David H. O’Connor

Putative Cyclospora cayetanensis detection in wastewater metagenomic datasets

The paper detects putative Cyclospora cayetanensis in wastewater metagenomic data using 31-mers, finding 3.5% of runs positive and seasonal patterns matching cyclosporiasis.

Spondweni virus infection in pregnant rhesus macaques causes placental pathology without apparent fetal harm

This study infects pregnant rhesus macaques with Spondweni virus and finds placental pathology without fetal harm, contrasting with ZIKV-DAK-induced fetal demise.

Metagenomic surveillance of undiagnosed febrile illness in Nigeria does not reveal the etiological agent for most patients

The paper uses metagenomic sequencing to investigate undiagnosed febrile illness in Nigeria, identifying viruses and bacteria but finding no clear etiological agent for most cases.

Multiple full-length homozygous IGH haplotypes from Mauritian cynomolgus macaques

The paper reports the assembly of multiple IGH haplotypes from Mauritian cynomolgus macaques using long-read sequencing, revealing genetic diversity and novel alleles not previously cataloged.

Mpox virus (MPXV) vertical transmission and fetal demise in a pregnant rhesus macaque model

This study infects pregnant rhesus macaques with clade IIb Mpox virus and finds vertical transmission to the fetus and adverse pregnancy outcomes.

Complete genomic assembly of Mauritian cynomolgus macaque killer immunoglobulin-like receptor and natural killer group 2 haplotypes

The paper assembles KIR and NKG2 genomic haplotypes in Mauritian cynomolgus macaques using long-read sequencing and develops a strategy for genotyping using short-read data.

Complete sequencing of a cynomolgus macaque major histocompatibility complex haplotype

The paper fully assembles and annotates a cynomolgus macaque MHC haplotype using long-read sequencing, revealing structural diversity and gene counts different from previous rhesus macaque haplotypes.

Construction of a new chromosome-scale, long-read reference genome assembly for the Syrian hamster, Mesocricetus auratus

The paper presents an improved chromosome-scale genome assembly for the Syrian hamster using long-read sequencing, resulting in higher continuity and gene annotation accuracy.

Consistent ultra-long DNA sequencing with automated slow pipetting

SNAILS improves long-read sequencing by automating slow pipetting, increasing read length and consistency in Oxford Nanopore library preparation.

Characterization of 100 extended major histocompatibility complex haplotypes in Indonesian cynomolgus macaques

The paper characterizes 100 extended MHC haplotypes in Indonesian cynomolgus macaques using sequencing and haplotype analysis to improve preclinical research applications.

Using Barcoded Zika Virus to Assess virus Population Structure in vitro and in Aedes aegypti Mosquitoes

This study uses barcoded Zika virus to track genetic bottlenecks during transmission in vitro and in mosquitoes, showing stochasticity in viral dissemination.

Novel full-length major histocompatibility complex class I allele discovery and haplotype definition in pig-tailed macaques

This study identifies full-length MHC class I alleles and haplotypes in pig-tailed macaques using Pacific Biosciences sequencing, providing resources for HIV and transplant research.

Improved full-length killer cell immunoglobulin-like receptor transcript discovery in Mauritian cynomolgus macaques

The paper improves KIR allele discovery in Mauritian cynomolgus macaques using high-throughput sequencing and develops a new target capture reagent, finding nine novel alleles.

Major histocompatibility complex haplotyping and long-amplicon allele discovery in cynomolgus macaques from Chinese breeding facilities

The paper identifies MHC class I haplotypes and full-length alleles in cynomolgus macaques using PacBio sequencing, expanding the reference database with novel and extended sequences.