The Virus Characterization, Isolation, Production, and Sequencing (VCIPS) Core is housed within the Division of Microbiology.
The Virus Characterization, Isolation, Production and Sequencing Core provides services to TNPRC, Tulane University, and affiliate investigators. The VCIPS core is divided into two primary components: 1) Virus characterization, isolation, and production and 2) Next generation sequencing.
Virus Characterization, Production, and Isolation
Provides virus expansion and characterization, viral titer by plaque and TCID50 assays, live virus neutralization and inhibition assays, and training in virological techniques.
BSL-3 virology
The VCIPS core provides live virus work with BSL-2/3 viruses including Simian Immunodeficiency Virus (SIV), Zika virus, and SARS-CoV-2, with capacity to expand to any BSL-2 or BSL-3 virus as needs arise. Available SIV isolates include SIVmac239, SIVmac251, and others. For SARS-CoV-2, the VCIPS core provides well-characterized stocks of multiple viral variants, including WA1/2020, Alpha, Beta, Gamma, Delta, Omicron (including subvariants BA.2, BA.2.11.2, BA.4, BA.5), and others, as well as mouse adapted (MA10 and MA30) and WA1/2020 modified to express eGFP. BSL-2/3 assays provided by the VCIPS core include:
- Virus expansion and characterization, including from primary (e.g. clinical) samples
- Viral sequencing
- Viral titer by plaque and TCID50 assays
- Live virus neutralization assays using traditional (plaque reduction) and modern assays including microneutralization assays
- Impedance and imaging- based assays for viral replication and inhibition (BSL-3 only).
Next Generation Sequencing
Provides expertise in next generation sequencing and timely genomic services including whole genome, epigenetics, targeted amplicons, and 16S metagenomics. Some area of investigation that can be examined with next generation sequencing include identification of unknow organisms, de-novo assemblies, resequencing, variant detection, epigenetics, gene expression, and microbiomes (including 16S.)
Illumina
The Sequencing core houses an Illumina MiSeq which is capable of sequencing for numerous types of sequencing projects. The MiSeq is a short read technology producing highly accurate short sequencing reads from 50-300bps.
MiSeq - Whole Genome Sequencing (bacteria, virus), Amplicon Sequencing | |||
Instrument Flow Cells - Cycles | Millions of Reads / Run | Bases / Read | Gbp / Run |
Nano - 300 cycles | 1 | 300 | 0.3 |
Nano - 500 cycles | 1 | 500 | 0.5 |
Micro - 300 cycles | 4 | 300 | 1.2 |
v2 - 50 cycles | 15 | 50 | 0.9 |
v2 - 300 cycles | 15 | 300 | 5.1 |
v2 - 500 cycles | 15 | 500 | 8.5 |
v3 - 150 cycles | 25 | 150 | 3.8 |
v3 - 600 cycles | 25 | 600 | 15 |
Oxford Nanopore
The Sequencing core houses an Oxford Nanopore MinIon/Flongle. The MinIon is a long-read technology that can produce individual sequencing reads >100,000 bps. Oxford Nanopore technology is capable of both direct RNA sequencing as well as direct methylation detection.
MinION – Whole genome, amplicons, Direct DNA and RNA | |||
Instrument Flow Cells - Cycles | Millions of Reads / Run | Bases / Read | Gbp / Run |
Flongle | 0.1 | 100-1M | 2 |
MinION | 0.8 | 100-1M | 50 |
Contact Information
Nicholas Maness, PhD, Director of VCIPS
Preston Marx, PhD, Associate Director of VCIPS
Lori Rowe, PhD, Assistant Director of Sequencing for VCIPS
Kelly Goff, Laboratory Manager for VCIPS
Sarah Scheuermann, Laboratory Supervisor for VCIPS
Acknowledgments
When utilizing research resources made possible by the TNPRC Virus Characterization, Isolation, Production and Sequencing Core, please cite RRID:SCR_024679. For additional information on acknowledging Tulane National Primate Research Center resources, please see here.
