HPC Cloud Research on Lab Leak Hypothesis Published in Scientific Reports

By Oliver Peckham

July 12, 2021

When the pandemic began accelerating in spring 2020, the lab leak hypothesis – which suggests that COVID-19 may have emerged from a virology lab, rather than originating purely zoonotically – was broadly viewed as a fringe conspiracy theory. Over the past six months, however, that perception has changed, thanks in large part to revelations that a group of workers from the Wuhan Institute of Virology fell ill in early November 2019 and renewed credibility and attention from government officials, including President Biden. Now, HPC cloud-powered research delving into the origins of the pandemic – first reported by HPCwire in May – has been published in Scientific Reports.

The work, led by David Winkler (a professor at La Trobe University, Monash University and the University of Nottingham), sought to identify animal vectors that could have helped transfer the SARS-CoV-2 virus to humans. Beginning in early 2020, the research team used models of the SARS-CoV-2 spike protein and the ACE2 receptors of various host organisms to study how likely it was that the virus could infect those organisms and, in turn, infect a human. To conduct this research, they used a state-of-the-art protein docking package (HDOCK) and GROMACS, a molecular dynamics package, running on Oracle Cloud HPC resources.

After a series of simulations, they came to some surprising conclusions. “Surprisingly, we found that humans had the highest affinity,” Winkler said. “You would expect the virus – like the flu virus or a coronavirus – to adapt to its host over time and become more tightly bound, but this was a structure that we had from the very, very early part of the pandemic before the virus would have had time to adapt to a human host.”

Affinity (blue) and infectivity (orange) by species. Image courtesy of the researchers.

“Pangolins were a little bit lower,” he continued. “Bat was quite a long way down. That was where people considered the virus originated, and it needed to pass through an intermediate animal, which at this stage most likely to be a pangolin based on these calculations. But there are other things, like [the] snake, which was also considered a potential source of the coronavirus, and it was way, way down on the binding energy – so it seems very unlikely.”

“We didn’t really expect the human to come out on top,” he added. “Because we would have thought that if the virus had come from a bat, probably that would come out to be the top – possibly a pangolin. So based on this information, you can’t really exclude the possibility that the virus could have escaped from a lab. I’m not saying it did, but those calculations suggest that it could have come from a lab.”

When HPCwire first reported on Winkler’s research, it had not yet been published. Now, that’s changed: the research has been published in the June 2021 issue of Scientific Reports. The article, titled “In silico comparison of SARS-CoV-2 spike protein-ACE2 binding affinities across species and implications for virus origin,” was written by Sakshi Piplani, Puneet Kumar Singh, David Winkler and Nikolai Petrovsky. It can be accessed here.

To read HPCwire‘s original reporting on this research, click here.

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!

Why HPC Storage Matters More Now Than Ever: Analyst Q&A

September 17, 2021

With soaring data volumes and insatiable computing driving nearly every facet of economic, social and scientific progress, data storage is seizing the spotlight. Hyperion research analyst and noted storage expert Mark No Read more…

GigaIO Gets $14.7M in Series B Funding to Expand Its Composable Fabric Technology to Customers

September 16, 2021

Just before the COVID-19 pandemic began in March 2020, GigaIO introduced its Universal Composable Fabric technology, which allows enterprises to bring together any HPC and AI resources and integrate them with networking, Read more…

What’s New in HPC Research: Solar Power, ExaWorks, Optane & More

September 16, 2021

In this regular feature, HPCwire highlights newly published research in the high-performance computing community and related domains. From parallel programming to exascale to quantum computing, the details are here. Read more…

Cerebras Brings Its Wafer-Scale Engine AI System to the Cloud

September 16, 2021

Five months ago, when Cerebras Systems debuted its second-generation wafer-scale silicon system (CS-2), co-founder and CEO Andrew Feldman hinted of the company’s coming cloud plans, and now those plans have come to fruition. Today, Cerebras and Cirrascale Cloud Services are launching... Read more…

AI Hardware Summit: Panel on Memory Looks Forward

September 15, 2021

What will system memory look like in five years? Good question. While Monday's panel, Designing AI Super-Chips at the Speed of Memory, at the AI Hardware Summit, tackled several topics, the panelists also took a brief glimpse into the future. Unlike compute, storage and networking, which... Read more…

AWS Solution Channel

Supporting Climate Model Simulations to Accelerate Climate Science

The Amazon Sustainability Data Initiative (ASDI), AWS is donating cloud resources, technical support, and access to scalable infrastructure and fast networking providing high performance computing (HPC) solutions to support simulations of near-term climate using the National Center for Atmospheric Research (NCAR) Community Earth System Model Version 2 (CESM2) and its Whole Atmosphere Community Climate Model (WACCM). Read more…

ECMWF Opens Bologna Datacenter in Preparation for Atos Supercomputer

September 14, 2021

In January 2020, the European Centre for Medium-Range Weather Forecasts (ECMWF) – a juggernaut in the weather forecasting scene – signed a four-year, $89-million contract with European tech firm Atos to quintuple its supercomputing capacity. With the deal approaching the two-year mark, ECMWF... Read more…

Why HPC Storage Matters More Now Than Ever: Analyst Q&A

September 17, 2021

With soaring data volumes and insatiable computing driving nearly every facet of economic, social and scientific progress, data storage is seizing the spotlight Read more…

Cerebras Brings Its Wafer-Scale Engine AI System to the Cloud

September 16, 2021

Five months ago, when Cerebras Systems debuted its second-generation wafer-scale silicon system (CS-2), co-founder and CEO Andrew Feldman hinted of the company’s coming cloud plans, and now those plans have come to fruition. Today, Cerebras and Cirrascale Cloud Services are launching... Read more…

AI Hardware Summit: Panel on Memory Looks Forward

September 15, 2021

What will system memory look like in five years? Good question. While Monday's panel, Designing AI Super-Chips at the Speed of Memory, at the AI Hardware Summit, tackled several topics, the panelists also took a brief glimpse into the future. Unlike compute, storage and networking, which... Read more…

ECMWF Opens Bologna Datacenter in Preparation for Atos Supercomputer

September 14, 2021

In January 2020, the European Centre for Medium-Range Weather Forecasts (ECMWF) – a juggernaut in the weather forecasting scene – signed a four-year, $89-million contract with European tech firm Atos to quintuple its supercomputing capacity. With the deal approaching the two-year mark, ECMWF... Read more…

Quantum Computer Market Headed to $830M in 2024

September 13, 2021

What is one to make of the quantum computing market? Energized (lots of funding) but still chaotic and advancing in unpredictable ways (e.g. competing qubit tec Read more…

Amazon, NCAR, SilverLining Team for Unprecedented Cloud Climate Simulations

September 10, 2021

Earth’s climate is, to put it mildly, not in a good place. In the wake of a damning report from the Intergovernmental Panel on Climate Change (IPCC), scientis Read more…

After Roadblocks and Renewals, EuroHPC Targets a Bigger, Quantum Future

September 9, 2021

The EuroHPC Joint Undertaking (JU) was formalized in 2018, beginning a new era of European supercomputing that began to bear fruit this year with the launch of several of the first EuroHPC systems. The undertaking, however, has not been without its speed bumps, and the Union faces an uphill... Read more…

How Argonne Is Preparing for Exascale in 2022

September 8, 2021

Additional details came to light on Argonne National Laboratory’s preparation for the 2022 Aurora exascale-class supercomputer, during the HPC User Forum, held virtually this week on account of pandemic. Exascale Computing Project director Doug Kothe reviewed some of the 'early exascale hardware' at Argonne, Oak Ridge and NERSC (Perlmutter), while Ti Leggett, Deputy Project Director & Deputy Director... Read more…

Ahead of ‘Dojo,’ Tesla Reveals Its Massive Precursor Supercomputer

June 22, 2021

In spring 2019, Tesla made cryptic reference to a project called Dojo, a “super-powerful training computer” for video data processing. Then, in summer 2020, Tesla CEO Elon Musk tweeted: “Tesla is developing a [neural network] training computer called Dojo to process truly vast amounts of video data. It’s a beast! … A truly useful exaflop at de facto FP32.” Read more…

Berkeley Lab Debuts Perlmutter, World’s Fastest AI Supercomputer

May 27, 2021

A ribbon-cutting ceremony held virtually at Berkeley Lab's National Energy Research Scientific Computing Center (NERSC) today marked the official launch of Perlmutter – aka NERSC-9 – the GPU-accelerated supercomputer built by HPE in partnership with Nvidia and AMD. Read more…

Google Launches TPU v4 AI Chips

May 20, 2021

Google CEO Sundar Pichai spoke for only one minute and 42 seconds about the company’s latest TPU v4 Tensor Processing Units during his keynote at the Google I Read more…

Esperanto, Silicon in Hand, Champions the Efficiency of Its 1,092-Core RISC-V Chip

August 27, 2021

Esperanto Technologies made waves last December when it announced ET-SoC-1, a new RISC-V-based chip aimed at machine learning that packed nearly 1,100 cores onto a package small enough to fit six times over on a single PCIe card. Now, Esperanto is back, silicon in-hand and taking aim... Read more…

Enter Dojo: Tesla Reveals Design for Modular Supercomputer & D1 Chip

August 20, 2021

Two months ago, Tesla revealed a massive GPU cluster that it said was “roughly the number five supercomputer in the world,” and which was just a precursor to Tesla’s real supercomputing moonshot: the long-rumored, little-detailed Dojo system. “We’ve been scaling our neural network training compute dramatically over the last few years,” said Milan Kovac, Tesla’s director of autopilot engineering. Read more…

CentOS Replacement Rocky Linux Is Now in GA and Under Independent Control

June 21, 2021

The Rocky Enterprise Software Foundation (RESF) is announcing the general availability of Rocky Linux, release 8.4, designed as a drop-in replacement for the soon-to-be discontinued CentOS. The GA release is launching six-and-a-half months after Red Hat deprecated its support for the widely popular, free CentOS server operating system. The Rocky Linux development effort... Read more…

Intel Completes LLVM Adoption; Will End Updates to Classic C/C++ Compilers in Future

August 10, 2021

Intel reported in a blog this week that its adoption of the open source LLVM architecture for Intel’s C/C++ compiler is complete. The transition is part of In Read more…

Iran Gains HPC Capabilities with Launch of ‘Simorgh’ Supercomputer

May 18, 2021

Iran is said to be developing domestic supercomputing technology to advance the processing of scientific, economic, political and military data, and to strengthen the nation’s position in the age of AI and big data. On Sunday, Iran unveiled the Simorgh supercomputer, which will deliver.... Read more…

Leading Solution Providers

Contributors

AMD-Xilinx Deal Gains UK, EU Approvals — China’s Decision Still Pending

July 1, 2021

AMD’s planned acquisition of FPGA maker Xilinx is now in the hands of Chinese regulators after needed antitrust approvals for the $35 billion deal were receiv Read more…

Hot Chips: Here Come the DPUs and IPUs from Arm, Nvidia and Intel

August 25, 2021

The emergence of data processing units (DPU) and infrastructure processing units (IPU) as potentially important pieces in cloud and datacenter architectures was 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…

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…

HPE Wins $2B GreenLake HPC-as-a-Service Deal with NSA

September 1, 2021

In the heated, oft-contentious, government IT space, HPE has won a massive $2 billion contract to provide HPC and AI services to the United States’ National Security Agency (NSA). Following on the heels of the now-canceled $10 billion JEDI contract (reissued as JWCC) and a $10 billion... 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…

Quantum Roundup: IBM, Rigetti, Phasecraft, Oxford QC, China, and More

July 13, 2021

IBM yesterday announced a proof for a quantum ML algorithm. A week ago, it unveiled a new topology for its quantum processors. Last Friday, the Technical Univer Read more…

Frontier to Meet 20MW Exascale Power Target Set by DARPA in 2008

July 14, 2021

After more than a decade of planning, the United States’ first exascale computer, Frontier, is set to arrive at Oak Ridge National Laboratory (ORNL) later this year. Crossing this “1,000x” horizon required overcoming four major challenges: power demand, reliability, extreme parallelism and data movement. Read more…

  • arrow
  • Click Here for More Headlines
  • arrow
HPCwire