Steven Sanche, PhD, Ethan Romero-Severson, PhD, Nick Hengartner, PhD
medRxiv, doi: https://www.medrxiv.org/content/10.1101/2020.04.04.20050427v1.full.pdf
Findings: In all countries, the early epidemic period was characterized by exponential growth with rates between 0.19-0.29/day (epidemic doubling times between 2.4-3.7 days). However, the proportion of cases that had been detected was low … With such high epidemic growth rates, moderate intervention efforts will have little impact on the public health outcome; high levels of efforts to achieve greater than 77-86% reduction in transmission are needed, no matter whether the goal is to slow down the growth to protect a large fraction of population from infection within 18 months, or to reverse the growth all together.
Interpretation: The extremely fast spread of COVID-19 in Europe and the US suggest a highly infectious virus with a high R0. Early, strong and comprehensive intervention efforts are necessary, whether the aim is mitigation or containment.
High Contagiousness and Rapid Spread of Severe Acute Respiratory Syndrome Coronavirus 2
Steven Sanche, Yen Ting Lin, Chonggang Xu, Ethan Romero-Severson, Nick Hengartner, Ruian Ke
EID Journal: https://wwwnc.cdc.gov/eid/article/26/7/20-0282_article
Severe acute respiratory syndrome coronavirus 2 is the causative agent of the 2019 novel coronavirus disease pandemic. Initial estimates of the early dynamics of the outbreak in Wuhan, China, suggested a doubling time of the number of infected persons of 6–7 days and a basic reproductive number (R0) of 2.2–2.7. We collected extensive individual case reports across China and estimated key epidemiologic parameters, including the incubation period. We then designed 2 mathematical modeling approaches to infer the outbreak dynamics in Wuhan by using high-resolution domestic travel and infection data. Results show that the doubling time early in the epidemic in Wuhan was 2.3–3.3 days. Assuming a serial interval of 6–9 days, we calculated a median R0 value of 5.7 (95% CI 3.8–8.9). We further show that active surveillance, contact tracing, quarantine, and early strong social distancing efforts are needed to stop transmission of the virus.
Emergence of SARS-CoV-2 through Recombination and Strong Purifying Selection
Xiaojun Li, Elena E. Giorgi, Manukumar Honnayakanahalli Marichann, Brian Foley, Chuan Xiao, Xiang-peng Kong, Yue Chen, Bette Korber, Feng Gao
bioRxiv, doi: https://doi.org/10.1101/2020.03.20.000885
Our team demonstrated, by looking at the genetic sequence of the virus and comparing it to other known coronaviruses, that it originated from animals. More specifically, it most likely came from a family of bat viruses that acquired the ability to infect human cells from another family of coronaviruses found in pangolins.
School dismissal as a pandemic influenza response: When, where and for how long
Timothy C. Germann, Hongjiang Gao, Manoj Gambhir, Andrew Plummer, Matthew Biggerstaff, Carrie Reed, Amra Uzicanin
Epidemics, 2019 – Elsevier
We used individual-based computer simulation models at community, regional and national levels to evaluate the likely impact of coordinated pre-emptive school dismissal policies during an influenza pandemic. Such policies involve three key decisions: when, over what geographical scale, and how long to keep schools closed. Our evaluation includes uncertainty and sensitivity analyses, as well as model output uncertainties arising from variability in serial intervals and presumed modifications of social contacts during school dismissal periods.
The following are links to recent articles and clips related to LANL COVID-19 science:
Race for vaccine intensifies as coronavirus hits Asia with a second wave of outbreaks —Los Angeles Times (4/9)
Los Alamos National Lab has been working in biological sciences since 1945 and is applying its earlier pioneering research on HIV and influenza to the new coronavirus, said, a biochemist program manager at the federal facility.
Virus May Spread Twice as Fast as Earlier Thought, Study Says —Bloomberg News (4/8)
Each person infected early in the epidemic in Wuhan probably passed the virus to an average of 5.7 other people, according to a mathematical analysis from Los Alamos National Laboratory. That’s more than twice what the World Health Organization and other public health authorities reported in February.
Coronavirus might spread much quicker than health officials thought —New York Post (4/8)
The research, from the Los Alamos National Laboratory, found that people infected during the initial outbreak in Wuhan probably passed the virus to an average 5.7 others — more than double the 2 or 2.5 other people estimated by health officials and the World Health Organization.
Federal Research Is the Key to Solving the COVID-19 Crisis —Inside Higher Ed (4/7)
Researchers across the University of California and our associated health centers are now engaged in more than 300 research initiatives designed to combat COVID-19… A new public-private consortium that includes UC San Diego and the UC-affiliated Lawrence Livermore and Los Alamos National Laboratories is using supercomputers to answer questions about the virus in hours or days, rather than weeks or months.
Inside the Global Race to Fight COVID-19 Using the World’s Fastest Supercomputers —Scientific American Observations (4/6)
More than 25 U.S.-based supercomputers with more than 400 petaflops of computing power – are now available for free to scientists searching for a vaccine or treatment against the virus, through the COVID-19 High Performance Computing Consortium.
Supercomputers join the global fight against COVID-19 —Channelwise (3/30)
IBM, in collaboration with the White House Office of Science and Technology Policy, the US Department of Energy and others, is helping launch the COVID-19 High Performance Computing Consortium.
Ordinary people, extraordinary times —Santa Fe New Mexican (3/28)
Emergency surgeries haven’t stopped in the time of COVID-19. Neither have Eva Birnbaum nor her team at Los Alamos National Laboratory, which is ensuring medical isotopes, critical for positron emission tomography scans and other medical imaging, remain available.
Aid to New Mexico will exceed $1.25 billion from virus relief bill —Albuquerque Journal (3/28)
U.S. Rep. Ben Ray Luján said the state will get its share of the $100 million for national laboratories, which will provide resources for Sandia National Laboratories and Los Alamos National Laboratory to help with coronavirus research. Part of the funding will protect employment at the labs.
DOE Expands on Role of COVID-19 Supercomputing Consortium —HPC Wire (3/25)
After announcing the launch of the COVID-19 High Performance Computing Consortium on Sunday, the Department of Energy yesterday provided more details on its scope and operation in a briefing led by Undersecretary of Energy Paul Dabbar and attended by HPC leaders from national labs.
DHS wound down pandemic models before coronavirus struck —Politico (3/24)
The Department of Homeland Security stopped updating its annual models of the havoc that pandemics would wreak on America’s critical infrastructure in 2017, according to current and former DHS officials with direct knowledge of the matter. NISAC, the DHS office that oversaw the models, began as a partnership between the Los Alamos and Sandia national laboratories in 1999 but in 2003 was folded into DHS by the USA Patriot Act and in 2014 put under OCIA, which has listed analyzing “pandemic influenza” as a top priority.
Governor tells MSNBC she wants all New Mexicans tested for virus —Santa Fe New Mexican (3/24)
The governor told Williams the state’s efforts to track and test the virus are helped by the presence of two of the country’s national laboratories — Los Alamos National Laboratory and Sandia National Laboratories — and the research ability and instruments they have to address the issue.
Roles national labs in New Mexico have to help combat coronavirus —KRQE (3/24)
Gov. Michelle Lujan Grisham is grabbing national attention for New Mexico’s coronavirus response. She also mentioned getting help from the state’s two national labs. So what exactly is their role?
“The position that New Mexico is in is a bit different,” said Gov. Lujan Grisham on MSNBC. “Is that we are a state that has two of the five national laboratories.”
Navigating the Coronavirus Epidemic —Seeking Alpha (3/24)
Current measures such as self-quarantine, social distances, contact tracing, case isolation, etc. will not hinder exponential growth. With no precautionary measures taken, virulence of COVID-19 (R0) is 4.7, according to the lower end of the range proposed by Los Alamos National Laboratory. This means that one infected person will go on to infect 4.7 people on average.
Supercomputers rallied to combat coronavirus —NBC News (3/23)
The consortium includes a slate of 16 supercomputers housed at labs across the country including Los Alamos National Laboratory, the National Science Foundation, NASA, the Massachusetts Institute of Technology and Rensselaer Polytechnic Institute.
IBM and Honeywell sign on with White House to help fight COVID-19 —USA Today (3/23)
IBM says it’s working with Lawrence Livermore National Lab, Argonne National Lab, Oak Ridge National Laboratory, Sandia National Laboratory, Los Alamos National Laboratory, the National Science Foundation, NASA and Rensselaer Polytechnic Institute.
Opinion: Why we need to lock everything down —Australian Financial Review (3/23)
Important studies at Imperial College and Oxford in the UK, and at the Santa Fe Institute, New England Complex Systems Institute and Los Alamos National Laboratory in the US all show that, in highly connected systems, viral pandemics can be contained, and then stamped out, if a massive effort is put into the initial infection zone.
Coronavirus: Experts, data say WNC is ‘underwater’ in having hospital beds to fight COVID-19 —Asheville Citizen Times (3/21)
A pre-print study of Chinese cases by Los Alamos National Laboratory sets the average hospital stay of COVID-19 patients at 11 days.
Mesa Biotech to Receive Funding from US Health and Human Services for Development of a 30-minute Molecular (PCR) Point-of-Care SARS-CoV-2 Test —Monterey County Weekly (3/20)
Today, Mesa Biotech announced it has been awarded a $561K contract from the US Department of Health and Human Services (HHS) Biomedical Advanced Research and Development Authority (BARDA) for development of its rapid molecular diagnostic test for detection of SARS-CoV-2 for ‘near patient’ testing. Mesa Biotech’s molecular technology was developed at Los Alamos National Lab.
NNSA forms Coronavirus 2019 watch group, considering scaling back events —Exchange Monitor (3/11)
Meanwhile, the Los Alamos National Laboratory in New Mexico is pitching in on the effort to understand how the disease — which is not influenza — may spread. A lab spokesperson said Los Alamos had four funded COVID-19 research projects underway, as of Thursday.
Scientists in New Mexico studying link between coronavirus and animals —KOAT (3/10)
Scientists in New Mexico are studying the new coronavirus and other infectious diseases, trying to help stop a pandemic. Researchers at Los Alamos National Laboratory are looking into the cause and how to stop it.
They say there is a link between people and animals and believe that the more people come in contact with animals, the more diseases like the coronavirus will spread.
Mutations can reveal how the coronavirus moves—but they’re easy to overinterpret —Science (3/9)
It was a case study in the power and pitfalls of real-time analysis of viral genomes. “This is an incredibly important disease. We need to understand how it is moving,” says Bette Korber, a biologist at Los Alamos National Laboratory who is also studying the genome of SARS-CoV-2. “With very limited evolution during the outbreak, [these researchers] are doing what they can and they are making suggestions, which I think at this point should be taken as suggestions.”
Mesa Biotech Developing Molecular Point-Of-Care (PCR) Diagnostic Test For Novel Coronavirus (COVID-19) —Laboratory Network (3/6)
“With a proven platform and a China clinical trial already underway for influenza, we are uniquely positioned to rapidly bring accurate and easily deployable coronavirus testing closer to the patient and away from the central lab,” said Hong Cai, Co-founder and Chief Executive Officer, Mesa Biotech, Inc. “Our technology development started at Los Alamos National Lab supported by NIH grants from the National Institute of Allergy and Infectious Diseases (NIAID) and the Western Regional Centers for Excellence in Biodefense and Emerging Infectious Disease program.
How Computer Modeling Of COVID-19’s Spread Could Help Fight The Virus —NPR (3/5)
Scientists who use math and computers to simulate the course of epidemics are taking on the new coronavirus to try to predict how this global outbreak might evolve and how best to tackle it. Sara Del Valle, a mathematical and computational epidemiologist at Los Alamos National Laboratory, says she’d like to see a global center set up to constantly collect information about circulating infectious illnesses.
Much like how the National Weather Service provides forecasts to help people prepare for their local weather, she says, such a center could tell people about their local risk of infectious diseases.
Mesa Biotech developing molecular point-of-care diagnostic test for Novel Coronavirus (COVID-19) —Associated Press (3/4)
“Our technology development started at Los Alamos National Lab supported by NIH grants from the National Institute of Allergy and Infectious Diseases (NIAID) and the Western Regional Centers for Excellence in Biodefense and Emerging Infectious Disease program. Since the beginning we have focused on technology suited for emergency defense and rapid deployment for SARS, Ebola and other emerging infectious diseases. Mesa’s platform was specifically designed for use outside the lab to enable rapid responses to global pandemics, such as COVID-19.”
To Defeat Coronavirus, Win the Containment Battle —Bloomberg (2/25)
The coronavirus epidemic keeps defying predictions. New research suggests that the virus is also far more contagious than initially believed. Early estimates of the basic reproductive number r0 — a key epidemiological figure that reflects the number of new cases, on average, resulting from a single infection in a fully susceptible population — looked to be in the range of 2 to 3.
The largest estimate of r0 so far, in the range of 4.7 to 6.6, comes from a new study by a modeling group at Los Alamos National Laboratory in New Mexico.
Going Viral: Los Alamos National Lab scientists discuss coronavirus modeling, data and prevention —Santa Fe Reporter (2/25)
As governments grapple with responses to the new coronavirus, scientists continue modeling its outbreak and determining its cause. Two such scientists from Los Alamos National Laboratory spoke with me recently about their work.
Sara Del Valle, the deputy group leader for LANL’s Information Systems and Modeling Group, develops mathematical and computational models for infectious diseases. She has developed epidemiological models for smallpox, anthrax, HIV, Ebola, influenza, among others. She has also worked on investigating the role of internet data streams on monitoring emergent behavior during outbreaks and forecasting infectious diseases. LANL Deputy Group Leader for Biosecurity & Public Health Jeanne Fair focuses on epidemiology and animal disease ecology, and was the principle investigator for a 24-year research project on the impacts of environmental stress on avian populations and infectious diseases.
Disease modeller says COVID-19 risk to NZ is very low —Radio New Zealand (2/25)
Sara Del Valle is an applied mathematician and disease modeller at Los Alamos National Laboratory. Like a weather forecaster, she uses mathematical equations to identify patterns in the hope of being able to predict trends that could be a threat to global security. Del Valle and other disease modellers have gazed into their computers to see the future of COVID-19 and the news is not bad for New Zealand.
The Next Coronavirus Nightmare Is Closer Than You Think —Daily Beast (2/20)
Global warming can accelerate displacement by thawing, burning, flooding, or drying out habitats in response to hotter temperatures and stronger storms. “As habitats change and people move and wildlife moves, they’re going to be coming into contact more with each other,” said Jeanne Fair, a biosecurity and public health expert at Los Alamos National Laboratory in Los Alamos, New Mexico. Increasingly close contact, in turn, significantly raises the risk that an animal disease will spill over into humans.
Disease modelers gaze into their computers to see the future of COVID-19, and it isn’t good —STAT (2/15)
Like weather forecasters, researchers who use mathematical equations to project how bad a disease outbreak might become are used to uncertainties and incomplete data, and COVID-19, the disease caused by the new-to-humans coronavirus that began circulating in Wuhan, China, late last year, has those everywhere you look.
“Our overarching goal is to minimize the spread and burden of infectious disease,” said Sara Del Valle, an applied mathematician and disease modeler at Los Alamos National Laboratory. By calculating the effects of countermeasures such as social isolation, travel bans, vaccination, and using face masks, modelers can “understand what’s going on and inform policymakers,” she said.