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Highly divergent integration profile of adeno-associated virus serotype 5 revealed by high-throughput sequencing.

TitleHighly divergent integration profile of adeno-associated virus serotype 5 revealed by high-throughput sequencing.
Publication TypeJournal Article
Year of Publication2014
AuthorsJanovitz T, Oliveira T, Sadelain M, Falck-Pedersen E
JournalJ Virol
Volume88
Issue5
Pagination2481-8
Date Published2014 Mar
ISSN1098-5514
KeywordsBase Sequence, Binding Sites, Cell Line, Chromosome Mapping, Consensus Sequence, Dependovirus, DNA-Binding Proteins, Endonucleases, Gene Order, Genome, Viral, High-Throughput Nucleotide Sequencing, Humans, Nucleotide Motifs, Position-Specific Scoring Matrices, Viral Proteins, Virus Integration
Abstract

UNLABELLED: Adeno-associated virus serotype 5 (AAV-5) is a human parvovirus that infects a high percentage of the population. It is the most divergent AAV, the DNA sequence cleaved by the viral endonuclease is distinct from all other described serotypes and, uniquely, AAV-5 does not cross-complement the replication of other serotypes. In contrast to the well-characterized integration of AAV-2, no published studies have investigated the genomic integration of AAV-5. In this study, we analyzed more than 660,000 AAV-5 integration junctions using high-throughput integrant capture sequencing of infected human cells. The integration activity of AAV-5 was 99.7% distinct from AAV-2 and favored intronic sequences. Genome-wide integration was highly correlated with viral replication protein binding and endonuclease sites, and a 39-bp consensus integration motif was revealed that included these features. Algorithmic scanning identified 126 AAV-5 hot spots, the largest of which encompassed 3.3% of all integration events. The unique aspects of AAV-5 integration may provide novel tools for biotechnology and gene therapy.

IMPORTANCE: Viral integration into the host genome is an important aspect of virus host cell biology. Genomic integration studies of the small single-stranded AAVs have largely focused on site preferential integration of AAV-2, which depends on the viral replication protein (Rep). We have now established the first genome wide integration profile of the highly divergent AAV-5 serotype. Using integrant capture sequencing, more than 600,000 AAV-5 integration junctions in human cells were analyzed. AAV-5 integration hot spots were 99.7% distinct from AAV-2. Integration favored intronic sequences, occurred on all chromosomes, and integration hot spot distribution was correlated with human genomic GAGC repeats and transcriptional activity. These features support expansion of AAV-5 based vectors for gene transfer considerations.

DOI10.1128/JVI.03419-13
Alternate JournalJ Virol
PubMed ID24335317
PubMed Central IDPMC3958079
Grant ListR01 AI094050 / AI / NIAID NIH HHS / United States
T32 GM007739 / GM / NIGMS NIH HHS / United States
T32GM07739 / GM / NIGMS NIH HHS / United States

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