Research specialist Max Bobholz (left) and William Vuyk discuss an animated-computer timeline showing the evolution of the the COVID-19 pandemic across the state of Wisconsin – based on community zipcode and virus variant – while discussing their work on environmental surveillance of SARS-CoV-2 (COVID-19) and other viruses at the AIDS Vaccine Research Laboratory (AVRL) at the University of Wisconsin–Madison on Sept. 21, 2022. (Photo by Jeff Miller / UW–Madison)

Max Bobholz and Will Vuyk reviewing census level SARS-CoV-2 cases in Wisconsin

Mike, Adam, and Trent analyzing macaque genome data.

Christina looking at genetically modified mosquitoes designed to fight Zika virus.

Viral air sampling sequencing team

Lab staff attend training for new air sampling instrumentation

Nanopore Day, April 2023 Chicago

Sequencing group attend Nanopore Day, April 2023 Chicago

The overarching goal of the O’Connor lab is to contribute meaningfully to the global response to viral infections impacting human health. We do this by studying the interplay of viral pathogenesis, host genomics, and immunity. The lab currently has several major research areas (described below) with most of our research support coming from the National Institutes of Health and the Centers for Disease Control and Prevention.

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In close collaboration with Dr. Tom Friedrich and Shelby O’Connor,  we are using our expertise in virology to respond to COVID-19 in Wisconsin. Our lab is sequencing viruses from around the state to understand how variants are spreading through space and time. We are also detecting SARS-CoV-2 and other respiratory viruses in air samples from congregate spaces such as schools, hospitals, shelters, and other vulnerable settings. Information on our COVID-19 research including real-time data can be found at

For more information:

  • SARS-CoV-2 and other respiratory pathogens are detected in continuous air samples from congregate settings. Medrxiv. PMID: 35378751.
  • Revealing fine-scale spatiotemporal differences in SARS-CoV-2 introduction and spread. Nat Comm. PMID: 33144575
  • Construction of a new chromosome-scale, long-read reference genome assembly for the Syrian hamster, Mesocricetus auratus. GigaScience. PMID: 35640223
  • Viral Sequencing to Investigate Sources of SARS-CoV-2 Infection in US Healthcare Personnel. Clin Infect Dis. PMID: 33857303
  • Characteristic and quantifiable COVID-19-like abnormalities in CT- and PET/CT-imaged lungs of SARS-CoV-2-infected crab-eating macaques ( Macaca fascicularis). BioRxiv. PMID: 32511338

Zika virus association with fetal abnormalities

Zika virus can cause microcephaly and other fetal abnormalities. We have developed a rhesus macaque model for studying Zika virus during pregnancy and recently showed that African lineage Zika virus frequently causes pregnancy loss. The goal of this model is to define when during pregnancy a woman is at greatest risk of adverse fetal outcomes and test interventions that could prevent or reverse these outcomes.

For more information:

  • Fetal loss in pregnant rhesus macaques infected with high-dose African-lineage Zika virus. BioRxiv.
  • Early Embryonic Loss Following Intravaginal Zika Virus Challenge in Rhesus Macaques. Front Immunol. PMID: 34079560
  • Miscarriage and stillbirth following maternal Zika virus infection in nonhuman primates. Nat Med. PMID: 29967348.
  • A rhesus macaque model of Asian-lineage Zika virus infection. Nat Commun. PMC4931337.

Primate immune genetics and genomics

Macaque monkeys are widely used in biomedical research. A major research emphasis in our lab is understanding how macaque genetics influence susceptibility and resistance to infectious diseases as well as transplant rejection. We are particularly interested in the major histocompatibility complex (MHC), a cluster of genes that bind and present peptides to T cells. We are also characterizing variation in other macaque immune gene families, such as the killer immunoglobulin receptors (KIR) and FC gamma receptors. We are currently using ultra-long Oxford Nanopore sequencing and Pacific Biosciences HiFi sequencing to create exceptionally high quality genomes from Mauritian macaques with restricted genetic diversity.

Current job openings

Research analyst. A computational biology position to analyze MHC and KIR variants from exome and genome datasets, contribute to the discovery and curation of MHC and KIR allele databases, and manage and organize sequencing datasets. Candidates with a strong computer or biology background encouraged to apply.

Research specialist. A laboratory position ideal for someone who enjoys designing, performing, and analyzing molecular biology and sequencing experiments. This candidate will determine which MHC and KIR genes are present in macaques used in organ transplantation, infectious disease, and cancer biology research.

For more information:

  • Consistent ultra-long DNA sequencing with automated slow pipetting. BMC Genomics. 33711930
  • Characterization of 100 extended major histocompatibility complex haplotypes in Indonesian cynomolgus macaques. Immunogenetics. PMID: 32112172
  • O’Connor lab MHC contract web portal
  • No assembly required: Full-length MHC class I allele discovery by PacBio circular consensus sequencing. Hum Immunol 76:891.