Pavitra Roychoudhury

HIV-SEQ REVEALS GLOBAL HOST GENE EXPRESSION DIFFERENCES BETWEEN HIV-TRANSCRIBING CELLS FROM VIREMIC AND SUPPRESSED PEOPLE WITH HIV

The paper develops HIV-seq to capture HIV transcripts for scRNA-seq, revealing distinct transcriptional features of HIV-transcribing cells in viremic and ART-suppressed HIV patients.

ARTIC RSV amplicon sequencing reveals global RSV genotype dynamics.

This study introduces two novel amplicon sequencing schemes for RSV A and B, demonstrating their effectiveness in generating high-quality genomes globally and revealing minimal geographic clustering of RSV sequences.

Clinical performance evaluation of a tiling amplicon panel for whole genome sequencing of respiratory syncytial virus

The paper evaluates a tiling amplicon panel for RSV whole genome sequencing, showing high sensitivity, specificity, and accuracy in clinical and contrived samples.

Minimization of gene editing off-target effects by tissue restriction of expression

This study shows that restricting meganuclease expression to specific tissues reduces off-target gene editing in vivo.

Convergence of immune escape strategies highlights plasticity of SARS-CoV-2 spike

This study identifies two SARS-CoV-2 variants with NTD deletions that reshape the antigenic surface and reduce antibody binding, highlighting the plasticity of the NTD for immune escape.

Differences in expression of tumor suppressor, innate immune, inflammasome, and potassium/gap junction channel host genes significantly predict viral reservoir size during treated HIV infection

This study identifies host gene expression patterns associated with HIV reservoir size in treated individuals, linking inflammation, innate immunity, and potassium/gap junction channels to viral persistence.

Genome sequencing of 196 Treponema pallidum strains from six continents reveals additional variability in vaccine candidate genes and dominance of Nichols clade strains in Madagascar

Host Variation in Type I Interferon Signaling Genes (MX1), CCR5{triangleup}32, and MHC Class I Alleles in Treated HIV+ Non-Controllers Predict Viral Reservoir Size

The paper investigates host genetic variations in MX1, CCR5Δ32, and MHC class I alleles in HIV+ non-controllers on ART and finds associations with HIV reservoir size.

The impact of interspecies recombination on human herpes simplex virus evolution and host immune recognition

This study identifies interspecies recombination events in HSV-2 genomes and shows their impact on genetic variation and T-cell recognition.

Viral diversity is an obligate consideration in CRISPR/Cas9 designs for HIV cure

This paper identifies highly-conserved CRISPR guide RNAs for HIV cure and models the impact of viral diversity on therapeutic success.

Ultrasensitive capture of human herpes simplex virus genomes directly from clinical samples reveals extraordinarily limited evolution in cell culture

The paper develops tools to directly sequence HSV genomes from clinical samples with high sensitivity and low viral load, revealing limited evolution during cell culture.

Copy number heterogeneity, large origin tandem repeats, and interspecies recombination in HHV-6A and HHV-6B reference strains

The paper uses next-generation sequencing to analyze copy number variations and interspecies recombination in HHV-6A and HHV-6B reference strains, revealing large tandem repeats and a novel recombinant strain.