LANL Researchers Study HIV Virus Through Computer Modeling

November 19, 2013

LOS ALAMOS, N.M., Nov. 19 — Researchers at Los Alamos National Laboratory are investigating the complex relationships between the spread of the HIV virus in a population (epidemiology) and the actual, rapid evolution of the virus (phylogenetics) within each patient’s body.

“We have developed novel ways of estimating epidemics dynamics such as who infected whom, and the true population incidence of infection versus mere diagnoses dates,” said Thomas Leitner, principal investigator. “Obviously, knowledge about these things is important for public health monitoring, decision making and intervention campaigns, and further to forensic investigations.”

The team models the uninfected population using traditional differential equations on the computer; this is done for computational speed, because an agent-based component is much more demanding. Once a person is infected, he/she becomes an “agent” in computer modeling terms, and the model starts following their behavior individually, as well as the viral HIV evolution within the person.

Agent-based Modeling Clarifies Infection History

This new modeling approach distinguishes between susceptible and infected individuals to capture the full infection history, including contact tracing data for infected individuals. The uninfected individuals are modeled at a population level and stratified by transmission risk and social group. The social network in this model forms – and can change – during the simulation. Thus, the model is much more realistic than traditional models.

The advantage of this epidemiological model, Leitner said, is that “it allows us to simulate many possible outcomes of epidemics with known parameters of human interactions, where social networks form as part of the agent interactions. It is a flexible system that has the ability to describe realistic human populations.”

Within a National Institutes of Health-supported project “Reconstructing HIV Epidemics from HIV Phylogenetics,” the team has published 10 papers describing new mathematical models and results from real data addressing these issues. Most recently, they published a Nature correspondence on the limitations of HIV forensics and the need for better standards.

Who Infected Whom

A key question is on the fundamental limitations to the inference of who infected whom, based on a concept known as the pre-transmission interval (which this group first described back in 1999). Another publication, published in Epidemics, developed a new hybrid model to simulate and analyze the spread of HIV or other pathogens spread in a human population. The work also appeared in PLoS-ONE Public Library of Science online publication.

As an example, the team modeled a Latvian HIV-1 epidemic, and they showed that injecting drug users fueled the heterosexual population, thereby sustaining the overall epidemic. The researchers are now expanding this hybrid model to also include HIV genetic evolution, which occurs in every infected individual.

The researchers have shown that in fast HIV epidemics – such as among individuals injecting themselves with drugs – HIV viral evolution is slow, resulting in little diversification at the population level. Meanwhile, slower-spreading epidemics display more HIV evolution over the same amount of time.

New Field of Phylodynamics Evolves

Understanding HIV’s genetic evolution will soon allow investigations of how accurately researchers can reconstruct different epidemiological scenarios using pathogen genetic materials, an important and growing field called phylodynamics.

The team also has developed a new mathematical model that facilitates estimation of when a person was infected with HIV based on a previously used biomarker (BED IgG).

“This is important because most HIV infected persons are not discovered shortly after infection rather, they are often discovered long after, often years after infection, said Leitner. “Thus, to estimate true incidence, that is when infections actually occurred, cannot be done based on diagnosis dates.”

Using Swedish surveillance data, the team has shown that the common assumption that infection occurred on average half way between last negative test and first positive test, is wrong. Instead, the actual infection is strongly skewed towards the first positive sample.

This finding should have large impact on epidemiological models used worldwide by public health organizations, Leitner says. “Currently, we have further developed this model to also correct for unknown cases, such as infected people not yet discovered but who contribute to new infections and thereby the true incidence of the disease.”

The Team Behind the Insights

Researchers include Frederik Graw, Thomas Leitner, Ruy M. Ribeiro, and Helena Skar (Los Alamos National Laboratory) and Jan Albert (Karolinska Institute and Karolinska University Hospital). The National Institutes of Health funded the research.

About Los Alamos National Laboratory (www.lanl.gov)

Los Alamos National Laboratory, a multidisciplinary research institution engaged in strategic science on behalf of national security, is operated by Los Alamos National Security, LLC, a team composed of Bechtel National, the University of California, The Babcock & Wilcox Company, and URS Corporation for the Department of Energy’s National Nuclear Security Administration.

—–

Source: Los Alamos National Laboratory

Subscribe to HPCwire's Weekly Update!

Be the most informed person in the room! Stay ahead of the tech trends with industy updates delivered to you every week!

Q&A with Altair CEO James Scapa, an HPCwire Person to Watch in 2021

May 14, 2021

Chairman, CEO and co-founder of Altair James R. Scapa closed several acquisitions for the company in 2020, including the purchase and integration of Univa and Ellexus. Scapa founded Altair more than 35 years ago with two Read more…

HLRS HPC Helps to Model Muscle Movements

May 13, 2021

The growing scale of HPC is allowing simulation of more and more complex systems at greater detail than ever before, particularly in the biological research spheres. Now, researchers at the University of Stuttgart are le Read more…

Behind the Met Office’s Procurement of a Billion-Dollar Microsoft System

May 13, 2021

The UK’s national weather service, the Met Office, caused shockwaves of curiosity a few weeks ago when it formally announced that its forthcoming billion-dollar supercomputer – expected to be the most powerful weather and climate-focused supercomputer in the world when it launches in 2022... Read more…

AMD, GlobalFoundries Commit to $1.6 Billion Wafer Supply Deal

May 13, 2021

AMD plans to purchase $1.6 billion worth of wafers from GlobalFoundries in the 2022 to 2024 timeframe, the chipmaker revealed today (May 13) in an SEC filing. In the face of global semiconductor shortages and record-high demand, AMD is renegotiating its Wafer Supply Agreement and bumping up capacity. Read more…

Hyperion Offers Snapshot of Quantum Computing Market

May 13, 2021

The nascent quantum computer (QC) market will grow 27 percent annually (CAGR) reaching $830 million in 2024 according to an update provided today by analyst firm Hyperion Research at the HPC User Forum being held this we Read more…

AWS Solution Channel

Numerical weather prediction on AWS Graviton2

The Weather Research and Forecasting (WRF) model is a numerical weather prediction (NWP) system designed to serve both atmospheric research and operational forecasting needs. Read more…

Hyperion: HPC Server Market Ekes 1 Percent Gain in 2020, Storage Poised for ‘Tipping Point’

May 12, 2021

The HPC User Forum meeting taking place virtually this week (May 11-13) kicked off with Hyperion Research’s market update, covering the 2020 period. Although the HPC server market had been facing a 6.7 percent COVID-re Read more…

Behind the Met Office’s Procurement of a Billion-Dollar Microsoft System

May 13, 2021

The UK’s national weather service, the Met Office, caused shockwaves of curiosity a few weeks ago when it formally announced that its forthcoming billion-dollar supercomputer – expected to be the most powerful weather and climate-focused supercomputer in the world when it launches in 2022... Read more…

AMD, GlobalFoundries Commit to $1.6 Billion Wafer Supply Deal

May 13, 2021

AMD plans to purchase $1.6 billion worth of wafers from GlobalFoundries in the 2022 to 2024 timeframe, the chipmaker revealed today (May 13) in an SEC filing. In the face of global semiconductor shortages and record-high demand, AMD is renegotiating its Wafer Supply Agreement and bumping up capacity. Read more…

Hyperion Offers Snapshot of Quantum Computing Market

May 13, 2021

The nascent quantum computer (QC) market will grow 27 percent annually (CAGR) reaching $830 million in 2024 according to an update provided today by analyst fir Read more…

Hyperion: HPC Server Market Ekes 1 Percent Gain in 2020, Storage Poised for ‘Tipping Point’

May 12, 2021

The HPC User Forum meeting taking place virtually this week (May 11-13) kicked off with Hyperion Research’s market update, covering the 2020 period. Although Read more…

IBM Debuts Qiskit Runtime for Quantum Computing; Reports Dramatic Speed-up

May 11, 2021

In conjunction with its virtual Think event, IBM today introduced an enhanced Qiskit Runtime Software for quantum computing, which it says demonstrated 120x spe Read more…

AMD Chipmaker TSMC to Use AMD Chips for Chipmaking

May 8, 2021

TSMC has tapped AMD to support its major manufacturing and R&D workloads. AMD will provide its Epyc Rome 7702P CPUs – with 64 cores operating at a base cl Read more…

Fast Pass Through (Some of) the Quantum Landscape with ORNL’s Raphael Pooser

May 7, 2021

In a rather remarkable way, and despite the frequent hype, the behind-the-scenes work of developing quantum computing has dramatically accelerated in the past f Read more…

IBM Research Debuts 2nm Test Chip with 50 Billion Transistors

May 6, 2021

IBM Research today announced the successful prototyping of the world's first 2 nanometer chip, fabricated with silicon nanosheet technology on a standard 300mm Read more…

AMD Chipmaker TSMC to Use AMD Chips for Chipmaking

May 8, 2021

TSMC has tapped AMD to support its major manufacturing and R&D workloads. AMD will provide its Epyc Rome 7702P CPUs – with 64 cores operating at a base cl Read more…

Intel Launches 10nm ‘Ice Lake’ Datacenter CPU with Up to 40 Cores

April 6, 2021

The wait is over. Today Intel officially launched its 10nm datacenter CPU, the third-generation Intel Xeon Scalable processor, codenamed Ice Lake. With up to 40 Read more…

Julia Update: Adoption Keeps Climbing; Is It a Python Challenger?

January 13, 2021

The rapid adoption of Julia, the open source, high level programing language with roots at MIT, shows no sign of slowing according to data from Julialang.org. I Read more…

CERN Is Betting Big on Exascale

April 1, 2021

The European Organization for Nuclear Research (CERN) involves 23 countries, 15,000 researchers, billions of dollars a year, and the biggest machine in the worl Read more…

HPE Launches Storage Line Loaded with IBM’s Spectrum Scale File System

April 6, 2021

HPE today launched a new family of storage solutions bundled with IBM’s Spectrum Scale Erasure Code Edition parallel file system (description below) and featu Read more…

10nm, 7nm, 5nm…. Should the Chip Nanometer Metric Be Replaced?

June 1, 2020

The biggest cool factor in server chips is the nanometer. AMD beating Intel to a CPU built on a 7nm process node* – with 5nm and 3nm on the way – has been i Read more…

Saudi Aramco Unveils Dammam 7, Its New Top Ten Supercomputer

January 21, 2021

By revenue, oil and gas giant Saudi Aramco is one of the largest companies in the world, and it has historically employed commensurate amounts of supercomputing Read more…

Quantum Computer Start-up IonQ Plans IPO via SPAC

March 8, 2021

IonQ, a Maryland-based quantum computing start-up working with ion trap technology, plans to go public via a Special Purpose Acquisition Company (SPAC) merger a Read more…

Leading Solution Providers

Contributors

AMD Launches Epyc ‘Milan’ with 19 SKUs for HPC, Enterprise and Hyperscale

March 15, 2021

At a virtual launch event held today (Monday), AMD revealed its third-generation Epyc “Milan” CPU lineup: a set of 19 SKUs -- including the flagship 64-core, 280-watt 7763 part --  aimed at HPC, enterprise and cloud workloads. Notably, the third-gen Epyc Milan chips achieve 19 percent... Read more…

Can Deep Learning Replace Numerical Weather Prediction?

March 3, 2021

Numerical weather prediction (NWP) is a mainstay of supercomputing. Some of the first applications of the first supercomputers dealt with climate modeling, and Read more…

Livermore’s El Capitan Supercomputer to Debut HPE ‘Rabbit’ Near Node Local Storage

February 18, 2021

A near node local storage innovation called Rabbit factored heavily into Lawrence Livermore National Laboratory’s decision to select Cray’s proposal for its CORAL-2 machine, the lab’s first exascale-class supercomputer, El Capitan. Details of this new storage technology were revealed... Read more…

African Supercomputing Center Inaugurates ‘Toubkal,’ Most Powerful Supercomputer on the Continent

February 25, 2021

Historically, Africa hasn’t exactly been synonymous with supercomputing. There are only a handful of supercomputers on the continent, with few ranking on the Read more…

GTC21: Nvidia Launches cuQuantum; Dips a Toe in Quantum Computing

April 13, 2021

Yesterday Nvidia officially dipped a toe into quantum computing with the launch of cuQuantum SDK, a development platform for simulating quantum circuits on GPU-accelerated systems. As Nvidia CEO Jensen Huang emphasized in his keynote, Nvidia doesn’t plan to build... Read more…

New Deep Learning Algorithm Solves Rubik’s Cube

July 25, 2018

Solving (and attempting to solve) Rubik’s Cube has delighted millions of puzzle lovers since 1974 when the cube was invented by Hungarian sculptor and archite Read more…

The History of Supercomputing vs. COVID-19

March 9, 2021

The COVID-19 pandemic poses a greater challenge to the high-performance computing community than any before. HPCwire's coverage of the supercomputing response t Read more…

Microsoft to Provide World’s Most Powerful Weather & Climate Supercomputer for UK’s Met Office

April 22, 2021

More than 14 months ago, the UK government announced plans to invest £1.2 billion ($1.56 billion) into weather and climate supercomputing, including procuremen Read more…

  • arrow
  • Click Here for More Headlines
  • arrow
HPCwire