Differences in cynomolgus macaque populations used for infectious disease research

Abstract

Cynomolgus macaques, a species of Old World primate native to southeastern and eastern Asia and the island of Mauritius, are one of the most important nonhuman primate models for infectious disease. Although the closely related rhesus macaque is classified into subspecies based on geographic origin, no such subdivision exists for cynomolgus macaques, and they continue to be used interchangeably in infectious disease research, reducing the comparability of data produced from these studies. Research into the population genetics of cynomolgus macaques has found significant differences between macaques native to different areas, including their genetic diversity, with macaques from insular populations such as Mauritius and the Philippines exhibiting highly restricted heterozygosity compared to mainland populations native to Indonesia or Cambodia. In the context of infectious disease studies, research into pathogens, including Ebola virus, Crimean-Congo hemorrhagic fever virus, and Mycobacterium tuberculosis have found differences in study outcomes, survival times, and immune cell responses between different populations of macaques. This review provides an overview of the differences between cynomolgus macaque populations in the context of genetic diversity, and in response to infection, and highlights the need for clear reporting of geographic origin of primates used in research. This will improve data comparison between studies and help to further refine this important animal model.

Keywords

animal models / communicable diseases / genetic variation / Macaca fascicularis / population genetics

References

[1] Fooden J. Comparative review of Fascicularis-group species of macaques (primates: Macaca). Fieldiana Zool. 2006; 107: 1-44.

[2] Wu SJ, Luo J, Li QQ, et al. Ecological genetics of Chinese rhesus macaque in response to mountain building: all things are not equal. PLoS One. 2013; 8(2):e55315.

[3] Baxter A, Home Office. Statistics of scientific procedures on living animals, Great Britain: 2022. 2024. Accessed June 27, 2024. https://www.gov.uk/government/statistics/statistics-of-scientific-procedures-on-living-animals-great-britain-2022

[4] National Academies of Sciences E, and Medicine; Division on Earth and Life Studies; Health and Medicine Division; Institute for Laboratory Animal Research; Board on Health Sciences Policy; Committee on the State of the Science and Future Needs for Nonhuman Primate Model Systems. Current landscape of use and availability of nonhuman primates for NIH-supported biomedical research. In: OC Yost, A Downey, KS Ramos, eds. Nonhuman Primate Models in Biomedical Research: State of the Science and Future Needs. National Academies Press (US); 2023 chap 3. The National Academies Collection: Reports funded by National Institutes of Health.

[5] How CITES Works. Accessed October 28, 2024. https://cites.org/eng/disc/how.php

[6] CITES Trade Database. 2024. Accessed October 28, 2024. https://trade.cites.org/

[7] Robinson JE, Sinovas P. Challenges of analyzing the global trade in CITES-listed wildlife. Conserv Biol. 2018; 32(5): 1203-1206.

[8] Weinbauer G, Mecklenburg L. Does geographical origin of long-tailed macaques (Macaca fascicularis) matter in drug safety assessment?: a literature review and proposed conclusion. Toxicol Pathol. 2022; 50(5): 552-559.

[9] Liepnieks M, Carter C, Caruso MJ, Lloyd Z, Muzyka M, Patrick D. A comparison of historical control data from cynomolgus macaques (Macaca fascicularis) of Chinese, Cambodian, and Vietnamese origin. Toxicol Pathol. 2022; 50(5): 560-573.

[10] Kozlosky JC, Mysore J, Clark SP, et al. Comparison of physiologic and pharmacologic parameters in Asian and Mauritius cynomolgus macaques. Regul Toxicol Pharmacol. 2015; 73(1): 27-42.

[11] Arndt T, Meindel M, Clarke J, Shaw A, Gregori M. Comparison of routine hematology, coagulation, and clinical chemistry parameters of cynomolgus macaques of Mauritius origin with cynomolgus macaques of Cambodia, China, and Vietnam origin. Toxicol Pathol. 2022; 50(5): 591-606.

[12] Fooden J. Systematic review of the rhesus macaque, Macaca mulatta (Zimmermann, 1780). Fieldiana. 2000; 96: 1-180.

[13] Fooden J. Systematic review of southeast Asian longtail macaques, Macaca fascicularis (Raffles, [1821]). Fieldiana. 1985; 81: 1-206.

[14] GBIF.org. GBIF Occurrence Download. The Global Biodiversity Information Facility; 2025. Accessed October 1, 2025. https://www.gbif.org

[15] GBIF.org. GBIF Occurrence Download. The Global Biodiversity Information Facility; 2025. Accessed October 2, 2025. https://www.gbif.org

[16] IUCN (International Union for Conservation of Nature). Macaca fascicularis (spatial data). IUCN Red List Threat Species. 2022. 2025;(2). Accessed October 1, 2025. https://www.iucnredlist.org

[17] IUCN (International Union for Conservation of Nature). Macaca mulatta (spatial data). IUCN Red List Threat Species. 2020. 2025;(2). Accessed October 2, 2025. https://www.iucnredlist.org

[18] Smith DG, McDonough JW, George DA. Mitochondrial DNA variation within and among regional populations of longtail macaques (Macaca fascicularis) in relation to other species of the fascicularis group of macaques. Am J Primatol. 2007; 69(2): 182-198.

[19] Eudey AA. The crab-eating macaque (Macaca fascicularis): widespread and rapidly declining. Primate Conserv. 2008; 23(1): 129-132, 4.

[20] Zhang X, Meng Y, Houghton P, et al. Ancestry, plasmodium cynomolgi prevalence and rhesus macaque admixture in cynomolgus macaques (Macaca fascicularis) bred for export in Chinese breeding farms. J Med Primatol. 2017; 46(2): 31-41.

[21] Bonhomme M, Cuartero S, Blancher A, Crouau-Roy B. Assessing natural introgression in 2 biomedical model species, the rhesus macaque (Macaca mulatta) and the long-tailed macaque (Macaca fascicularis). J Hered. 2009; 100(2): 158-169.

[22] Tosi AJ, Morales JC, Melnick DJ. Y-chromosome and mitochondrial markers in Macaca fascicularis indicate introgression with Indochinese M. mulatta and a biogeographic barrier in the Isthmus of Kra. Int J Primatol. 2002; 23(1): 161-178.

[23] Schmidt LH, Cramer DV, Rossan RN, Harrison J. The characteristics of plasmodium cynomolgi infections in various old world primates. Am J Trop Med Hyg. 1977; 26(3): 356-372.

[24] Reinegger RD, Oleksy RZ, Gazagne E, Jones G. Foraging strategies of invasive Macaca fascicularis may promote plant invasion in Mauritius. Int J Primatol. 2023; 44(1): 140-170.

[25] Blancher A, Bonhomme M, Crouau-Roy B, Terao K, Kitano T, Saitou N. Mitochondrial DNA sequence phylogeny of 4 populations of the widely distributed cynomolgus macaque (Macaca fascicularis fascicularis). J Hered. 2008; 99(3): 254-264.

[26] Tosi AJ, Coke CS. Comparative phylogenetics offer new insights into the biogeographic history of Macaca fascicularis and the origin of the Mauritian macaques. Mol Phylogenet Evol. 2007; 42(2): 498-504.

[27] Kawamoto Y, Kawamoto S, Matsubayashi K, et al. Genetic diversity of longtail macaques (Macaca fascicularis) on the Island of Mauritius: an assessment of nuclear and mitochondrial DNA polymorphisms. J Med Primatol. 2008; 37(1): 45-54.

[28] Kanthaswamy S, Ng J, Satkoski Trask J, et al. The genetic composition of populations of cynomolgus macaques (Macaca fascicularis) used in biomedical research. J Med Primatol. 2013; 42(3): 120-131.

[29] Satkoski Trask J, George D, Houghton P, Kanthaswamy S, Smith DG. Population and landscape genetics of an introduced species (M. fascicularis) on the Island of Mauritius. PLoS One. 2013; 8(1):e53001.

[30] Bonhomme M, Blancher A, Cuartero S, Chikhi L, Crouau-Roy B. Origin and number of founders in an introduced insular primate: estimation from nuclear genetic data. Mol Ecol. 2008; 17(4): 1009-1019.

[31] Osada N, Hettiarachchi N, Adeyemi Babarinde I, Saitou N, Blancher A. Whole-genome sequencing of six Mauritian cynomolgus macaques (Macaca fascicularis) reveals a genome-wide pattern of polymorphisms under extreme population bottleneck. Genome Biol Evol. 2015; 7(3): 821-830.

[32] Lawler SH, Sussman RW, Taylor LL. Mitochondrial DNA of the Mauritian macaques (Macaca fascicularis): an example of the founder effect. Am J Phys Anthropol. 1995; 96(2): 133-141.

[33] Barton NH, Charlesworth B. Genetic revolutions, founder effects, and speciation. Annu Rev Ecol Evol Syst. 1984; 15: 133-164.

[34] Esselstyn J, Widmann P, Heaney L. The mammals of Palawan Island, Philippines. Proc Biol Soc Wash. 2004; 117(3): 271-302.

[35] Fooden J. Systematic Review of Philippine Macaques (Primates, Cercopithecidae: Macaca fascicularis Subspp.). Field Museum of Natural History; 1991.

[36] Smith DG, Ng J, George D, et al. A genetic comparison of two alleged subspecies of Philippine cynomolgus macaques. Am J Phys Anthropol. 2014; 155(1): 136-148.

[37] de Groot NG, de Groot N, de Vos-Rouweler AJM, Louwerse A, Bruijnesteijn J, Bontrop RE. Dynamic evolution of Mhc haplotypes in cynomolgus macaques of different geographic origins. Immunogenetics. 2022; 74(4): 409-429.

[38] Kanthaswamy S, Satkoski J, George D, Kou A, Erickson BJ, Smith DG. Hybridization and stratification of nuclear genetic variation in Macaca mulatta and M. fascicularis. Int J Primatol. 2008; 29(5): 1295-1311.

[39] Street SL, Kyes RC, Grant R, Ferguson B. Single nucleotide polymorphisms (SNPs) are highly conserved in rhesus (Macaca mulatta) and cynomolgus (Macaca fascicularis) macaques. BMC Genomics. 2007; 8:480.

[40] Ferguson B, Street SL, Wright H, et al. Single nucleotide polymorphisms (SNPs) distinguish Indian-origin and Chinese-origin rhesus macaques (Macaca mulatta). BMC Genomics. 2007; 8:43.

[41] Hayasaka K, Fujii K, Horai S. Molecular phylogeny of macaques: implications of nucleotide sequences from an 896-base pair region of mitochondrial DNA. Mol Biol Evol. 1996; 13(7): 1044-1053.

[42] Kanthaswamy S, Gill L, Satkoski J, et al. Development of a Chinese-Indian hybrid (Chindian) rhesus macaque colony at the California National Primate Research Center by introgression. J Med Primatol. 2009; 38(2): 86-96.

[43] Mee ET, Badhan A, Karl JA, et al. MHC haplotype frequencies in a UK breeding colony of Mauritian cynomolgus macaques mirror those found in a distinct population from the same geographic origin. J Med Primatol. 2009; 38(1): 1-14.

[44] Mitchell JL, Mee ET, Almond NM, Cutler K, Rose NJ. Characterisation of MHC haplotypes in a breeding colony of Indonesian cynomolgus macaques reveals a high level of diversity. Immunogenetics. 2012; 64(2): 123-129.

[45] Lodoen MB, Lanier LL. Natural killer cells as an initial defense against pathogens. Curr Opin Immunol. 2006; 18(4): 391-398.

[46] Prall TM, Graham ME, Karl JA, et al. Improved full-length killer cell immunoglobulin-like receptor transcript discovery in Mauritian cynomolgus macaques. Immunogenetics. 2017; 69(5): 325-339.

[47] Hu Q, Huang X, Jin Y, et al. Long-read assembly of major histocompatibility complex and killer cell immunoglobulin-like receptor genome regions in cynomolgus macaque. Biol Direct. 2022; 17(1):36.

[48] Bimber BN, Moreland AJ, Wiseman RW, Hughes AL, O'Connor DH. Complete characterization of killer Ig-like receptor (KIR) haplotypes in Mauritian cynomolgus macaques: novel insights into nonhuman primate KIR gene content and Organization. J Immunol. 2008; 181(9): 6301-6308.

[49] Bruijnesteijn J, de Groot N, van der Wiel MKH, et al. Unparalleled rapid evolution of KIR genes in rhesus and cynomolgus macaque populations. J Immunol. 2020; 204(7): 1770-1786.

[50] Albrecht C, Malzahn D, Brameier M, Hermes M, Ansari AA, Walter L. Progression to AIDS in SIV-infected rhesus macaques is associated with distinct KIR and MHC class I polymorphisms and NK cell dysfunction. Front Immunol. 2014; 5:2014.

[51] Uno Y, Murayama N, Yamazaki H. Novel cytochrome P450 2C119 enzymes in cynomolgus and rhesus macaques metabolize progesterone, diclofenac, and omeprazole. Drug Metab Dispos. 2024; 52(3): 266-273.

[52] Uno Y, Yamazaki H. Expression of cytochrome P450 regulators in cynomolgus macaque. Xenobiotica. 2018; 48(7): 695-703.

[53] Uno Y, Uehara S, Kohara S, Osada N, Murayama N, Yamazaki H. CYP2D44 polymorphisms in cynomolgus and rhesus macaques. Mol Biol Rep. 2015; 42(7): 1149-1155.

[54] He ZX, Chen XW, Yang Y, Zhou SF. A comparison of non-human primate cytochrome P450 2D members and the implication in drug discovery. Curr Drug Metab. 2016; 17(6): 520-527.

[55] Uno Y, Matsushita A, Shukuya M, Matsumoto Y, Murayama N, Yamazaki H. CYP2C19 polymorphisms account for inter-individual variability of drug metabolism in cynomolgus macaques. Biochem Pharmacol. 2014; 91(2): 242-248.

[56] Ise R, Nakanishi Y, Kohara S, et al. Expression profile of hepatic genes in cynomolgus macaques bred in Cambodia, China, and Indonesia: implications for cytochrome P450 genes. Drug Metab Pharmacokinet. 2012; 27(3): 307-316.

[57] Rougeron V, Feldmann H, Grard G, Becker S, Leroy EM. Ebola and Marburg haemorrhagic fever. J Clin Virol. 2015; 64: 111-119.

[58] World Health Organization. Ebola outbreak 2014-2016—West Africa—Overview. 2024. Accessed August 16, 2024. https://www.who.int/emergencies/situations/ebola-outbreak-2014-2016-West-Africa

[59] Feldmann H, Jones S, Klenk HD, Schnittler HJ. Ebola virus: from discovery to vaccine. Nat Rev Immunol. 2003; 3(8): 677-685.

[60] Geisbert TW, Strong JE, Feldmann H. Considerations in the use of nonhuman primate models of Ebola virus and Marburg virus infection. J Infect Dis. 2015; 212(Suppl 2): 91-97.

[61] Bennett RS, Huzella LM, Jahrling PB, Bollinger L, Olinger GG, Hensley LE. Nonhuman primate models of Ebola virus disease. Curr Top Microbiol Immunol. 2017; 411: 171-193.

[62] Piorkowski G, Jacquot F, Querat G, et al. Implementation of a non-human primate model of Ebola disease: infection of Mauritian cynomolgus macaques and analysis of virus populations. Antivir Res. 2017; 140: 95-105.

[63] Johnson DM, Brasel T, Massey S, et al. Characterization of Ebola virus mucosal challenge routes in cynomolgus macaques. J Virol. 2023; 97(5):e0188822.

[64] Cross RW, Prasad AN, Woolsey CB, et al. Natural history of nonhuman primates after conjunctival exposure to Ebola virus. Sci Rep. 2023; 13(1):4175.

[65] Johnston SC, Wilhelmsen CL, Shamblin J, et al. Delayed disease in cynomolgus macaques exposed to Ebola virus by an intranasal route. Front Immunol. 2021; 12:709772.

[66] Alfson KJ, Avena LE, Beadles MW, et al. Particle-to-PFU ratio of Ebola virus influences disease course and survival in cynomolgus macaques. J Virol. 2015; 89(13): 6773-6781.

[67] Alfson KJ, Avena LE, Worwa G, Carrion R, Griffiths A. Development of a lethal intranasal exposure model of Ebola virus in the cynomolgus macaque. Viruses. 2017; 9(11).

[68] Sullivan NJ, Hensley L, Asiedu C, et al. CD8+ cellular immunity mediates rAd5 vaccine protection against Ebola virus infection of nonhuman primates. Nat Med. 2011; 17(9): 1128-1131.

[69] Niemuth NA, Fallacara D, Triplett CA, et al. Natural history of disease in cynomolgus monkeys exposed to Ebola virus Kikwit strain demonstrates the reliability of this non-human primate model for Ebola virus disease. PLoS One. 2021; 16(7):e0252874.

[70] Zumbrun EE, Garvey CB, Wells JB, et al. Characterization of the cynomolgus macaque model of Marburg virus disease and assessment of timing for therapeutic treatment testing. Viruses. 2023; 15(12).

[71] Nakayama E, Saijo M. Animal models for Ebola and Marburg virus infections. Front Microbiol. 2013; 4:267.

[72] World Health Organization. Crimean-Congo haemorrhagic fever Factsheet. 2024. Accessed September 25, 2024. https://www.who.int/news-room/fact-sheets/detail/crimean-congo-haemorrhagic-fever

[73] Bente DA, Forrester NL, Watts DM, McAuley AJ, Whitehouse CA, Bray M. Crimean-Congo hemorrhagic fever: history, epidemiology, pathogenesis, clinical syndrome and genetic diversity. Antivir Res. 2013; 100(1): 159-189.

[74] Garrison AR, Smith DR, Golden JW. Animal models for Crimean-Congo hemorrhagic fever human disease. Viruses. 2019; 11(7).

[75] Hoogstraal H. The epidemiology of tick-borne Crimean-Congo hemorrhagic fever in Asia, Europe, and Africa. J Med Entomol. 1979; 15(4): 307-417.

[76] Weidmann M, Avsic-Zupanc T, Bino S, et al. Biosafety standards for working with Crimean-Congo hemorrhagic fever virus. J Gen Virol. 2016; 97(11): 2799-2808.

[77] Haddock E, Feldmann F, Hawman DW, et al. A cynomolgus macaque model for Crimean-Congo haemorrhagic fever. Nat Microbiol. 2018; 3(5): 556-562.

[78] Hawman DW, Ahlen G, Appelberg KS, et al. A DNA-based vaccine protects against Crimean-Congo haemorrhagic fever virus disease in a cynomolgus macaque model. Nat Microbiol. 2021; 6(2): 187-195.

[79] Cross RW, Prasad AN, Borisevich V, et al. Crimean-Congo hemorrhagic fever virus strains Hoti and Afghanistan cause viremia and mild clinical disease in cynomolgus monkeys. PLoS Negl Trop Dis. 2020; 14(8):e0008637.

[80] Furin J, Cox H, Pai M. Tuberculosis. Lancet. 2019; 393(10181): 1642-1656.

[81] Capuano SV, Croix DA, Pawar S, et al. Experimental mycobacterium tuberculosis infection of cynomolgus macaques closely resembles the various manifestations of human M. tuberculosis infection. Infect Immun. 2003; 71(10): 5831-5844.

[82] Pena JC, Ho WZ. Non-human primate models of tuberculosis. Microbiol Spectr. 2016; 4(4).

[83] Langermans JA, Andersen P, van Soolingen D, et al. Divergent effect of bacillus Calmette-Guerin (BCG) vaccination on mycobacterium tuberculosis infection in highly related macaque species: implications for primate models in tuberculosis vaccine research. Proc Natl Acad Sci USA. 2001; 98(20): 11497-11502.

[84] Sharpe SA, White AD, Sibley L, et al. An aerosol challenge model of tuberculosis in Mauritian cynomolgus macaques. PLoS One. 2017; 12(3):e0171906.

[85] Sibley L, Gooch K, Wareham A, et al. Differences in monocyte: lymphocyte ratio and tuberculosis disease progression in genetically distinct populations of macaques. Sci Rep. 2019; 9(1):3340.

[86] Naranbhai V, Hill AV, Abdool Karim SS, et al. Ratio of monocytes to lymphocytes in peripheral blood identifies adults at risk of incident tuberculosis among HIV-infected adults initiating antiretroviral therapy. J Infect Dis. 2014; 209(4): 500-509.

[87] Sibley L, Daykin-Pont O, Sarfas C, Pascoe J, White AD, Sharpe S. Differences in host immune populations between rhesus macaques and cynomolgus macaque subspecies in relation to susceptibility to mycobacterium tuberculosis infection. Sci Rep. 2021; 11(1):8810.

[88] Stevison LS, Kohn MH. Determining genetic background in captive stocks of cynomolgus macaques (Macaca fascicularis). J Med Primatol. 2008; 37(6): 311-317.

[89] Karp NA, Berdoy M, Gray K, et al. The sex inclusive research framework to address sex bias in preclinical research proposals. Nat Commun. 2025; 16(1):3763.

[90] Evans BJ, Pin L, Melnick DJ, Wright SI. Sex-linked inheritance in macaque monkeys: implications for effective population size and dispersal to Sulawesi. Genetics. 2010; 185(3): 923-937.

[91] Mao P, Gallagher P, Nedungadi S, et al. Mitochondrial DNA deletions and differential mitochondrial DNA content in rhesus monkeys: implications for aging. Biochim Biophys Acta (BBA) - Mol Basis Dis. 2012; 1822(2): 111-119.

[92] Guo S, Zhou Y, Zeng P, Xu G, Wang G, Cui Q. Identification and analysis of the human sex-biased genes. Brief Bioinform. 2018; 19(2): 188-198.

[93] Batdorj E, AlOgayil N, Zhuang QK, et al. Genetic variation in the Y chromosome and sex-biased DNA methylation in somatic cells in the mouse. Mamm Genome. 2023; 34(1): 44-55.

[94] Rovie-Ryan JJ, Khan FAA, Abdullah MT. Evolutionary pattern of Macaca fascicularis in Southeast Asia inferred using Y-chromosomal gene. BMC Ecol Evol. 2021; 21(1):26.

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