@article{mao_harvey_porubsky_munson_hoekzema_lewis_audano_rozanski_yang_zhang_et al._2024, title={Structurally divergent and recurrently mutated regions of primate genomes}, volume={187}, ISSN={["1097-4172"]}, DOI={10.1016/j.cell.2024.01.052}, abstractNote={We sequenced and assembled using multiple long-read sequencing technologies the genomes of chimpanzee, bonobo, gorilla, orangutan, gibbon, macaque, owl monkey, and marmoset. We identified 1,338,997 lineage-specific fixed structural variants (SVs) disrupting 1,561 protein-coding genes and 136,932 regulatory elements, including the most complete set of human-specific fixed differences. We estimate that 819.47 Mbp or ∼27% of the genome has been affected by SVs across primate evolution. We identify 1,607 structurally divergent regions wherein recurrent structural variation contributes to creating SV hotspots where genes are recurrently lost (e.g., CARD, C4, and OLAH gene families) and additional lineage-specific genes are generated (e.g., CKAP2, VPS36, ACBD7, and NEK5 paralogs), becoming targets of rapid chromosomal diversification and positive selection (e.g., RGPD gene family). High-fidelity long-read sequencing has made these dynamic regions of the genome accessible for sequence-level analyses within and between primate species.}, number={6}, journal={CELL}, author={Mao, Yafei and Harvey, William T. and Porubsky, David and Munson, Katherine M. and Hoekzema, Kendra and Lewis, Alexandra P. and Audano, Peter A. and Rozanski, Allison and Yang, Xiangyu and Zhang, Shilong and et al.}, year={2024}, month={Mar} }
 @article{kiehl_hodo_hamer_hamer_wilkerson_2023, title={Exclusion of Horizontal and Vertical Transmission as Major Sources of Trypanosoma cruzi Infections in a Breeding Colony of Rhesus Macaques (Macaca mulatta)}, volume={73}, ISSN={["1532-0820"]}, DOI={10.30802/AALAS-CM-23-000005}, abstractNote={The vector-borne protozoal parasiteTrypanosoma cruzicauses Chagas disease in humans and animals. This parasite is endemic to the southern United States where outdoor-housed NHP at biomedical facilities are at risk of infection. In addi- tion to the direct morbidity caused byT. cruzi, infected animals are of limited biomedical research use because infections can produce confounding pathophysiologic changes even in animals with no clinical disease. In part due to concerns for directT. cruzitransmission between animals, infected NHP at some institutions have been culled, removed, or otherwise isolated from uninfected animal populations. However, data that document horizontal or vertical transmission in captive NHP in the United States are not available. To evaluate the potential for inter-animal transmission and to identify environmental factors that affect the distribution of new infections in NHPs, we conducted a retrospective epidemiologic study of a rhesus macaque (Macaca mulatta) breeding colony in south Texas. We used archived biologic samples and husbandry records to identify the time and location of macaque seroconversion. These data were used to perform a spatial analysis of how geographic location and animal associations affected the spread of disease and to infer the importance of horizontal or vertical routes of transmission. The majority ofT. cruziinfections were spatially clustered, suggesting that environmental factors promoted vector exposure in various areas of the facility. Although we cannot not rule out horizontal transmission, our data suggest that horizontal transmission was not a critical route for spread for the disease. Vertical transmission was not a contributing factor in this colony. In conclusion, our findings suggest that local triatome vectors were the major source ofT. cruziinfections in captive macaques in our colony. Therefore, limiting contact with vectors, rather than segregation of infected macaques, is a key strategy for disease prevention at institutions that house macaques outdoors in the southern United States.}, number={3}, journal={COMPARATIVE MEDICINE}, author={Kiehl, Whitney M. and Hodo, Carolyn L. and Hamer, Gabriel L. and Hamer, Sarah A. and Wilkerson, Gregory K.}, year={2023}, month={Jun}, pages={229–241} }
 @article{bustamante_white_wilkerson_hodo_auckland_wang_mccain_hamer_saunders_tarleton_2023, title={Frequency Variation and Dose Modification of Benznidazole Administration for the Treatment of Trypanosoma cruzi Infection in Mice, Dogs, and Nonhuman Primates}, ISSN={["1098-6596"]}, DOI={10.1128/aac.00132-23}, abstractNote={
            Trypanosoma cruzi
            naturally infects a broad range of mammalian species and frequently results in the pathology that has been most extensively characterized in human Chagas disease. Currently employed treatment regimens fail to achieve parasitological cure of
            T. cruzi
            infection in the majority of cases.
          }, journal={ANTIMICROBIAL AGENTS AND CHEMOTHERAPY}, author={Bustamante, Juan M. and White, Brooke E. and Wilkerson, Gregory K. and Hodo, Carolyn L. and Auckland, Lisa D. and Wang, Wei and McCain, Stephanie and Hamer, Sarah A. and Saunders, Ashley B. and Tarleton, Rick L.}, year={2023}, month={Apr} }
 @article{hensel_rodrigues-hoffmann_dray_wilkerson_baze_sulkosky_hodo_2023, title={Gastrointestinal tract pathology of the owl monkey (<i>Aotus</i> spp.)}, ISSN={["1544-2217"]}, DOI={10.1177/03009858231204260}, abstractNote={ Owl monkeys are small nocturnal new world primates in the genus Aotus that are most used in biomedical research for malaria. Cardiomyopathy and nephropathy are well-described common diseases contributing to their morbidity and mortality; less is known about lesions affecting the gastrointestinal tract. Records from a 14-year period (2008-2022) at the Keeling Center for Comparative Medicine and Research were queried to identify instances of spontaneous gastrointestinal disease that directly contributed to the cause of death from the 235 adult owl monkeys submitted for necropsy. Of the 235, 10.6% (25/235) had gastrointestinal disease listed as a significant factor that contributed to morbidity and mortality. Diagnoses included candidiasis (3/25), gastric bloat (4/25), and intestinal incarceration and ischemia secondary (11/25), which included intussusception (4/25), mesenteric rent (3/25), strangulating lipoma (2/25), intestinal torsion (1/25), and an inguinal hernia (1/25). Intestinal adenocarcinomas affecting the jejunum (4/25) were the most common neoplasia diagnosis. Oral squamous cell carcinoma (1/25) and intestinal lymphoma (2/25) were also diagnosed. This report provides evidence of spontaneous lesions in the species that contribute to morbidity and mortality. }, journal={VETERINARY PATHOLOGY}, author={Hensel, Martha E. and Rodrigues-Hoffmann, Aline and Dray, Beth K. and Wilkerson, Gregory K. and Baze, Wally B. and Sulkosky, Sarah and Hodo, Carolyn L.}, year={2023}, month={Oct} }
 @article{kuderna_ulirsch_rashid_ameen_sundaram_hickey_cox_gao_kumar_aguet_et al._2023, title={Identification of constrained sequence elements across 239 primate genomes}, ISSN={["1476-4687"]}, DOI={10.1038/s41586-023-06798-8}, abstractNote={Abstract}, journal={NATURE}, author={Kuderna, Lukas F. K. and Ulirsch, Jacob C. and Rashid, Sabrina and Ameen, Mohamed and Sundaram, Laksshman and Hickey, Glenn and Cox, Anthony J. and Gao, Hong and Kumar, Arvind and Aguet, Francois and et al.}, year={2023}, month={Nov} }
 @article{gao_hamp_ede_schraiber_mcrae_singer-berk_yang_dietrich_fiziev_kuderna_et al._2023, title={The landscape of tolerated genetic variation in humans and primates}, volume={380}, ISSN={["1095-9203"]}, DOI={10.1126/science.abn8197}, abstractNote={Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole-genome sequencing data for 809 individuals from 233 primate species and identified 4.3 million common protein-altering variants with orthologs in humans. We show that these variants can be inferred to have nondeleterious effects in humans based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases.}, number={6648}, journal={SCIENCE}, author={Gao, Hong and Hamp, Tobias and Ede, Jeffrey and Schraiber, Joshua G. and McRae, Jeremy and Singer-Berk, Moriel and Yang, Yanshen and Dietrich, Anastasia S. D. and Fiziev, Petko P. and Kuderna, Lukas F. K. and et al.}, year={2023}, month={Jun}, pages={929-+} }
 @article{warren_yu_peters_barbachano-guerrero_yang_burris_worwa_huang_wilkerson_goldberg_et al._2022, title={Primate hemorrhagic fever-causing arteriviruses are poised for spillover to humans}, volume={185}, ISSN={["1097-4172"]}, DOI={10.1016/j.cell.2022.09.022}, abstractNote={Simian arteriviruses are endemic in some African primates and can cause fatal hemorrhagic fevers when they cross into primate hosts of new species. We find that CD163 acts as an intracellular receptor for simian hemorrhagic fever virus (SHFV; a simian arterivirus), a rare mode of virus entry that is shared with other hemorrhagic fever-causing viruses (e.g., Ebola and Lassa viruses). Further, SHFV enters and replicates in human monocytes, indicating full functionality of all of the human cellular proteins required for viral replication. Thus, simian arteriviruses in nature may not require major adaptations to the human host. Given that at least three distinct simian arteriviruses have caused fatal infections in captive macaques after host-switching, and that humans are immunologically naive to this family of viruses, development of serology tests for human surveillance should be a priority.}, number={21}, journal={CELL}, author={Warren, Cody J. and Yu, Shuiqing and Peters, Douglas K. and Barbachano-Guerrero, Arturo and Yang, Qing and Burris, Bridget L. and Worwa, Gabriella and Huang, I-Chueh and Wilkerson, Gregory K. and Goldberg, Tony L. and et al.}, year={2022}, month={Oct}, pages={3980-+} }