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Natural Killer Cells Regulate Acute SIV Replication, Dissemination, and Inflammation, but Do Not Impact Independent Transmission Events. J Virol 2023; 97:e0151922. [PMID: 36511699 PMCID: PMC9888193 DOI: 10.1128/jvi.01519-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Natural killer (NK) cells are potent effector cells of the innate immune system possessing both cytotoxic and immunoregulatory capabilities, which contribute to their crucial role in controlling human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) infections. However, despite significant evidence for NK cell modulation of HIV disease, their specific contribution to transmission and control of acute infection remains less clear. To elucidate the contribution of NK cells during acute SIV infection, we performed an acute necropsy study, where rhesus macaques (RM) were subjected to preinfection depletion of systemic NK cells using established methods of IL-15 neutralization, followed by subsequent challenge with barcoded SIVmac239X. Our study showed that depletion was highly effective, resulting in near total ablation of all NK cell subsets in blood, liver, oral, and rectal mucosae, and lymph nodes (LN) that persisted through the duration of the study. Meanwhile, frequencies and phenotypes of T cells remained virtually unchanged, indicating that our method of NK cell depletion had minimal off-target effects. Importantly, NK cell-depleted RM demonstrated an early and sustained 1 to 2 log increase in viremia over controls, but sequence analysis suggested no difference in the number of independent transmission events. Acute bulk, central memory (CM), and CCR5+ CD4+ T cell depletion was similar between experimental and control groups, while CD8+ T cell activation was higher in NK cell-depleted RM as measured by Ki67 and PD-1 expression. Using 27-plex Luminex analyses, we also found modestly increased inflammatory cytokines in NK cell-depleted RM compared to control animals. In the effort to determine the impact of NK cells on HIV/SIV transmission and acute viremia, future studies will be necessary to better harness these cells for future viral therapies. Collectively, these data suggest NK cells are important modulators of lentivirus dissemination and disease but may not have the capacity to independently eliminate individual transmission events. IMPORTANCE Natural killer (NK) cells as major effector cells of the innate immune system can contribute significantly to human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) control. However, a specific role for NK cells in blocking lentivirus transmission remains incompletely clear. In this study, we depleted NK cells prior to challenge with a barcoded SIV. Importantly, our studied showed systemic NK cell depletion was associated with a significant increase in acute viremia, but did not impact the number of independent transmission events. Collectively, these data suggest NK cells are critical modulators of early lentivirus replication but may not regulate individual transmission events at mucosal portals of entry.
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Bhebhe L, Moyo S, Gaseitsiwe S, Pretorius-Holme M, Yankinda EK, Manyake K, Kgathi C, Mmalane M, Lebelonyane R, Gaolathe T, Bachanas P, Ussery F, Letebele M, Makhema J, Wirth KE, Lockman S, Essex M, Novitsky V, Ragonnet-Cronin M. Epidemiological and viral characteristics of undiagnosed HIV infections in Botswana. BMC Infect Dis 2022; 22:710. [PMID: 36031617 PMCID: PMC9420270 DOI: 10.1186/s12879-022-07698-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 08/17/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
HIV-1 is endemic in Botswana. The country’s primary challenge is identifying people living with HIV who are unaware of their status. We evaluated factors associated with undiagnosed HIV infection using HIV-1 phylogenetic, behavioural, and demographic data.
Methods
As part of the Botswana Combination Prevention Project, 20% of households in 30 villages were tested for HIV and followed from 2013 to 2018. A total of 12,610 participants were enrolled, 3596 tested HIV-positive at enrolment, and 147 participants acquired HIV during the trial. Extensive socio-demographic and behavioural data were collected from participants and next-generation sequences were generated for HIV-positive cases. We compared three groups of participants: (1) those previously known to be HIV-positive at enrolment (n = 2995); (2) those newly diagnosed at enrolment (n = 601) and (3) those who tested HIV-negative at enrolment but tested HIV-positive during follow-up (n = 147). We searched for differences in demographic and behavioural factors between known and newly diagnosed group using logistic regression. We also compared the topology of each group in HIV-1 phylogenies and used a genetic diversity-based algorithm to classify infections as recent (< 1 year) or chronic (≥ 1 year).
Results
Being male (aOR = 2.23) and younger than 35 years old (aOR = 8.08) was associated with undiagnosed HIV infection (p < 0.001), as was inconsistent condom use (aOR = 1.76). Women were more likely to have undiagnosed infections if they were married, educated, and tested frequently. For men, being divorced increased their risk. The genetic diversity-based algorithm classified most incident infections as recent (75.0%), but almost none of known infections (2.0%). The estimated proportion of recent infections among new diagnoses was 37.0% (p < 0.001).
Conclusion
Our results indicate that those with undiagnosed infections are likely to be young men and women who do not use condoms consistently. Among women, several factors were predictive: being married, educated, and testing frequently increased risk. Men at risk were more difficult to delineate. A sizeable proportion of undiagnosed infections were recent based on a genetic diversity-based classifier. In the era of “test and treat all”, pre-exposure prophylaxis may be prioritized towards individuals who self-identify or who can be identified using these predictors in order to halt onward transmission in time.
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Brenner BG, Ibanescu RI, Osman N, Cuadra-Foy E, Oliveira M, Chaillon A, Stephens D, Hardy I, Routy JP, Thomas R, Baril JG, Leblanc R, Tremblay C, Roger M. The Role of Phylogenetics in Unravelling Patterns of HIV Transmission towards Epidemic Control: The Quebec Experience (2002-2020). Viruses 2021; 13:1643. [PMID: 34452506 PMCID: PMC8402830 DOI: 10.3390/v13081643] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/09/2021] [Accepted: 08/11/2021] [Indexed: 01/23/2023] Open
Abstract
Phylogenetics has been advanced as a structural framework to infer evolving trends in the regional spread of HIV-1 and guide public health interventions. In Quebec, molecular network analyses tracked HIV transmission dynamics from 2002-2020 using MEGA10-Neighbour-joining, HIV-TRACE, and MicrobeTrace methodologies. Phylogenetics revealed three patterns of viral spread among Men having Sex with Men (MSM, n = 5024) and heterosexuals (HET, n = 1345) harbouring subtype B epidemics as well as B and non-B subtype epidemics (n = 1848) introduced through migration. Notably, half of new subtype B infections amongst MSM and HET segregating as solitary transmissions or small cluster networks (2-5 members) declined by 70% from 2006-2020, concomitant to advances in treatment-as-prevention. Nonetheless, subtype B epidemic control amongst MSM was thwarted by the ongoing genesis and expansion of super-spreader large cluster variants leading to micro-epidemics, averaging 49 members/cluster at the end of 2020. The growth of large clusters was related to forward transmission cascades of untreated early-stage infections, younger at-risk populations, more transmissible/replicative-competent strains, and changing demographics. Subtype B and non-B subtype infections introduced through recent migration now surpass the domestic epidemic amongst MSM. Phylodynamics can assist in predicting and responding to active, recurrent, and newly emergent large cluster networks, as well as the cryptic spread of HIV introduced through migration.
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Affiliation(s)
- Bluma G. Brenner
- McGill Centre for Viral Diseases, Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; (R.-I.I.); (N.O.); (E.C.-F.); (M.O.)
- Department of Microbiology and Immunology, McGill University, Montréal, QC H4A 3J1, Canada
- Department of Medicine (Surgery, Infectious Disease), McGill University, Montréal, QC H3A 2M7, Canada
| | - Ruxandra-Ilinca Ibanescu
- McGill Centre for Viral Diseases, Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; (R.-I.I.); (N.O.); (E.C.-F.); (M.O.)
| | - Nathan Osman
- McGill Centre for Viral Diseases, Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; (R.-I.I.); (N.O.); (E.C.-F.); (M.O.)
- Department of Microbiology and Immunology, McGill University, Montréal, QC H4A 3J1, Canada
| | - Ernesto Cuadra-Foy
- McGill Centre for Viral Diseases, Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; (R.-I.I.); (N.O.); (E.C.-F.); (M.O.)
- Department of Microbiology and Immunology, McGill University, Montréal, QC H4A 3J1, Canada
| | - Maureen Oliveira
- McGill Centre for Viral Diseases, Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; (R.-I.I.); (N.O.); (E.C.-F.); (M.O.)
| | - Antoine Chaillon
- Department of Medicine, University of California, San Diego, CA 93903, USA;
| | - David Stephens
- Department of Mathematics and Statistics, McGill University, Montréal, QC H3A 0B9, Canada;
| | - Isabelle Hardy
- Département de Microbiologie et d’Immunologie et Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CHUM), Montréal, QC H2X 0C1, Canada; (I.H.); (C.T.); (M.R.)
| | - Jean-Pierre Routy
- Chronic Viral Illness Service, McGill University Health Centre, Montréal, QC H3A 3J1, Canada;
| | - Réjean Thomas
- Clinique Médicale l’Actuel, Montréal, QC H2L 4P9, Canada;
| | - Jean-Guy Baril
- Clinique Médicale Urbaine du Quartier Latin, Montréal, QC H2L 4E9, Canada;
| | - Roger Leblanc
- Clinique Médicale OPUS, Montréal, QC H3A 1T1, Canada;
| | - Cecile Tremblay
- Département de Microbiologie et d’Immunologie et Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CHUM), Montréal, QC H2X 0C1, Canada; (I.H.); (C.T.); (M.R.)
| | - Michel Roger
- Département de Microbiologie et d’Immunologie et Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CHUM), Montréal, QC H2X 0C1, Canada; (I.H.); (C.T.); (M.R.)
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