IntroductionMpox (formerly known as monkeypox), previously considered endemic to several Western and Central African countries1, has been declared a public health emergency of international concern (PHEIC) by the World Health Organization (WHO) for the second time2. The ongoing outbreak also prompted the Africa Centers for Disease Control and Prevention (Africa CDC) to declare its first-ever public-health emergency on 13th August3. Before this, WHO had declared mpox a PHEIC by on July 23, 20224. Mpox has sparked a global public health crisis, with over 117,600 cases and over 200 deaths reported5. In the Democratic Republic of the Congo (DRC) alone, approximately 18,000 suspected cases, many involving children6, and at least 600 deaths potentially attributable to the disease in 20247,8. Only one week in September 2024, more than 100 mpox-related deaths were recorded across African countries9. Efforts to contain the virus have been complicated by the emergence of viral variants10,11, the lack of effective and widely accessible vaccines7,12, and dashed hope of tecovirimat against a spreading type of mpox virus (MPXV)13, increasing the challenge of curbing further transmission both in Africa and globally.The co-infection of human immunodeficiency virus (HIV) and MPXV significantly increases the complexity of the disease and the burden on public health. During both the 2022 mpox outbreak and its recent resurgence, high transmission rates were recorded among sex workers and men who have sex with men (MSM)14,15. These populations also suffer a higher risk of other sexually transmitted diseases, particularly HIV infection. Their high rates of immunosuppression make them more vulnerable to MPXV infection and associated mortality16,17,18. In DRC, HIV prevalence is estimated at 7.5% among sex workers and 7.1% among MSM19. During the 2022 mpox outbreak, approximately 40% of MPXV cases in the MSM population were co-infected with HIV15. Similarly, an investigation in Shenzhen, China, reported about 56.5% (52/92) of enrolled mpox cases were also diagnosed with HIV11. The larger skin lesions, more prolonged illness, and higher rates of genital ulcers and bacterial superinfection were observed in the populations infected with HIV-1 and MPXV when compared to HIV-negative cases1. Notably, 15% mortality in patients with HIV-related disease characterized by CD4+ T cell counts below 200 cells per mm³ were uncovered in a large case series17. Moreover, the safety and tolerability of drugs and vaccines targeting mpox in immunocompromised populations have also raised concerns among the public. Given the epidemiological overlap between mpox and HIV infection, the possible serious consequences of co-infection, and the limitations of medication and vaccines for HIV-infected individuals, it is both meaningful and necessary to explore the differences in symptoms, underlying mechanisms, and treatment targets between co-infected individuals and those with mpox infection alone.Omics analysis has recently become a crucial tool in studying pathogens, providing essential information for viral prevention and drug development, as demonstrated with ZIKV and SARS-CoV-2. The integrated proteomics approach, including proteome and phosphoproteome, used in research associated with ZIKV identified the proteins, the host factors involving the cellular responses to viral infection and phosphorylation sites that are specifically up- or down-regulated after ZIKV infection20. In the global responses to the COVID-19 pandemic, multi-omics (interactome, proteome, transcriptome, and bibliome) data and subsequent integrated analysis were used to identify biomarkers for understanding the pathogenesis of severe COVID-19, providing the hotspots that could be targeted by existing drugs and may be used to guide rational design of virus- and host-directed therapies21,22,23,24. Such information forms a central pillar of global pandemic preparedness programs25. However, there remains a significant gap in omics research on MPXV. Few studies exist, including limited transcriptomic analyses26,27,28,29, a plasma proteomic study of MPXV-infected patients30, a pulmonary fluid proteomic study of MPXV-infected macaques31, and a multi-omics study of MPXV infection in primary human cells in vitro32. The plasma proteomic study revealed correlations between plasma proteins and disease severity, identifying strong responses among nutritional and acute-phase proteins30. Increased expression of inflammatory proteins was observed in response to MPXV in the pulmonary fluid proteomic study of MPXV-infected macaques31. Meanwhile, multi-omics studies uncovered regulation of the HIPPO and TGF-β pathways, dynamic phosphorylation of H5 affecting its binding to dsDNA, and the role of MAPKs as key regulators of differential phosphorylation in MPXV-infected cells32. Despite these findings, there is still a lack of proteomic data directly examining MPXV-induced tissue damage in vivo. Furthermore, no comprehensive studies have yet compared the multi-organ molecular and pathological differences between individuals infected with MPXV alone and those co-infected with both HIV and MPXV. Using proteomics and phosphoproteomics analysis to predict kinase targets can provide effective candidate drugs for screening antiviral agents against the monkeypox virus. To understand how HIV-MPXV co-infection leads to more severe clinical outcomes than MPXV infection alone, we inoculated rhesus macaques with simian immunodeficiency virus (SIV) to model HIV infection in humans. Furthermore, we developed rhesus macaque models for both SIV-MPXV co-infection and MPXV infection alone. Macaques co-infected with SIV-MPXV exhibited more extensive skin lesions than those with MPXV infection alone. In-depth proteomic and phosphoproteomic analyses revealed distinct protein and phosphosite profiles in the skin lesions of co-infected versus singly infected macaques. Further proteomic and phosphoproteomic analyses across eight other organs (lymph node, spleen, cerebral cortex, lung, heart, liver, kidney, and rectum) showed that SIV-induced systematic dysfunction in MPXV-infected macaques. These findings enhanced our understanding of MPXV biology and provide valuable datasets for further MPXV study.ResultsChronic SIV-infected rhesus macaques develop increased lesions following MPXV infectionTo mimic mpox cases with and without HIV co-infection and compare their pathogenicity, we enrolled six rhesus macaques with chronic simian immunodeficiency virus (SIVmac239) infection into the SIV-MPXV (MS) group and six naïve macaques into the MPXV-alone (MP) group (Fig.1a and Supplementary Data S1). Prior to the MPXV challenge, the six macaques in the MS group were intravenously inoculated with 100 TCID50 of SIVmac239 and monitored for plasma viral loads over 115 days. During this period, all six macaques exhibited persistent SIV replication in peripheral blood (Supplementary Fig. S1a and Fig.1b) along with a decreased CD4+/CD8+ T cell ratio and CD4+ T cell counts (Supplementary Fig. S1b), confirming the successful establishment of a chronic and stable SIV infection model. Subsequently, all twelve macaques were intravenously challenged with 1 × 107 TCID50 of MPXV clade IIb (MPXV-B.1-China-C-Tan-CQ01), isolated from the first imported mpox case in China in 2022.Fig. 1: Study design and comparison of skin lesions in rhesus macaques from the MPXV and SIV-MPXV groups.a Study design. Group A (MS, SIV-MPXV, n = 6) and Group B (MP, MPXV, n = 6). b SIV RNA and MPXV DNA loads in the plasma of monkeys before (n = 6) and after 10 dpi (n = 3). The shaded areas within the dashed lines indicate the standard deviation (SD). c,d Skin lesion counts (n = 6 before 10 dpi, n = 3 after 10 dpi) and duration from onset to resolution. Statistical differences between groups were analyzed using two-way ANOVA. ****P