Center for Viral Systems Biology

What Center for Viral Systems Biology does

Center for Viral Systems Biology (CViSB) is a multi-institutional academic research consortium founded in 2018 and led by Scripps Research under the direction of Kristian Andersen, with funding from the NIH National Institute of Allergy and Infectious Diseases (NIAID, Award U19AI135995). The consortium integrates Scripps Research, Tulane University, MIT, UCLA, the Ragon Institute of MGH/MIT/Harvard, Kenema Government Hospital, and the Sierra Leone Ministry of Health to study the genetic, immunological, and physiological factors that determine outcomes from viral infections, with primary focus on Ebola virus, Lassa virus, and SARS-CoV-2.

CViSB's core offerings center on the CViSB Data Portal (compiling data on 7,000+ Ebola patients, 6,500+ Lassa patients, 5,000+ COVID-19 patients, plus thousands of viral sequences, serology samples, and HLA sequences) and an integrated suite of open-source bioinformatics tools, including iVar for viral amplicon sequencing, Freyja for SARS-CoV-2 lineage abundance estimation in mixed samples such as wastewater, Bjorn for parallelized mutation counting, and Outbreak.info, a public-facing variant tracking platform adopted by the CDC and FDA. The technology stack extends to BEAST/BEAGLE for phylogenetic analysis and Clonify, AbStar, and AbUtils for antibody repertoire analysis, with newer AI/ML capabilities spanning ESM2, DeBERTa, LLMs, and autoencoders.

CViSB operates as a non-profit, grant-funded research consortium rather than a commercial entity. All data and software tools are released openly without restrictions, and there are no commercial products, licensing fees, or paid services. The customer base comprises academic researchers studying viral systems biology and clinical/public health entities (Kenema Government Hospital, Sierra Leone Ministry of Health) supporting field operations. Go-to-market is community-led through scientific publications, open-source software distribution, conferences, training programs, and internships, with adoption among public health agencies (CDC, FDA) serving as the primary form of validation rather than revenue.

Name

Center for Viral Systems Biology

Legal name

Center for Viral Systems Biology

Website

https://cvisb.org

Company type

Private

Founded year

2018

Operating status

Operating

Headcount range

11–50 employees

Short description

CViSB is a multi-institutional research consortium founded in 2018 that uses systems biology to study Ebola, Lassa, and COVID-19 infections. It serves academic researchers and public health agencies through open-access data portals and widely-adopted bioinformatics tools.

Ownership category

akta.pro rank

Product category

Bioinformatics and Genomic Surveillance Software

NAICS

Research and Development in Biotechnology (except Nanobiotechnology) (541714), Medical Laboratories (621511)

SIC

Services-Medical Laboratories (8071), Services-Prepackaged Software (7372)

akta.pro primary industry

Digital Epidemiology & Event-Based Surveillance (media/mobility) (HLAJABAJ)

akta.pro secondary industry

Microbiology & Infectious Disease Diagnostics (culture, rapid antigen, syndromic panels) (HLAAALAC)

Keywords

• Viral systems biology
• Bioinformatics software tools
• Genomic surveillance platforms
• Infectious disease research
• Open science data portals

Headquarters

HQ city

La Jolla

HQ country

United States

HQ region

North America

Offices6 records

Markets served

GTM type

B2B

Offering type

Software

Cost components

Personnel, Technology or R&D, Operations, Infrastructure

Revenue model

1. NIH/NIAID Research Grant: Primary funding from National Institutes of Health National Institute of Allergy and Infectious Diseases (NIAID) awarded to Scripps Research-led Center for Viral Systems Biology. Initial grant awarded in 2018, renewed for up to $12.8M over 5 years ($2.5M annually). Also received $1.3M supplement for SARS-CoV-2 research collaboration with Johns Hopkins University.

Go-to-market motion2 records

Distribution channels4 records

Marketing channels6 records

Core offering

The Center for Viral Systems Biology (CViSB) is a multi-institutional research consortium that conducts systems biology research on viral infections (Ebola, Lassa, SARS-CoV-2) and distributes open-source bioinformatics tools (iVar, Freyja, Bjorn, Outbreak.info) along with a public data portal containing patient and viral sequence data for the infectious disease research community.

Product overview

CViSB is a research consortium focused on understanding viral disease outcomes through systems biology approaches. The core offering is the CViSB Data Portal, which provides centralized access to patient and viral sequence data for Lassa fever, Ebola, and COVID-19 research. The product portfolio includes specialized bioinformatics tools: iVar for viral amplicon-based sequencing analysis; Freyja for SARS-CoV-2 lineage abundance estimation from wastewater; Bjorn for mutation counting from viral genomes; and Outbreak.info as a public-facing web resource for COVID-19 variant tracking. Additional tools include BEAST/RBeast for Bayesian phylogenetic analysis, BEAGLE for high-performance phylogenetic computations, Tracer for MCMC trace analysis, and antibody analysis tools (Clonify, AbStar, AbUtils). VIC Explorer and VIC Network provide specialized visualization of Ebola antibody data. These tools work together as an integrated ecosystem for viral genomics and systems immunology research, with many tools distributed via Docker containers and available through the outbreak.info API.

Differentiator

Problem solved

Functional benefit

Products and services

• CViSB Data Portal A collaborative data platform that compiles Ebola, Lassa fever, and COVID-19 patient data in one easy-to-access site for the global infectious disease research community, including data from Kenema Government Hospital in Sierra Leone and partners in Nigeria.
• iVar A computational package for viral amplicon-based sequencing with functions for trimming primers and low-quality bases, consensus calling, variant calling (iSNVs and insertions/deletions), and identifying mismatches to primer sequences. Used by CDC and FDA for viral surveillance.
• Freyja A tool to estimate relative abundance of SARS-CoV-2 lineages from sequencing of mixed-lineage virus samples like wastewater. Uses SNV frequency estimation and depth-weighted demixing using constrained least absolute deviation regression.
• Bjorn A pipeline to count mutations from given sets of genomes in a parallelized manner. Used by outbreak.info to count substitutions and deletions in all SARS-CoV-2 genomes available on GISAID.
• Outbreak.info An online resource that tracks SARS-CoV-2 variants using sequencing data repositories, providing dashboards for daily situation reports, a standardized searchable platform for COVID-19 resources, and genomic reports for scalable surveillance of SARS-CoV-2 variants and mutations.
• BEAST A cross-platform program for Bayesian analysis of molecular sequences using MCMC (Markov Chain Monte Carlo), used for reconstructing rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models.
• BEAGLE A high-performance library that performs core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages, utilizing GPUs for parallel processing of phylogenetic likelihood evaluations.
• Clonify A software package for unseeded lineage assignment on very large sets of antibody sequences, enabling comprehensive study of antibody clonal lineages for understanding humoral response to infection and immunization.
• AbStar A software package for VDJ assignments and primary annotation of antibody and TCR sequencing data, scalable from a single sequence to billions of sequences and conforming with AIRR data formatting standards.
• AbUtils A programming package providing utilities for interactive sequence processing, analysis, and visualization of BCR and TCR sequencing data, conforming with AIRR data formatting standards.
• systemsseRology A collection of functions used to analyse multivariate systems serology data for characterizing humoral immune responses.
• VIC Explorer A data explorer application for browsing and analyzing Ebola antibody data generated from the VIC (Viral Hemorrhagic Fever Immunotherapeutics Consortium) consortium.
• VIC Network A network analysis application to investigate interactions between data in the Ebola antibody dataset generated from the VIC consortium.

Quantifiable outcome

• Tools like iVar, Freyja, and Outbreak.info are used by CDC and FDA for viral surveillance
• +1 more outcomes

Named customers2 records

Segments2 records

Ideal customer profiles3 records

Technology focussed Yes

API detail

Has API

Yes

API docs

API detail

Core technology

AI maturity

App detail

Integration5 records

AI capability13 records

Feature9 records

Partnerships

Eleven partnerships are on record, tiered major and core.

• GISAIDmajorTechnology or Integration · 1 January 2022Collaboration with GISAID, a global data science initiative facilitating public access to SARS-CoV-2 genomic data. CViSB developed an API enabling access to all processed data on Outbreak.info for tracking global SARS-CoV-2 variant evolution.
• Johns Hopkins UniversitymajorStrategic or Co-development Partner · 1 January 2020Collaboration with Lauren Gardner at Johns Hopkins University funded through $1.3M grant supplement. CViSB data scientists design computational models and visualization software for analyzing SARS-CoV-2 transmission.
• Scripps ResearchcoreStrategic or Co-development Partner · 1 January 2018CViSB is led by Scripps Research as the primary institution. Kristian Andersen serves as Director & Principal Investigator at Scripps Research. Bryan Briney leads the Technology Core from Scripps Research. The center is funded through NIH NIAID award to Scripps Research.
• Tulane UniversitycoreStrategic or Co-development Partner · 1 January 2018Robert Garry serves as Co-Director from Tulane. John Schieffelin serves as Clinical Director from Tulane. Tulane researchers lead Project 1 investigating host responses to Ebola and Lassa viruses and oversee clinical operations in Sierra Leone.
• Massachusetts Institute of Technology (MIT)coreStrategic or Co-development Partner · 1 January 2018Douglas Lauffenburger leads the Modeling Core from MIT. His lab develops machine learning methods for analyzing longitudinal multivariate datasets produced by CViSB.
• University of California, Los Angeles (UCLA)coreStrategic or Co-development Partner · 1 January 2018Marc Suchard co-leads the Modeling Core from UCLA. He develops statistical tools for large-scale data analysis and oversees CViSB analyses.
• Ragon Institute of MGH, MIT, and HarvardcoreStrategic or Co-development Partner · 1 January 2018Ryan McNamara directs the Systems Serology Laboratory at the Ragon Institute and co-leads Project 1. His research focuses on molecular aspects of host-virus interactions for SARS-CoV-2, Lassa, and Ebola.
• Kenema Government Hospital (KGH)coreStrategic or Co-development Partner · 1 January 2018Long-term collaborator and primary clinical site. KGH's Lassa Fever Ward was at the center of the 2014-2016 West African Ebola outbreak. Donald Grant serves as Chief Physician overseeing patient management. The hospital provides essential data for the CViSB data portal.
• Sierra Leone Ministry of Health and SanitationcoreStrategic or Co-development Partner · 1 January 2018Government health authority working closely with CViSB and Kenema Government Hospital for infectious disease surveillance and research operations in Sierra Leone.
• Viral Hemorrhagic Fever Consortium (VHFC)coreStrategic or Co-development Partner · 1 January 2018Consortium partner developing countermeasures including diagnostics, immunotherapeutics, and vaccines against Lassa virus, Ebola and Marburg viruses, and other high consequence pathogens. Based at Tulane University.
• African Center of Excellence for Genomics of Infectious Diseases (ACEGID)majorStrategic or Co-development Partner · 1 January 2018Research collaboration with ACEGID for Lassa fever studies in Nigeria. Partnership with Professor Christian Happi supporting multi-site clinical studies.

Scale indicators9 records

Recent moves4 records

Expansion highlights6 records

Direct peers

• GISAID: GISAID is a global data science initiative providing public access to SARS-CoV-2 and influenza genomic data. CViSB collaborated with GISAID on the outbreak.info API, and Bjorn uses the GISAID API to download SARS-CoV-2 genomes, making it a tightly intertwined peer.
• Nextstrain: Nextstrain provides real-time tracking of pathogen evolution using genomic data, with tools for phylogenetic visualization. It is explicitly referenced as a related platform to CViSB's Bjorn pipeline and Outbreak.info, making it the most direct peer in viral genomic surveillance.
• African Center of Excellence for Genomics of Infectious Diseases (ACEGID): ACEGID at Redeemer's University is a research partner of CViSB for Lassa fever studies in Nigeria, led by Professor Christian Happi. It operates as a parallel African genomics center with overlapping pathogen focus and complementary surveillance capabilities.
• Viral Hemorrhagic Fever Consortium (VHFC): VHFC is a Tulane-led sister consortium developing diagnostics, immunotherapeutics, and vaccines against Lassa, Ebola, and Marburg viruses. It shares core PIs (Robert Garry), overlapping pathogen focus, and complementary clinical operations in West Africa.
• Ragon Institute of MGH, MIT and Harvard: Ragon Institute is a core CViSB partner institution whose Systems Serology Laboratory (directed by Ryan McNamara) co-leads Project 1 on antibody responses to SARS-CoV-2, Lassa, and Ebola. It is directly comparable as an immunology-focused infectious disease research center.

Broad incumbents

• Broad Institute: Broad Institute is a major genomics and infectious disease research organization where CViSB's director Kristian Andersen did his postdoctoral work. It represents a much larger, well-funded institution operating in the same host-pathogen genomics and viral surveillance space.
• Scripps Research: Scripps Research is the lead institution hosting CViSB and employs its director (Kristian Andersen) and Technology Core lead (Bryan Briney). It is the broader biomedical research enterprise of which CViSB is a specialized center.
• Fred Hutchinson Cancer Center: Fred Hutch operates a comparable consortium-style research model with major infectious disease and immunology programs. It represents a broader biomedical research enterprise with similar multi-investigator, multi-institutional structure to CViSB.
• Chan Zuckerberg Biohub: CZ Biohub is a large, well-funded biomedical research consortium with an Infectious Disease initiative focused on pathogen surveillance. It operates as a comparable multi-institutional research model but at significantly larger scale and broader scope than CViSB.
• Howard Hughes Medical Institute: HHMI funds and operates large-scale biomedical research labs, including infectious disease work by Kristian Andersen (a former PEW scholar in adjacent networks). It represents a much larger funder-operator in the biomedical research ecosystem with overlapping scientific interests.

Market position

Strengths5 records

Weaknesses5 records

Competitive moat5 records

Key risks4 records

Key highlights7 records

Customer concentration

• Xx.com/cvisb
• GitHubgithub.com/cvisb
• Instagraminstagram.com/cvisb

Revenue estimate

Valuation estimate

Number of profiles

Profiles10 records

Funding overview

Funding rounds

Investors

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M&A

Investments

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Frequently asked questions about Center for Viral Systems Biology