Los Alamos National Labs with logo 2021

COVID-19 science updates

Los Alamos is focusing its scientific and technical capabilities in response to COVID-19 in several key areas: modeling, laboratory testing options, manufacturing, application of AI and machine learning, medical countermeasures, and high performance computing.

LANL's broad effort to fight COVID-19  




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Craft employees receive State proclamation for work during COVID-19

Posted: May 3, 2021

When the pandemic hit last spring, an essential group of employees remained on-site to keep our mission-essential functions operating. Among these were Capital Projects and Facilities and Operations-Logistics craft team members, who continued to come on-site to ensure the Laboratory could fulfill its national security mission in the midst of a global health crisis.

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New AI tool tracks evolution of COVID-19 conspiracy theories on social media

Posted: April 19, 2021

A new machine-learning program accurately identifies COVID-19-related conspiracy theories on social media and models how they evolved over time—a tool that could someday help public health officials combat misinformation online.

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Simulations reveal how dominant SARS-CoV-2 strain binds to host, succumbs to antibodies

Posted: April 16, 2021

Large-scale supercomputer simulations at the atomic level show that the dominant G form variant of the COVID-19-causing virus is more infectious partly because of its greater ability to readily bind to its target host receptor in the body, compared to other variants. These research results from a Los Alamos National Laboratory–led team illuminate the mechanism of both infection by the G form and antibody resistance against it, which could help in future vaccine development.

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Vaccine development software shows promise in influenza effort, could help defeat coronavirus

Posted: March 1, 2021

A novel computer algorithm that could create a broadly reactive influenza vaccine for swine flu also offers a path toward a pan-influenza vaccine and possibly a pan-coronavirus vaccine as well, according to a new paper published in Nature Communications.

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COVID-19 vaccine critical but it's not silver bullet

Posted: January 5, 2021

After months of anticipation, the COVID-19 vaccine has been delivered to every state in the nation and inoculations are underway. But vaccinating more than 250 million adults throughout the country is a monumental task that requires careful planning and assessments of different approaches to distribution — without which herd immunity can take longer to achieve.

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Answering the what-if questions on COVID Interventions with MEDIAN

Posted: Thursday, Dec. 10 3:05 p.m.

With the COVID-19 pandemic bringing masses of uncertainty and variability, it’s essential for the government policy makers to understand the many variations of biological, policy, sociological and infrastructure responses. How much testing is enough? How much of a problem are false-negative results? Does contact tracing really help? How long will this go on?

This is where Los Alamos shines, in assessing complex data and making sense of it for decision makers. Los Alamos’ Modeling Epidemics for Decision Support with Infrastructure Analysis (MEDIAN) project evolved to help identify asymptomatic people in the population, understanding the balances between maintaining critical infrastructures and public health measures such as contact tracing and diagnostics.

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Special Report: Los Alamos Versus the Virus

Posted: Thursday, Aug. 13 9:10 a.m.

Los Alamos responded to the COVID-19 threat with rigorous worker isolation and a massive mobilization of scientific resources

When the virus hit the United States in force, Los Alamos did what many other organizations across the nation did: sent most of its workforce home. Apart from key national security personnel who continued to work on-site, Laboratory employees worked on laptops from home with various forms of connectivity software to keep their programs going. Of course, this approach had its limitations; for example, most scientists no longer had access to their laboratories or experiments. But far from giving up and watching soap operas in their pajamas, they instead answered a new call to serve the nation. Within just a few weeks, the Lab’s considerable supercomputer resources and expert personnel were allocated to national COVID-19 research efforts, and a rush of new internal research programs were variously proposed, approved, and underway.

Read full story in Lab's 1663 magazine


Identifying existing drugs to speed up prevention, treatment of COVID-19

Posted: Wednesday, July 22 7:34 a.m.

Research targets how the coronavirus spike protein binds to its host cell receptor in the human body, aiding and abetting viral entry

LOS ALAMOS, N.M., July 22—By focusing on host proteins that help the SARS-CoV-2 virus enter cells in the body, a Los Alamos National Laboratory research team is supporting the effort to rapidly identify already-approved FDA drugs that could be used to treat people who have COVID-19. 

“The research aims to boost the growing repertoire of identified drug compounds that could be part of a comprehensive prevention and treatment plan for those infected with the SARS-CoV-2 virus that causes COVID-19, while vaccine development continues,” said Julian Chen, B-11, who is leading the project team with internal funding from the Laboratory Directed Research and Development program.

Viral infection requires host proteins to aid the virus in replicating, so it is important to understand these host factors as well. In the long run, Chen said, the team of computational biologists hopes to lay a foundation for efficiently and quickly addressing future pandemics.

Chen and his collaborators at Los Alamos have been studying how the coronavirus spike (S) protein binds to its host cell receptor in the human body, and how host proteins unwillingly aid and abet viral entry.

“In the short term, we hope to identify FDA-approved drugs that can be repurposed to treat COVID-19 cases,” Chen said. “There is of course an intensive effort towards FDA-approved drugs targeting the viral proteins. With new drug candidates in mind, we can engage with academic groups and biotechnology companies to further drug development efforts.”

With Chen, the Los Alamos team includes postdoc Jacob Miner and staff members Ramesh Jha, Jurgen Schmidt, Karissa Sanbonmatsu, and Chang-Shung Tung.

Funding: This work was supported by the Laboratory Directed Research and Development program at Los Alamos National Laboratory.



EpiGrid models disease spread for decision support

Posted: Friday, June 26 10:34 a.m.

Los Alamos, N.M., June 26— Since the outbreak of COVID-19, scientists at Los Alamos National Laboratory have been providing critical decision support to government agencies such as the Defense Threat Reduction Agency (DTRA). Their work enables military planners to simulate progression patterns and develop better ways to guide and support policy decisions, as well as analyze alternatives when implementing a layered defense in near-real-time.

EpiGrid is the epidemiological tool at the heart of this effort. Developed to model the spread of infectious biological agents with different modes of disease transmission (i.e. close-contact/droplet, water-borne and vector-borne diseases), EpiGrid “tracks the range of disease severity in the population so that the timeliness of interventions and mitigations can be accurately modeled,” according to project lead, Paul Fenimore.

Within the EpiGrid framework, the population of any geographical area is partitioned by disease progression so that the range of disease-states—from susceptible, through exposed, various states of severity, and then recovery or death—is captured in the model. The population numbers for hospitalized, treated, or deceased individuals are predicted over the course of an outbreak. Starting with initial disease cases in particular geographic locales, individuals within the population enter the disease progression over the course of the outbreak based on the force of infection.

Mitigations such as vaccination and hospitalization can be varied over time and across the geography of the outbreak, and thus capture the degree to which interventions either slow or divert the flow of individuals through the different disease states.

In short, EpiGrid allows analysts to model the force of infection and the spread of a disease through populations and provide robust decision support during the course of a disease outbreak.

This work is funded by DTRA CB10621.


Computer model forecasts COVID-19 confirmed cases and deaths

Posted: Thursday, June 25 3:04 p.m.

Los Alamos National Laboratory has developed a computer model that forecasts the number of future confirmed COVID-19 cases and deaths around the globe. It is a featured model on the Centers for Disease Control’s website and has been recognized as one of the most accurate COVID-19 forecasting models. It is also providing decision-making support at the state and national level.

Using data from the Johns Hopkins University (JHU) Coronavirus Resource Center dashboard, this statistical model generates a forecast for confirmed cases and deaths for any U.S. state that has at least one datapoint, and any country with at least 100 confirmed COVID-19 cases and 20 deaths. “When we initially started, many states had fewer than 100 confirmed cases,” said Dave Osthus, a statistician and member of the COVID-19 modeling team. “As a result, the model was quite unstable. As the case total rose, that data fed the model, which improved its accuracy.”

The Los Alamos model produces forecasts, not projections—meaning it does not explicitly model the effects of interventions or other “what-if” scenarios. “We distinguish forecasts as attempts to predict what will happen, versus projections as attempts to describe what would happen given certain hypotheses,” said Osthus. The model does, however, assume that interventions will be implemented and continue to be upheld in the future, resulting in an overall decrease in the growth rate of COVID-19. The model also allows for the possibility that the transmission rate may go up.

A strength of this model is that it adapts quickly to new data. So, for example, if a state implements a mitigation strategy such as a stay-at-home order that results in fewer confirmed cases, the model quickly changes course in accordance with this new information.

The model had already been test driven, so to speak, given that it is based on the Dante flu forecasting model that Osthus developed, which won the CDC’s FluSight Challenge last year. 

While having an existing, proven forecasting model already in place was helpful in getting the COVID-19 model up and running quickly, the lack of historical data for the novel coronavirus made it a challenge. “We have about two decades worth of flu data, so Dante had a lot of historical information to ‘learn’ from,” said Osthus. “Since COVID-19 is a new virus, we had no historical data to feed into the model. That’s why, initially, when there were very few cases, the model was not very accurate. When you look at various states’ forecasts, you can see them growing more accurate as the number of confirmed cases grew.”

Another challenge with forecasting COVID-19 is factoring in the role human behavior plays in the spread of the disease. The measures that communities, states, and nations have taken to curb the COVID-19 outbreak far exceeds what is typically done for seasonal flu. “This makes forecasting particularly challenging, as human behavior is notoriously difficult to predict,” said Osthus. “It also gives all of us agency. The choices we make as individuals—to socially distance, to wear masks, to frequently wash our hands—these all play a meaningful role in driving the infection to lower and lower levels.”

The model forecasts are probabilistic, so there is a high degree of uncertainty in future trajectories, given the possibilities of changing intervention strategies, changing case definitions, and changing rates of testing. “Our model does not explicitly model these different possible futures, as that would be nearly impossible,” said Osthus. “Instead, the model integrates over those potential futures.”

The forecasts are updated each Monday and Thursday, incorporating the latest data into the model.


Department of Energy Announces COVID-19 Innovation Portal and Assistance Program

Posted: Thursday, June 4 12:32 p.m.

WASHINGTON, D.C. – The U.S. Department of Energy’s (DOE’s) Office of Technology Transitions has announced new resources for innovators to combat COVID-19 through its Lab Partnering Service (LPS) and the COVID-19 Technical Assistance Program (CTAP). Supported by DOE’s Office of Technology Transitions (OTT), these initiatives will allow America’s innovators to readily access vital resources and connect and partner with experts at DOE’s 17 National Laboratories in the fight against the virus.

“Home to the best energy and science R&D enterprise, the Department of Energy has mobilized its considerable resources to better understand and combat the threat presented by the coronavirus pandemic,” said Secretary of Energy Dan Brouillette. “These programs will help transition those resources into the hands of America’s motivated and talented innovation community. We are grateful to all of DOE’s 17 National Labs, who have stepped up to facilitate access to their researchers, intellectual property, and facilities during this trying time.”

Visitors to the LPS COVID-19 portal can connect quickly with experienced researchers, browse existing patents available for licensing, and get information about facilities that may be useful in their efforts to contribute to the fight against the pandemic. The LPS previously created similar portals around events specific to the commercial space industry and artificial intelligence, but this is the first time the platform has been used to streamline access in an emergency. 

CTAP will provide targeted funding to DOE’s National Lab system to assist non-DOE entities working to combat the coronavirus pandemic. CTAP gives National Lab researchers the ability to offer short-term, limited assistance to U.S.-based entities dealing with particularly challenging technical hurdles. CTAP applicants should engage directly with the National Laboratory of their choosing through the Lab Partnering ServiceTo learn more, contact OTT at ctap-ott@hq.doe.gov.

The Lab Partnering Service was launched in 2018 to serve as a single online access point for investors, innovators, and institutions to identify, locate, and obtain information from DOE’s National Laboratories. This unique tool provides industry with a more efficient way to harness technical expertise and intellectual property housed at DOE’s Labs. The LPS is managed by the Office of Technology Transitions, which serves as the central hub for DOE’s lab-to-market activities and policy.


New website supports genetic understanding of COVID-19  

Posted: Friday, May 1 11:30 a.m.

LOS ALAMOS, N.M., May 1—A new website to facilitate analysis and interpretation of SARS-CoV-2 genomic data is aimed at improving the global response to the COVID-19 pandemic by helping researchers to detect and identify the virus and to analyze its evolution and how mutations impact diagnostic assays.

The COVID-19 Genome Analytics site launched by the Los Alamos National Laboratory Bioscience Division comprises several tools, including a tailored bioinformatics workflow based on the fully open-source EDGE Bioinformatics platform developed at Los Alamos. This mini-version of EDGE consists of a user-friendly interface that accommodates multiple different types of raw genomic sequencing data from COVID-19 patient samples as input, such as data being generated by the CDC and public health labs around the world. If the virus is present within the sample, EDGE COVID-19 can generate a complete SARS-CoV-2 genome that is ready to be shared with public data repositories such as GenBank, the nation’s primary repository for genomic data.  

Currently, over 13,000 SARS-COV-2 genomes have been sequenced, and with every new sequence comes a more comprehensive understanding of the virus and its evolution. The COVID-19 Genome Analytics site not only facilitates the assembly and addition of more high-quality genomes, but it also helps scientists analyze how the virus is evolving and how these changes impact our ability to detect and identify the virus.

For instance, Los Alamos scientists are also computationally screening published diagnostic assays against the increasing number of SARS-CoV-2 sequences to determine the most reliable assays for diagnosis. This computational assay validation is also available on the COVID-19 Genome Analytics site, as well as information tracking both the growth in genomic data and in confirmed COVID-19 cases in the USA and around the globe.

Research was supported by the DOE Office of Science through the National Virtual Biotechnology Laboratory, a consortium of DOE national laboratories focused on response to COVID-19, with funding provided by the Coronavirus CARES Act.

Link to site: https://covid19.edgebioinformatics.org/#/home 



Meeting the COVID-19 challenge head on

Posted: Monday, April 27 7:45 a.m.
By Thom Mason for the Santa Fe New Mexican

The COVID-19 pandemic has dramatically changed all of our lives — from how we work, to how we teach our children, to how we grocery shop. As we yearn to return to normal, we’re also called on to do what we can to protect ourselves, our loved ones and our communities.

Los Alamos National Laboratory is no different. We have responsibilities to the nation and to the communities where we live, and we take them very seriously. As one of the largest employers in Northern New Mexico, we’re doing what we can to answer the call to use our vast scientific and technical resources to help fight this disease, and protect our employees and the communities we call home.

To slow the spread of the virus, we took early and aggressive measures to get as much of our workforce as possible offsite, working from home. More than 85 percent of the laboratory’s workforce is teleworking.

The remaining employees are onsite because they are needed to assure the safety and security of our facilities or to perform essential national security work. For those onsite, measures are in place to keep them as safe as possible following CDC guidelines.

These measures are also helping to contain the spread of the virus in the communities where they live. About 75 percent of our employees live in Los Alamos, Rio Arriba and Santa Fe counties — where transmission rates have been lower than elsewhere in the state.

We are also bringing to bear our expertise, technology and materials to help the state combat COVID-19. By harnessing our capabilities in computer modeling, laboratory testing, manufacturing and medical countermeasures, we’re playing a crucial role in our country’s pandemic response.

For example, the laboratory’s HIV team, which designed an experimental HIV vaccine now in human trials, is deploying its expertise in genetic databases and bioinformatics against COVID-19. Specifically, we are developing a T-cell response vaccine approach, tracking the origin of the pathogen and building a robust bioinformatics pipeline to track the virus’s evolution, all of which are necessary for developing an effective vaccine.

Los Alamos has also partnered with Sandia and other national laboratories to develop an integrated COVID-19 pandemic monitoring, modeling and analysis capability. The goal is to support decision-makers at the federal and state level, including New Mexico. This should help our government leaders make informed decisions about preparedness for our health care system. It will also provide us with a deeper understanding of the disease. More information can be found at cdc.gov/coronavirus/2019-ncov/covid-data/forecasting-us.html.

In addition to providing disease forecasts, we are also working hard on testing and manufacturing lifesaving ventilators. In fact, we are leading a Department of Energy-wide laboratory group on testing and participating in assessments of lab capabilities for near- and long-term testing requirements, both for public health and for the lab’s workforce. And we are evaluating the potential of advanced manufacturing, specifically 3D printing, to produce scarce medical equipment that is so badly needed.

Equally as important as all this scientific research and technological support is supporting the communities in which we live. Los Alamos employees and Triad National Security, the laboratory’s management and operations contractor, recently contributed more than $60,000 to the Food Depot to help serve hungry families during this difficult time.

And because the crisis continues to take a toll on the economy, we have redoubled efforts to work with community partners to develop our region’s workforce. Just last week, we — together with Santa Fe Community College — announced a new machinist training program to provide residents with the skills they need to get such jobs at the laboratory. This program, together with Northern New Mexico College’s radiation control technicians program and a new mechanical engineering program at UNM-LA, is part of our long-term commitment to create well-paying and secure jobs for New Mexicans — something that has always been a top priority for Northern New Mexico and will take on even greater importance in the coming months.

The laboratory is committed to helping our state and nation during this global crisis. Since World War II, we have demonstrated our ability to quickly and adeptly apply our scientific and technological capabilities to respond to national emergencies. This time is no exception. We are determined to meet this challenge head-on, while doing our part to keep our workforce and our communities safe.

Thom Mason is director of Los Alamos National Laboratory.


Lab leverages existing infrastructure to create new HPC system for COVID-19 research

Posted: Wednesday, April 29 10:25 a.m.

LOS ALAMOS, N.M., April 29, 2020—Los Alamos National Laboratory, partnering with Hewlett-Packard Enterprises, is building on existing infrastructure at Los Alamos to create a new high-performance computing system dedicated to COVID-19 researchers and applications.

“As part of its COVID-19 effort, the Laboratory is increasing its computational capabilities to support a variety of related research problems,” said Irene Qualters, Associate Laboratory Director for Simulation and Computation. “This is a unique opportunity to provide a broad range of researchers with the versatile, next-generation computing capabilities they need in the battle against COVID-19.”

As the Department of Energy continues to expand its efforts to fight COVID-19, the Laboratory is participating in a number of activities in concert with other DOE labs, federal and state agencies, universities, and industry partners.

The new HPC system will be a 500+ AMD Rome nodes or more than 64,000 cores occupying two HPE/Cray racks. It will be one of the most powerful machines that Los Alamos has dedicated to the COVID-19 High Performance Computing Consortium.

The system will align with Los Alamos’ and other DOE labs’ next generation machines, and will be made available on the Laboratory’s open network, which provides remote and local users with access to ultra-high-bandwidth connectivity.

By leveraging the space, power, cooling, hardware, networking infrastructure, systems management, and user support already available at Los Alamos, the new system will be quickly deployed and could be online before September.

The Laboratory has already dedicated a number of high performance computers to examine areas such as how artificial intelligence might apply in analyzing the spread of COVID-19, and in developing a path to a vaccine. Other important areas of study include optimizing the medical infrastructure to manage the anticipated number of patients and understanding the mitigating or correlating factors of COVID-19’s spread.

The research was supported by the DOE Office of Science through the National Virtual Biotechnology Laboratory, a consortium of DOE national laboratories focused on response to COVID-19, with funding provided by the Coronavirus CARES Act.



Los Alamos bringing broad experience to COVID-19 Supercomputing Consortium

Posted: Thursday, March 26 9:21 a.m.

Following Department of Energy leadership, Los Alamos is supporting the consortium by providing access to supercomputers and support for researchers.

“We have been working with Sandia National Laboratories and Lawrence Livermore National Laboratory, along with DOE Office of Science laboratories, to be ready to accommodate a variety of research problems at scale,” said Irene Qualters, Associate Laboratory Director for Simulation and Computation. “We are also working in areas where artificial intelligence might apply in analyzing the spread of COVID-19 and in developing a path to a vaccine. Other important areas of study include optimizing the medical infrastructure to manage the anticipated number of patients and understanding the mitigating or correlating factors of COVID-19’s spread.”

Read full Albuquerque Journal story:

Sandia, LANL help hunt for vaccine

By Scott Turner
Wednesday, March 25, 2020 at 9:38pm

ALBUQUERQUE, NM — Sandia National Laboratories and Los Alamos National Laboratory are playing roles in the search for a vaccine and other medications to halt the spread of COVID-19.

The two New Mexico facilities are part of a network of government and private laboratories providing computing resources and personnel to scientists involved in the hunt for a vaccine and treatments for coronavirus.

Their efforts could mean the difference in finding medications and vaccines in the next few weeks or months as opposed to years, Argonne National Laboratory Associate Director Rick Stevens said during a teleconference with representatives from the five national laboratories that are part of the effort.

“Our national laboratories house the top supercomputers in the country,” Department of Energy Under Secretary for Science Paul Dabbar said. Also involved in the effort are Lawrence Livermore and Oak Ridge national labs.

Although the labs are known more for their nuclear energy and nuclear weapons research, they’ve already been involved in the design of medications. Los Alamos has been involved with cancer research.

“This taps into an effort already underway in the industry and academia,” said Irene Qualters, Los Alamos associate director for simulation and computation.

The computing system being made available through the network will be able to process numbers of calculations related to bioinformatics, epidemiology and molecular modeling, Dabbar said.

“It will help scientists develop complex scientific questions about COVID-19 in hours or days,” he said.

But Qualters said providing computing space and data storage “was not enough.”

To that end, the labs will provide scientists and researchers who know how the systems work, Scott Collins of Sandia National Laboratories said.

He said both facilities and research talent would be made available.

The network of labs is part of the COVID-19 High Performance Computing Consortium launched by the Trump administration this week. The consortium also includes Amazon, IBM, Google, Microsoft, Hewlett Packard and NASA.

Researchers are invited to submit COVID-19-related proposals to the consortium, which will then be reviewed and matched with computing resources from one of the partner institutions, the DOE said.


HIV vaccine-research team shifts to SARS-CoV-2

Posted: Monday, April 20 6:45 a.m.

LOS ALAMOS, N.M., April 20, 2020—Building on previous work designing an experimental HIV vaccine being tested in two human vaccine efficacy trials, Los Alamos National Laboratory’s HIV team is now deploying its expertise in genetic databases and bioinformatics against the novel coronavirus SARS-CoV-2.

Three main thrusts are underway from the HIV team: developing a T-cell response vaccine approach, tracking the origin of the pathogen, and building a robust bioinformatics pipeline to track the virus’s evolution. While this work focuses on attacking the virus itself, other bioinformatics and modeling efforts across the lab aim at predicting disease spread to support decision making by government and health agencies.

Developing a T-cell response vaccine approach

Bette Korber, a computational biologist and the driving force behind the “mosaic” vaccine concept for HIV, together with fellow scientists Will Fischer and Sandrasegaram Gnanakaran, is shifting her attention from HIV, ebola, and influenza vaccines to developing a T-cell based vaccine design for the SARS CoV-2 coronavirus.

Traditional antibody vaccines are primarily intended to reduce rates of infection. Korber says they hope that vaccine-elicited T-cell responses could help ameliorate disease severity if people do get infected, and so this approach could be used to complement antibody-based vaccines. Korber and the HIV team members are in the Laboratory’s Theoretical Biology and Biophysics group.

Tracking the origin of the pathogen

Elena Giorgi, also of the Theoretical Biology and Biophysics group, recently published a pre-print paper on the origins of the virus,“Emergence of SARS-CoV-2 through Recombination and Strong Purifying Selection.”

“Our team demonstrated, by looking at the genetic sequence of the virus and comparing it to other known coronaviruses, that it originated from animals,” said Giorgi. “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.”

Coauthors are Xiaojun Li, Manukumar Honnayakanahalli Marichann, Brian Foley, Chuan Xiao, Xiang-peng Kong, Yue Chen, Bette Korber, Feng Gao, all of Los Alamos National Laboratory. The paper is on bioRxiv.org (doi: https://doi.org/10.1101/2020.03.20.000885).

Developing a robust bioinformatics pipeline

The LANL HIV database team led by Korber is now developing a real-time bioinformatics pipeline to track the evolution of the SARS Cov-2 spike protein, the target of the antibody-based vaccine approaches that are currently under development by many different groups worldwide. The implementation of this pipeline is being led by Will Fischer, Hyejin Yoon, and Werner Abfalterer.

The team is working to ensure that the evolving SARS Cov-2 variants that will be circulating when the vaccine is ready for delivery will remain sensitive to vaccine responses elicited using a spike protein based on the original strain that seeded the pandemic. As part of this effort, Gnanakaran will be modeling the molecular dynamics of the SARS Cov-2 spike protein and the sugars on its surface, to better understand the impact of the mutations that are beginning to accumulate in the circulating population.

They will also be adapting vaccine strategies they developed for HIV, which is a very diverse virus, to attempt to design vaccines that could work not only against the current pandemic virus, which is quite conserved, but also against highly diverse reservoir of coronaviruses that circulate in bats and other animals.

“One of the risks that we’ve recognized with this coronavirus is that there is an immense pool of other coronaviruses hiding in bats and pangolins and snakes and whatnot. We would like to come up with a strategy to protect us, not just against this particular strain, but maybe next year’s jump, too,” said Nick Hengartner, leader of the Theoretical Biology and Biophysics group.

Here's more information about previous LANL work in the HIV vaccine field.



RETRO Rx web tools aid public health organizations

Posted: Wednesday, April 8 3:33 p.m.

Los Alamos National Laboratory has years of experience developing tools that can now be applied to the battle against COVID-19, including the Rapid, Easy Tools for Responding to Outbreaks and Re-emergence Events (RETRO Rx), designed for disease forecasting and response.

RETRO Rx is actually two tools, Analytics for Investigation of Disease Outbreaks (AIDO), and Re-emerging Infectious Disease (RED) Alert. These tools put disease outbreak data into context to provide situational awareness and actionable information.

Read full story.


Outbreak analysis tool online at Los Alamos

Posted: Wednesday, April 8 2:21 p.m.

A Los Alamos project focused on situations such as the world now faces with COVID-19 is being put to the test. The web-based disease-outbreak tool is a quick analysis resource called AIDO (“I-do”) for Analytics for Investigation of Disease Outbreaks. The tool does not yet have a category for SARS-CoV2, but related coronavirus libraries (MERS and SARS) are included and can show the mitigation strategies found valuable for those diseases.

Read full Albuquerque Journal story. 


The COVID-19 Outbreak: Delivering Science and Technology to Protect Our Nation

Posted: Thursday, April 2 7:01 a.m.

Los Alamos National Laboratory is drawing on its rich history in the biological sciences to actively engage in the national effort to study, understand, and answer important questions about the COVID-19 outbreak.

In this video, Kirsten Taylor-McCabe, a biochemist and national defense and security program manager, and Nicolas Hengartner, group leader of the Theoretical Biology and Biophysics group at Los Alamos, discuss the Laboratory’s important contributions. Areas covered include disease detection and diagnostics, epidemic modeling, disease prediction and forecasting, decision support, data collection and integration, and medical countermeasures.

Fighting COVID-19 with computer modeling

Posted: Tuesday, March 31 11:15 a.m.

For at least the next three months, Los Alamos, Sandia, Argonne, and Oak Ridge national laboratories will collaborate to develop an integrated COVID-19 pandemic monitoring, modeling, and analysis capability.

"The work builds on existing spatial demography and human dynamics research, agent-based modeling systems, infrastructure-, and economic- and risk-modeling capabilities," said Kirsten Taylor-McCabe, a biochemist and National Defense and Security Program manager. "Integrating these components with scalable data and computing capabilities, the four laboratories will work together to rapidly develop a COVID-19 analysis framework and multiscale modeling system. They will also develop a scalable COVID-19 data collection process and integrated team that will respond to the near real-time needs of supporting U.S. policy makers."

The goal is to provide routine and frequent modeling and analysis deliverables to DOE and federal government leadership, and to revise the analysis and modeling goals on demand. This joint framework will answer questions about alternative options for interventions and preparedness for our healthcare system. It will also track the ongoing, deepening understanding of the disease and the risks to various demographic and age groups.

"In addition, the COVID-19 analysis framework will give U.S. government leadership improved situational awareness, offering improved insight into what is happening in different regions of the country, exploring how different areas and populations are responding and reacting to changing conditions and varied intervention strategies," Taylor-McCabe said.


Roles national labs in New Mexico have to help combat coronavirus

Posted: Thursday, March 26 7:32 a.m.

Read full KRQE news story and see video:

By Rachel Knapp
Posted:  Updated: 

ALBUQUERQUE, NM (KRQE)—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?

On MSNBC’s ‘The 11th Hour Show’ Monday night, Governor Lujan Grisham told a national audience that part of New Mexico’s success in processing hundreds of COVID-19 tests quickly is because of the equipment at the state lab and Tricore. She also gave credit to something New Mexico has that other states don’t.

“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.”

She’s referring to Sandia National Laboratories and Los Alamos National Laboratory, which are under the U.S. Department of Energy. KRQE News 13 asked the governor to clarify how the labs help in test processing but she declined an interview.

So we looked into what role the labs have in the fight against the coronavirus.

For Sandia, their supercomputers will help the government figure out how and where the government should put their resources.

“Where one should put test sites, where are we going to run out of medical supplies, doing those kind of predictions to help decision-makers how to best understand how to adapt and anticipate to mitigate the disease,” said Sandia National Labs Director of Computing Research, Scott Collis.

President Trump said they’ll also turn to LANL’s supercomputers to help make a vaccine.

“They’re going to be contributing a lot of different things but primarily computing resources to help researchers discover new treatments along with vaccines,” said President Trump.

That’s not all.

“Are looking at things like advanced manufacturing, how we could help make, rapidly make more masks for our medical professionals and other personal protective equipment,” said Collis.

There is still no explanation from the state for why New Mexico has the ability to process so many more tests than other states.


President Trump Announces New Effort to Unleash U.S. Supercomputing Resources to Fight COVID-19

Posted: Tuesday, March 24 7:32 p.m.

As part of the Department of Energy’s efforts to combat COVID-19, Los Alamos National Laboratory is making available to the broader research community its vast supercomputing capabilities,” said Laboratory Director Thom Mason. “This should accelerate the work of researchers studying the origins and development of COVID-19, as well help in the effort to develop urgently needed treatments and vaccines.

Read full DOE news release:

WASHINGTON, D.C.—President Donald J. Trump announced a new, unique public-private consortium, spearheaded by the White House Office of Science and Technology Policy (OSTP), the U.S. Department of Energy (DOE), and IBM, including government, industry, and academic leaders to unleash the power of America’s supercomputing resources to combat COVID-19.The launch of the COVID-19 High Performance Computing Consortium will provide COVID-19 researchers with access to the world’s most powerful high performance computing resources that can significantly advance the pace of scientific discovery in the fight to stop the virus.

Researchers are invited to submit COVID-19 related research proposals to the consortium via the online portal which will then be reviewed and matched with computing resources from one of the partner institutions. An expert panel of top scientists and computing researchers will work with proposers to quickly assess the public health benefit of the work and coordinate the allocation of the group’s powerful computing assets.

The COVID-19 High Performance Computing Consortium currently pools 16 systems that together offer over 330 petaflops of supercomputing capacity. Additional capacity, including cloud computing resources, will be added through present and future partners. The sophisticated computing systems available through this Consortium can process massive numbers of calculations related to bioinformatics, epidemiology, molecular modeling, and healthcare system response, helping scientists develop answers to complex scientific questions about COVID-19 in hours or days versus weeks or months.

“Under the Trump Administration, the United States has regained its position as the dominant global force in Supercomputing technology. The Department of Energy is home to the world’s fastest and most powerful supercomputers, and we are eager to partner with leaders across industry and the scientific community who will use our world class innovation and technology to combat COVID-19,” said U.S. Secretary of Energy Dan Brouillette.

“America is coming together to fight COVID-19, and that means unleashing the full capacity of our world-class supercomputers to rapidly advance scientific research for treatments and a vaccine. We thank the private sector and academic leaders who are joining the federal government as part of the Trump Administration’s whole-of-America response,” said Michael Kratsios, U.S. Chief Technology Officer.

“The Department of Energy’s National Labs have made profound advancements towards combatting COVID-19,” said DOE Under Secretary for Science Paul Dabbar. “By providing researchers access to world leading technology here in our own backyard, we take an additional leap towards ending this pandemic. We look forward to collaborating with scientists and researchers to bring an end to COVID-19.”

“DOE’s National Nuclear Security Administration is eagerly lending its world-class supercomputing resources to combat COVID-19 in collaboration with OSTP and other agencies,” said Lisa E. Gordon-Hagerty, DOE Under Secretary for Nuclear Security and NNSA Administrator. “NNSA supercomputers will be available, empowering researchers to understand the COVID-19 virus, develop treatments and vaccines, and ultimately bring an end to this pandemic.”

“Accelerating the process of discovery to unlock treatments and a cure for COVID-19 is of vital importance to us all. By bringing together the world's most advanced supercomputers and matching them with the best ideas and expertise, this consortium can drive real progress in this global fight. IBM is proud to have helped kick-start this important effort," said Dario Gil, Director of IBM Research.

Participants in this consortium will include:

Amazon Web Services
Google Cloud

Massachusetts Institute of Technology
Rensselaer Polytechnic Institute

U.S. Department of Energy National Laboratories
Argonne National Laboratory
Lawrence Livermore National Laboratory
Los Alamos National Laboratory
Oak Ridge National Laboratory
Sandia National Laboratories
Federal Agencies National Science Foundation