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Duncan MC, Omondi FH, Kinloch NN, Lapointe HR, Speckmaier S, Moran-Garcia N, Lawson T, DeMarco ML, Simons J, Holmes DT, Lowe CF, Bacani N, Sereda P, Barrios R, Harris M, Romney MG, Montaner JSG, Brumme CJ, Brockman MA, Brumme ZL. Effects of COVID-19 mRNA vaccination on HIV viremia and reservoir size. AIDS 2024:00002030-990000000-00434. [PMID: 38224350 DOI: 10.1097/qad.0000000000003841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
OBJECTIVE The immunogenic nature of COVID-19 mRNA vaccines led to some initial concern that these could stimulate the HIV reservoir. We analyzed changes in plasma HIV loads (pVL) and reservoir size following COVID-19 mRNA vaccination in 62 people with HIV (PWH) receiving antiretroviral therapy (ART), and analyzed province-wide trends in pVL before and after the mass vaccination campaign. DESIGN Longitudinal observational cohort and province-wide analysis. METHODS 62 participants were sampled pre-vaccination, and one month after their first and second COVID-19 immunizations. Vaccine-induced anti-SARS-CoV-2-Spike antibodies in serum were measured using the Roche Elecsys Anti-S assay. HIV reservoirs were quantified using the Intact Proviral DNA Assay; pVL were measured using the cobas 6800 (LLOQ:20 copies/mL). The province-wide analysis included all 290,401 pVL performed in British Columbia, Canada between 2012-2022. RESULTS Pre-vaccination, the median intact reservoir size was 77 (IQR:20-204) HIV copies/million CD4+ T-cells, compared to 74 (IQR:27-212) and 65 (IQR:22-174) post-first and -second dose, respectively (all comparisons p>0.07). Pre-vaccination, 82% of participants had pVL<20 copies/mL (max:110 copies/mL), compared to 79% post-first dose (max:183 copies/mL) and 85% post-second dose (max:79 copies/mL) (p > 0.4). There was no evidence that the magnitude of the vaccine-elicited anti-SARS-CoV-2-Spike immune response influenced pVL nor changes in reservoir size (p > 0.6). We found no evidence linking the COVID-19 mass vaccination campaign to population-level increases in detectable pVL frequency among all PWH in the province, nor among those who maintained pVL suppression on ART. CONCLUSION We found no evidence that COVID-19 mRNA vaccines induced changes in HIV reservoir size nor plasma viremia.
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Affiliation(s)
- Maggie C Duncan
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - F Harrison Omondi
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Natalie N Kinloch
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Hope R Lapointe
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Sarah Speckmaier
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | | | - Tanya Lawson
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
| | - Mari L DeMarco
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Janet Simons
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Daniel T Holmes
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Christopher F Lowe
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Nic Bacani
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Paul Sereda
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Rolando Barrios
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | - Marianne Harris
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Family Practice, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Marc G Romney
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Julio S G Montaner
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Mark A Brockman
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Zabrina L Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
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Kinloch NN, Shahid A, Dong W, Kirkby D, Jones BR, Beelen CJ, MacMillan D, Lee GQ, Mota TM, Sudderuddin H, Barad E, Harris M, Brumme CJ, Jones RB, Brockman MA, Joy JB, Brumme ZL. HIV reservoirs are dominated by genetically younger and clonally enriched proviruses. mBio 2023; 14:e0241723. [PMID: 37971267 PMCID: PMC10746175 DOI: 10.1128/mbio.02417-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 10/09/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Characterizing the human immunodeficiency virus (HIV) reservoir that endures despite antiretroviral therapy (ART) is critical to cure efforts. We observed that the oldest proviruses persisting during ART were exclusively defective, while intact proviruses (and rebound HIV) dated to nearer ART initiation. This helps explain why studies that sampled sub-genomic proviruses on-ART (which are largely defective) routinely found sequences dating to early infection, whereas those that sampled replication-competent HIV found almost none. Together with our findings that intact proviruses were more likely to be clonal, and that on-ART low-level/isolated viremia originated from proviruses of varying ages (including possibly defective ones), our observations indicate that (i) on-ART and rebound viremia can have distinct within-host origins, (ii) intact proviruses have shorter lifespans than grossly defective ones and thus depend more heavily on clonal expansion for persistence, and (iii) an HIV reservoir predominantly "dating" to near ART initiation will be substantially adapted to within-host pressures, complicating immune-based cure strategies.
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Affiliation(s)
- Natalie N. Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Winnie Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Don Kirkby
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Bradley R. Jones
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Bioinformatics Program, University of British Columbia, Vancouver, British Columbia, Canada
| | - Charlotte J. Beelen
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Daniel MacMillan
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Guinevere Q. Lee
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Talia M. Mota
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Hanwei Sudderuddin
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Experimental Medicine Program, University of British Columbia, Vancouver, British Columbia, Canada
| | - Evan Barad
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Marianne Harris
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Department of Family Practice, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - R. Brad Jones
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Mark A. Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Jeffrey B. Joy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Bioinformatics Program, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
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DeKoven S, Naccarato M, Brumme CJ, Tan DHS. Treatment-emergent reverse transcriptase resistance during antiretroviral therapy with bictegravir, tenofovir alafenamide, and emtricitabine: A case series. HIV Med 2023; 24:1137-1143. [PMID: 37317505 DOI: 10.1111/hiv.13520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/26/2023] [Indexed: 06/16/2023]
Abstract
OBJECTIVES Bictegravir/tenofovir alafenamide/emtricitabine (BIC/TAF/FTC) is a complete regimen for the treatment of HIV with a high barrier to resistance and few reported cases of treatment failure. We present three cases of treatment-emergent resistance to nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs) in patients with suboptimal treatment adherence and assess whether the resistance-associated mutations were present before BIC/TAF/FTC initiation or emerged during therapy. METHODS We used genotypic drug resistance testing by Sanger sequencing to identify emergent resistance mutations in plasma viral load specimens collected after combination antiretroviral therapy initiation in all participants. Additionally, we performed ultra-deep sequencing by Illumina MiSeq on the earliest available plasma HIV-1 viral load specimen and on any available specimens closest in time to the initiation of BIC/TAF/FTC therapy to identify low-abundance resistance mutations present in the viral quasispecies. RESULTS All three participants developed NRTI resistance after prolonged exposure and incomplete adherence to BIC/TAF/FTC. The T69N, K70E, M184I, and/or T215I mutations identified in clinical samples at the time of virological failure were not present on deep sequencing of either baseline samples or samples collected before BIC/TAF/FTC initiation. CONCLUSIONS Despite a generally high genetic barrier to resistance, NRTI resistance-associated mutations may emerge during therapy with BIC/TAF/FTC in the setting of suboptimal adherence.
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Affiliation(s)
- Samuel DeKoven
- Department of Family and Community Medicine, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Mark Naccarato
- Department of Pharmacy, Henry Ford Hospital, Detroit, Michigan, USA
| | - Chanson J Brumme
- BC Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Division of Infectious Diseases, University of British Columbia, Vancouver, British Columbia, Canada
| | - Darrell H S Tan
- Division of Infectious Diseases, St. Michael's Hospital, Toronto, Ontario, Canada
- MAP Centre for Urban Health Solutions, St. Michael's Hospital, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
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4
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Duncan MC, Omondi FH, Kinloch NN, Lapointe HR, Speckmaier S, Moran-Garcia N, Lawson T, DeMarco ML, Simons J, Holmes DT, Lowe CF, Bacani N, Sereda P, Barrios R, Harris M, Romney MG, Montaner JSG, Brumme CJ, Brockman MA, Brumme ZL. Effects of COVID-19 mRNA vaccination on HIV viremia and reservoir size. medRxiv 2023:2023.10.08.23296718. [PMID: 37873490 PMCID: PMC10593027 DOI: 10.1101/2023.10.08.23296718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Objective The immunogenic nature of COVID-19 mRNA vaccines led to some initial concern that these could stimulate the HIV reservoir. We analyzed changes in plasma HIV loads (pVL) and reservoir size following COVID-19 mRNA vaccination in 62 people with HIV (PWH) receiving antiretroviral therapy (ART), and analyzed province-wide trends in pVL before and after the mass vaccination campaign. Design Longitudinal observational cohort and province-wide analysis. Methods 62 participants were sampled pre-vaccination, and one month after their first and second COVID-19 immunizations. Vaccine-induced anti-SARS-CoV-2-Spike antibodies in serum were measured using the Roche Elecsys Anti-S assay. HIV reservoirs were quantified using the Intact Proviral DNA Assay; pVL were measured using the cobas 6800 (LLOQ:20 copies/mL). The province-wide analysis included all 290,401 pVL performed in British Columbia, Canada between 2012-2022. Results Pre-vaccination, the median intact reservoir size was 77 (IQR:20-204) HIV copies/million CD4+ T-cells, compared to 74 (IQR:27-212) and 65 (IQR:22-174) post-first and -second dose, respectively (all comparisons p>0.07). Pre-vaccination, 82% of participants had pVL<20 copies/mL (max:110 copies/mL), compared to 79% post-first dose (max:183 copies/mL) and 85% post-second dose (max:79 copies/mL) (p>0.4). The magnitude of the vaccine-elicited anti-SARS-CoV-2-Spike antibody response did not correlate with changes in reservoir size nor detectable pVL frequency (p>0.6). We found no evidence linking the COVID-19 mass vaccination campaign to population-level increases in detectable pVL frequency among all PWH in the province, nor among those who maintained pVL suppression on ART. Conclusion We found no evidence that COVID-19 mRNA vaccines induced changes in HIV reservoir size nor plasma viremia.
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Affiliation(s)
- Maggie C Duncan
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - F Harrison Omondi
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Natalie N Kinloch
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Hope R Lapointe
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Sarah Speckmaier
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | | | - Tanya Lawson
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
| | - Mari L DeMarco
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Janet Simons
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Daniel T Holmes
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Christopher F Lowe
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Nic Bacani
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Paul Sereda
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Rolando Barrios
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | - Marianne Harris
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Family Practice, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Marc G Romney
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Julio S G Montaner
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Mark A Brockman
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Zabrina L Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
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5
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Kinloch NN, Shahid A, Dong W, Kirkby D, Jones BR, Beelen CJ, MacMillan D, Lee GQ, Mota TM, Sudderuddin H, Barad E, Harris M, Brumme CJ, Jones RB, Brockman MA, Joy JB, Brumme ZL. HIV reservoirs are dominated by genetically younger and clonally enriched proviruses. bioRxiv 2023:2023.04.12.536611. [PMID: 37090500 PMCID: PMC10120704 DOI: 10.1101/2023.04.12.536611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
In order to cure HIV, we need to better understand the within-host evolutionary origins of the small reservoir of genome-intact proviruses that persists within infected cells during antiretroviral therapy (ART). Most prior studies on reservoir evolutionary dynamics however did not discriminate genome-intact proviruses from the vast background of defective ones. We reconstructed within-host pre-ART HIV evolutionary histories in six individuals and leveraged this information to infer the ages of intact and defective proviruses sampled after an average >9 years on ART, along with the ages of rebound and low-level/isolated viremia occurring during this time. We observed that the longest-lived proviruses persisting on ART were exclusively defective, usually due to large deletions. In contrast, intact proviruses and rebound HIV exclusively dated to the years immediately preceding ART. These observations are consistent with genome-intact proviruses having shorter lifespans, likely due to the cumulative risk of elimination following viral reactivation and protein production. Consistent with this, intact proviruses (and those with packaging signal defects) were three times more likely to be genetically identical compared to other proviral types, highlighting clonal expansion as particularly important in ensuring their survival. By contrast, low-level/isolated viremia sequences were genetically heterogeneous and sometimes ancestral, where viremia may have originated from defective proviruses. Results reveal that the HIV reservoir is dominated by clonally-enriched and genetically younger sequences that date to the untreated infection period when viral populations had been under within-host selection pressures for the longest duration. Knowledge of these qualities may help focus strategies for reservoir elimination.
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Affiliation(s)
- Natalie N. Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
| | - Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
| | - Winnie Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
| | - Don Kirkby
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
| | - Bradley R. Jones
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
- Bioinformatics Program, University of British Columbia, Vancouver, BC
| | | | - Daniel MacMillan
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
| | - Guinevere Q. Lee
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Talia M. Mota
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Hanwei Sudderuddin
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
- Experimental Medicine Program, University of British Columbia, Vancouver, BC
| | - Evan Barad
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
| | - Marianne Harris
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
- Department of Family Practice, Faculty of Medicine, University of British Columbia, Vancouver, BC
| | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
- Department of Medicine, University of British Columbia, Vancouver, BC
| | - R. Brad Jones
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Mark A. Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby BC
| | - Jeffrey B. Joy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
- Bioinformatics Program, University of British Columbia, Vancouver, BC
- Department of Medicine, University of British Columbia, Vancouver, BC
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
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6
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Lapointe HR, Mwimanzi F, Cheung PK, Sang Y, Yaseen F, Umviligihozo G, Kalikawe R, Speckmaier S, Moran-Garcia N, Datwani S, Duncan MC, Agafitei O, Ennis S, Young L, Ali H, Ganase B, Omondi FH, Dong W, Toy J, Sereda P, Burns L, Costiniuk CT, Cooper C, Anis AH, Leung V, Holmes DT, DeMarco ML, Simons J, Hedgcock M, Prystajecky N, Lowe CF, Pantophlet R, Romney MG, Barrios R, Guillemi S, Brumme CJ, Montaner JSG, Hull M, Harris M, Niikura M, Brockman MA, Brumme ZL. People With Human Immunodeficiency Virus Receiving Suppressive Antiretroviral Therapy Show Typical Antibody Durability After Dual Coronavirus Disease 2019 Vaccination and Strong Third Dose Responses. J Infect Dis 2023; 227:838-849. [PMID: 35668700 PMCID: PMC9214159 DOI: 10.1093/infdis/jiac229] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/19/2022] [Accepted: 06/02/2022] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Longer-term humoral responses to 2-dose coronavirus disease 2019 (COVID-19) vaccines remain incompletely characterized in people living with human immunodeficiency virus (HIV) (PLWH), as do initial responses to a third dose. METHODS We measured antibodies against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein receptor-binding domain, angiotensin-converting enzyme 2 (ACE2) displacement, and viral neutralization against wild-type and Omicron strains up to 6 months after 2-dose vaccination, and 1 month after the third dose, in 99 PLWH receiving suppressive antiretroviral therapy and 152 controls. RESULTS Although humoral responses naturally decline after 2-dose vaccination, we found no evidence of lower antibody concentrations or faster rates of antibody decline in PLWH compared with controls after accounting for sociodemographic, health, and vaccine-related factors. We also found no evidence of poorer viral neutralization in PLWH after 2 doses, nor evidence that a low nadir CD4+ T-cell count compromised responses. Post-third-dose humoral responses substantially exceeded post-second-dose levels, though Omicron-specific responses were consistently weaker than responses against wild-type virus. Nevertheless, post-third-dose responses in PLWH were comparable to or higher than controls. An mRNA-1273 third dose was the strongest consistent correlate of higher post-third-dose responses. CONCLUSION PLWH receiving suppressive antiretroviral therapy mount strong antibody responses after 2- and 3-dose COVID-19 vaccination. Results underscore the immune benefits of third doses in light of Omicron.
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Affiliation(s)
- Hope R Lapointe
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Francis Mwimanzi
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Peter K Cheung
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Yurou Sang
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Fatima Yaseen
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Gisele Umviligihozo
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Rebecca Kalikawe
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Sarah Speckmaier
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Nadia Moran-Garcia
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Sneha Datwani
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Maggie C Duncan
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Olga Agafitei
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Siobhan Ennis
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Landon Young
- Division of Medical Microbiology and Virology, St Paul’s Hospital, Vancouver, British Columbia, Canada
| | - Hesham Ali
- John Ruedy Clinic, St Paul’s Hospital, Vancouver, British Columbia, Canada
| | - Bruce Ganase
- AIDS Research Program, St Paul’s Hospital, Vancouver, British Columbia, Canada
| | - F Harrison Omondi
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Winnie Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Junine Toy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Paul Sereda
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Laura Burns
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, British Columbia, Canada
| | - Cecilia T Costiniuk
- Division of Infectious Diseases and Chronic Viral Illness Service, McGill University Health Centre and Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Curtis Cooper
- Department of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Aslam H Anis
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
- CIHR Canadian HIV Trials Network, University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Health Evaluation and Outcome Sciences, Vancouver, British Columbia, Canada
| | - Victor Leung
- Division of Medical Microbiology and Virology, St Paul’s Hospital, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Daniel T Holmes
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mari L DeMarco
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Janet Simons
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Natalie Prystajecky
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada
| | - Christopher F Lowe
- Division of Medical Microbiology and Virology, St Paul’s Hospital, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ralph Pantophlet
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Marc G Romney
- Division of Medical Microbiology and Virology, St Paul’s Hospital, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Rolando Barrios
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Silvia Guillemi
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Department of Family Practice, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Julio S G Montaner
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mark Hull
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marianne Harris
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Department of Family Practice, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Masahiro Niikura
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Mark A Brockman
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Zabrina L Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
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7
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Mwimanzi F, Lapointe HR, Cheung PK, Sang Y, Yaseen F, Kalikawe R, Datwani S, Burns L, Young L, Leung V, Ennis S, Brumme CJ, Montaner JSG, Dong W, Prystajecky N, Lowe CF, DeMarco ML, Holmes DT, Simons J, Niikura M, Romney MG, Brumme ZL, Brockman MA. Impact of Age and Severe Acute Respiratory Syndrome Coronavirus 2 Breakthrough Infection on Humoral Immune Responses After Three Doses of Coronavirus Disease 2019 mRNA Vaccine. Open Forum Infect Dis 2023; 10:ofad073. [PMID: 36910697 PMCID: PMC10003738 DOI: 10.1093/ofid/ofad073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 02/08/2023] [Indexed: 02/11/2023] Open
Abstract
Background Longer-term immune response data after 3 doses of coronavirus disease 2019 (COVID-19) mRNA vaccine remain limited, particularly among older adults and after Omicron breakthrough infection. Methods We quantified wild-type- and Omicron-specific serum immunoglobulin (Ig)G levels, angiotensin-converting enzyme 2 displacement activities, and live virus neutralization up to 6 months after third dose in 116 adults aged 24-98 years who remained COVID-19 naive or experienced their first severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection during this time. Results Among the 78 participants who remained COVID-19 naive throughout follow up, wild-type- and Omicron-BA.1-specific IgG concentrations were comparable between younger and older adults, although BA.1-specific responses were consistently significantly lower than wild-type-specific responses in both groups. Wild-type- and BA.1-specific IgG concentrations declined at similar rates in COVID-19-naive younger and older adults, with median half-lives ranging from 69 to 78 days. Antiviral antibody functions declined substantially over time in COVID-19-naive individuals, particularly in older adults: by 6 months, BA.1-specific neutralization was undetectable in 96% of older adults, versus 56% of younger adults. Severe acute respiratory syndrome coronavirus 2 infection, experienced by 38 participants, boosted IgG levels and neutralization above those induced by vaccination alone. Nevertheless, BA.1-specific neutralization remained significantly lower than wild-type, with BA.5-specific neutralization lower still. Higher Omicron BA.1-specific neutralization 1 month after third dose was an independent correlate of lower SARS-CoV-2 infection risk. Conclusions Results underscore the immune benefits of the third COVID-19 mRNA vaccine dose in adults of all ages and identify vaccine-induced Omicron-specific neutralization as a correlate of protective immunity. Systemic antibody responses and functions however, particularly Omicron-specific neutralization, decline rapidly in COVID-19-naive individuals, particularly in older adults, supporting the need for additional booster doses.
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Affiliation(s)
- Francis Mwimanzi
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Hope R Lapointe
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Peter K Cheung
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Yurou Sang
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Fatima Yaseen
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Rebecca Kalikawe
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Sneha Datwani
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Laura Burns
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
| | - Landon Young
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
| | - Victor Leung
- Department of Medicine, University of British Columbia, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Siobhan Ennis
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Julio S G Montaner
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Winnie Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Natalie Prystajecky
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, Canada
| | - Christopher F Lowe
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Mari L DeMarco
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Daniel T Holmes
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Janet Simons
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Masahiro Niikura
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | | | | | - Mark A Brockman
- Correspondence: Mark A. Brockman, PhD, Professor, Faculty of Health Sciences, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada ()
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8
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Appah A, Beelen CJ, Kirkby D, Dong W, Shahid A, Foley B, Mensah M, Ganu V, Puplampu P, Amoah LE, Nii-Trebi NI, Brumme CJ, Brumme ZL. Molecular Epidemiology of HIV-1 in Ghana: Subtype Distribution, Drug Resistance and Coreceptor Usage. Viruses 2022; 15:128. [PMID: 36680168 PMCID: PMC9865111 DOI: 10.3390/v15010128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 12/27/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023] Open
Abstract
The greatest HIV-1 genetic diversity is found in West/Central Africa due to the pandemic’s origins in this region, but this diversity remains understudied. We characterized HIV-1 subtype diversity (from both sub-genomic and full-genome viral sequences), drug resistance and coreceptor usage in 103 predominantly (90%) antiretroviral-naive individuals living with HIV-1 in Ghana. Full-genome HIV-1 subtyping confirmed the circulating recombinant form CRF02_AG as the dominant (53.9%) subtype in the region, with the complex recombinant 06_cpx (4%) present as well. Unique recombinants, most of which were mosaics containing CRF02_AG and/or 06_cpx, made up 37% of sequences, while “pure” subtypes were rare (<6%). Pretreatment resistance to at least one drug class was observed in 17% of the cohort, with NNRTI resistance being the most common (12%) and INSTI resistance being relatively rare (2%). CXCR4-using HIV-1 sequences were identified in 23% of participants. Overall, our findings advance our understanding of HIV-1 molecular epidemiology in Ghana. Extensive HIV-1 genetic diversity in the region appears to be fueling the ongoing creation of novel recombinants, the majority CRF02_AG-containing, in the region. The relatively high prevalence of pretreatment NNRTI resistance but low prevalence of INSTI resistance supports the use of INSTI-based first-line regimens in Ghana.
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Affiliation(s)
- Anna Appah
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
| | - Charlotte J. Beelen
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
| | - Don Kirkby
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
| | - Winnie Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
| | - Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
| | - Brian Foley
- Los Alamos National Laboratory, P.O. Box 1663, Los Alamos, NM 87545, USA
| | - Miriam Mensah
- Fevers Unit, Department of Medicine, Korle Bu Teaching Hospital, Accra P.O. Box KB 77, Ghana
| | - Vincent Ganu
- Department of Internal Medicine, Korle Bu Teaching Hospital, Accra P.O. Box KB 77, Ghana
| | - Peter Puplampu
- Department of Internal Medicine, Korle Bu Teaching Hospital, Accra P.O. Box KB 77, Ghana
| | - Linda E. Amoah
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra P.O. Box LG 581, Ghana
| | - Nicholas I. Nii-Trebi
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra P.O. Box LG 25, Ghana
| | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
- Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
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9
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Mwimanzi F, Lapointe HR, Cheung PK, Sang Y, Yaseen F, Umviligihozo G, Kalikawe R, Datwani S, Omondi FH, Burns L, Young L, Leung V, Agafitei O, Ennis S, Dong W, Basra S, Lim LY, Ng K, Pantophlet R, Brumme CJ, Montaner JSG, Prystajecky N, Lowe CF, DeMarco ML, Holmes DT, Simons J, Niikura M, Romney MG, Brumme ZL, Brockman MA. Older Adults Mount Less Durable Humoral Responses to Two Doses of COVID-19 mRNA Vaccine but Strong Initial Responses to a Third Dose. J Infect Dis 2022; 226:983-994. [PMID: 35543278 PMCID: PMC9129202 DOI: 10.1093/infdis/jiac199] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 05/10/2022] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Third coronavirus disease 2019 (COVID-19) vaccine doses are broadly recommended, but immunogenicity data remain limited, particularly in older adults. METHODS We measured circulating antibodies against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein receptor-binding domain, ACE2 displacement, and virus neutralization against ancestral and omicron (BA.1) strains from prevaccine up to 1 month following the third dose, in 151 adults aged 24-98 years who received COVID-19 mRNA vaccines. RESULTS Following 2 vaccine doses, humoral immunity was weaker, less functional, and less durable in older adults, where a higher number of chronic health conditions was a key correlate of weaker responses and poorer durability. One month after the third dose, antibody concentrations and function exceeded post-second-dose levels, and responses in older adults were comparable in magnitude to those in younger adults at this time. Humoral responses against omicron were universally weaker than against the ancestral strain after both the second and third doses. Nevertheless, after 3 doses, anti-omicron responses in older adults reached equivalence to those in younger adults. One month after 3 vaccine doses, the number of chronic health conditions, but not age, was the strongest consistent correlate of weaker humoral responses. CONCLUSIONS Results underscore the immune benefits of third COVID-19 vaccine doses, particularly in older adults.
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Affiliation(s)
- Francis Mwimanzi
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Hope R Lapointe
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Peter K Cheung
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Yurou Sang
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Fatima Yaseen
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | | | - Rebecca Kalikawe
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Sneha Datwani
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - F Harrison Omondi
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Laura Burns
- Division of Medical Microbiology and Virology, St Paul’s Hospital, Vancouver, Canada
| | - Landon Young
- Division of Medical Microbiology and Virology, St Paul’s Hospital, Vancouver, Canada
| | - Victor Leung
- Department of Medicine, University of British Columbia, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Olga Agafitei
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Siobhan Ennis
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Winnie Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Simran Basra
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Li Yi Lim
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Kurtis Ng
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Ralph Pantophlet
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Julio S G Montaner
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Natalie Prystajecky
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, Canada
| | - Christopher F Lowe
- Division of Medical Microbiology and Virology, St Paul’s Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Mari L DeMarco
- Division of Medical Microbiology and Virology, St Paul’s Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Daniel T Holmes
- Division of Medical Microbiology and Virology, St Paul’s Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Janet Simons
- Division of Medical Microbiology and Virology, St Paul’s Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Masahiro Niikura
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Marc G Romney
- Division of Medical Microbiology and Virology, St Paul’s Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Mark A Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
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10
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Lapointe HR, Mwimanzi F, Cheung PK, Sang Y, Yaseen F, Kalikawe R, Datwani S, Waterworth R, Umviligihozo G, Ennis S, Young L, Dong W, Kirkby D, Burns L, Leung V, Holmes DT, DeMarco ML, Simons J, Matic N, Montaner JS, Brumme CJ, Prystajecky N, Niikura M, Lowe CF, Romney MG, Brockman MA, Brumme ZL. Serial infection with SARS-CoV-2 Omicron BA.1 and BA.2 following three-dose COVID-19 vaccination. Front Immunol 2022; 13:947021. [PMID: 36148225 PMCID: PMC9485663 DOI: 10.3389/fimmu.2022.947021] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/16/2022] [Indexed: 11/30/2022] Open
Abstract
SARS-CoV-2 Omicron infections are common among individuals who are vaccinated or have recovered from prior variant infection, but few reports have immunologically assessed serial Omicron infections. We characterized SARS-CoV-2 humoral responses in an individual who acquired laboratory-confirmed Omicron BA.1.15 ten weeks after a third dose of BNT162b2, and BA.2 thirteen weeks later. Responses were compared to 124 COVID-19-naive vaccinees. One month post-second and -third vaccine doses, the participant's wild-type and BA.1-specific IgG, ACE2-displacement and virus neutralization activities were average for a COVID-19-naive triple-vaccinated individual. BA.1 infection boosted the participant's responses to the cohort ≥95th percentile, but even this strong "hybrid" immunity failed to protect against BA.2. Reinfection increased BA.1 and BA.2-specific responses only modestly. Though vaccines clearly protect against severe disease, results highlight the continued importance of maintaining additional protective measures to counteract the immune-evasive Omicron variant, particularly as vaccine-induced immune responses naturally decline over time.
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Affiliation(s)
- Hope R. Lapointe
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Francis Mwimanzi
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Peter K. Cheung
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Yurou Sang
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Fatima Yaseen
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Rebecca Kalikawe
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Sneha Datwani
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Rachel Waterworth
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | | | - Siobhan Ennis
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Landon Young
- Division of Medical Microbiology and Virology, St. Paul’s Hospital, Vancouver, BC, Canada
| | - Winnie Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Don Kirkby
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Laura Burns
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, BC, Canada
| | - Victor Leung
- Division of Medical Microbiology and Virology, St. Paul’s Hospital, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Daniel T. Holmes
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Mari L. DeMarco
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Janet Simons
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Nancy Matic
- Division of Medical Microbiology and Virology, St. Paul’s Hospital, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Julio S.G. Montaner
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Natalie Prystajecky
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada
| | - Masahiro Niikura
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Christopher F. Lowe
- Division of Medical Microbiology and Virology, St. Paul’s Hospital, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Marc G. Romney
- Division of Medical Microbiology and Virology, St. Paul’s Hospital, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Mark A. Brockman
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Zabrina L. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
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11
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Brockman MA, Mwimanzi F, Lapointe HR, Sang Y, Agafitei O, Cheung PK, Ennis S, Ng K, Basra S, Lim LY, Yaseen F, Young L, Umviligihozo G, Omondi FH, Kalikawe R, Burns L, Brumme CJ, Leung V, Montaner JSG, Holmes D, DeMarco ML, Simons J, Pantophlet R, Niikura M, Romney MG, Brumme ZL. Reduced Magnitude and Durability of Humoral Immune Responses to COVID-19 mRNA Vaccines Among Older Adults. J Infect Dis 2022; 225:1129-1140. [PMID: 34888688 PMCID: PMC8689804 DOI: 10.1093/infdis/jiab592] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 12/07/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The magnitude and durability of immune responses to coronavirus disease 2019 (COVID-19) mRNA vaccines remain incompletely characterized in the elderly. METHODS Anti-spike receptor-binding domain (RBD) antibodies, angiotensin-converting enzyme 2 (ACE2) competition, and virus neutralizing activities were assessed in plasma from 151 health care workers and older adults (range, 24-98 years of age) 1 month following the first vaccine dose, and 1 and 3 months following the second dose. RESULTS Older adults exhibited significantly weaker responses than younger health care workers for all humoral measures evaluated and at all time points tested, except for ACE2 competition activity after 1 vaccine dose. Moreover, older age remained independently associated with weaker responses even after correction for sociodemographic factors, chronic health condition burden, and vaccine-related variables. By 3 months after the second dose, all humoral responses had declined significantly in all participants, and remained significantly lower among older adults, who also displayed reduced binding antibodies and ACE2 competition activity towards the Delta variant. CONCLUSIONS Humoral responses to COVID-19 mRNA vaccines are significantly weaker in older adults, and antibody-mediated activities in plasma decline universally over time. Older adults may thus remain at elevated risk of infection despite vaccination.
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Affiliation(s)
- Mark A Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Francis Mwimanzi
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Hope R Lapointe
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Yurou Sang
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Olga Agafitei
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Peter K Cheung
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Siobhan Ennis
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Kurtis Ng
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Simran Basra
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
- Department of Chemistry, Simon Fraser University, Burnaby, Canada
| | - Li Yi Lim
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Fatima Yaseen
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Landon Young
- Division of Medical Microbiology and Virology, St Paul’s Hospital, Vancouver, Canada
| | | | - F Harrison Omondi
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Rebecca Kalikawe
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Laura Burns
- Division of Medical Microbiology and Virology, St Paul’s Hospital, Vancouver, Canada
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Victor Leung
- Division of Medical Microbiology and Virology, St Paul’s Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Julio S G Montaner
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Daniel Holmes
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada
| | - Mari L DeMarco
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada
| | - Janet Simons
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada
| | - Ralph Pantophlet
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Masahiro Niikura
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Marc G Romney
- Division of Medical Microbiology and Virology, St Paul’s Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
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12
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Lapointe HR, Mwimanzi F, Cheung PK, Sang Y, Yaseen F, Umviligihozo G, Kalikawe R, Speckmaier S, Moran-Garcia N, Datwani S, Duncan MC, Agafitei O, Ennis S, Young L, Ali H, Ganase B, Omondi FH, Dong W, Toy J, Sereda P, Burns L, Costiniuk CT, Cooper C, Anis AH, Leung V, Holmes D, DeMarco ML, Simons J, Hedgcock M, Prystajecky N, Lowe CF, Pantophlet R, Romney MG, Barrios R, Guillemi S, Brumme CJ, Montaner JSG, Hull M, Harris M, Niikura M, Brockman MA, Brumme ZL. People with HIV receiving suppressive antiretroviral therapy show typical antibody durability after dual COVID-19 vaccination, and strong third dose responses. medRxiv 2022. [PMID: 35350205 PMCID: PMC8963693 DOI: 10.1101/2022.03.22.22272793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Background: Longer-term humoral responses to two-dose COVID-19 vaccines remain incompletely characterized in people living with HIV (PLWH), as do initial responses to a third dose. Methods: We measured antibodies against the SARS-CoV-2 spike protein receptor-binding domain, ACE2 displacement and viral neutralization against wild-type and Omicron strains up to six months following two-dose vaccination, and one month following the third dose, in 99 PLWH receiving suppressive antiretroviral therapy, and 152 controls. Results: Though humoral responses naturally decline following two-dose vaccination, we found no evidence of lower antibody concentrations nor faster rates of antibody decline in PLWH compared to controls after accounting for sociodemographic, health and vaccine-related factors. We also found no evidence of poorer viral neutralization in PLWH after two doses, nor evidence that a low nadir CD4+ T-cell count compromised responses. Post-third-dose humoral responses substantially exceeded post-second-dose levels, though anti-Omicron responses were consistently weaker than against wild-type. Nevertheless, post-third-dose responses in PLWH were comparable to or higher than controls. An mRNA-1273 third dose was the strongest consistent correlate of higher post-third-dose responses. Conclusion: PLWH receiving suppressive antiretroviral therapy mount strong antibody responses after two- and three-dose COVID-19 vaccination. Results underscore the immune benefits of third doses in light of Omicron.
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Affiliation(s)
- Hope R Lapointe
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Francis Mwimanzi
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Peter K Cheung
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada.,Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Yurou Sang
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Fatima Yaseen
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | | | - Rebecca Kalikawe
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Sarah Speckmaier
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | | | - Sneha Datwani
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Maggie C Duncan
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada.,Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Olga Agafitei
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Siobhan Ennis
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Landon Young
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
| | - Hesham Ali
- John Ruedy Clinic, St, Paul's Hospital, Vancouver, Canada
| | - Bruce Ganase
- AIDS Research Program, St. Paul's Hospital, Vancouver, Canada
| | - F Harrison Omondi
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada.,Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Winnie Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Junine Toy
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Paul Sereda
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Laura Burns
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada
| | - Cecilia T Costiniuk
- Division of Infectious Diseases and Chronic Viral Illness Service, McGill University Health Centre and Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Curtis Cooper
- Department of Medicine, University of Ottawa, Ottawa, Canada.,Ottawa Hospital Research Institute, Ottawa, Canada
| | - Aslam H Anis
- School of Population and Public Health, University of British Columbia, Vancouver, Canada.,CIHR Canadian HIV Trials Network, University of British Columbia, Vancouver, Canada.,Centre for Health Evaluation and Outcome Sciences, Vancouver, Canada
| | - Victor Leung
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Daniel Holmes
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Mari L DeMarco
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Janet Simons
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | | | - Natalie Prystajecky
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada.,British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, Canada
| | - Christopher F Lowe
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Ralph Pantophlet
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Marc G Romney
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Rolando Barrios
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada.,School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | - Silvia Guillemi
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada.,Department of Family Practice, Faculty of Medicine, University of British Columbia, Canada
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada.,Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Julio S G Montaner
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada.,Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Mark Hull
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada.,Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Marianne Harris
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada.,Department of Family Practice, Faculty of Medicine, University of British Columbia, Canada
| | - Masahiro Niikura
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Mark A Brockman
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada.,Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Zabrina L Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada.,Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
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13
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Mwimanzi F, Lapointe HR, Cheung PK, Sang Y, Yaseen F, Umviligihozo G, Kalikawe R, Datwani S, Omondi FH, Burns L, Young L, Leung V, Agafitei O, Ennis S, Dong W, Basra S, Lim LY, Ng K, Pantophlet R, Brumme CJ, Montaner JS, Prystajecky N, Lowe CF, DeMarco ML, Holmes DT, Simons J, Niikura M, Romney MG, Brumme ZL, Brockman MA. Older Adults Mount Less Durable Humoral Responses to a Two-dose COVID-19 mRNA Vaccine Regimen, but Strong Initial Responses to a Third Dose. medRxiv 2022:2022.01.06.22268745. [PMID: 35018381 PMCID: PMC8750654 DOI: 10.1101/2022.01.06.22268745] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND Third COVID-19 vaccine doses are broadly recommended, but immunogenicity data remain limited, particularly in older adults. METHODS We measured circulating antibodies against the SARS-CoV-2 spike protein receptor-binding domain, ACE2 displacement, and virus neutralization against ancestral and Omicron (BA.1) strains from pre-vaccine up to one month following the third dose, in 151 adults aged 24-98 years who received COVID-19 mRNA vaccines. RESULTS Following two vaccine doses, humoral immunity was weaker, less functional and less durable in older adults, where a higher number of chronic health conditions was a key correlate of weaker responses and poorer durability. Third doses boosted antibody binding and function to higher levels than second-doses, and induced responses in older adults that were comparable in magnitude to those in younger adults. Humoral responses against Omicron were universally weaker than against the ancestral strain after both second and third doses; nevertheless, after three doses, anti-Omicron responses in older adults reached equivalence to those in younger adults. After three vaccine doses, the number of chronic health conditions, but not age per se, was the strongest consistent correlate of weaker humoral responses. CONCLUSION Results underscore the immune benefits of third COVID-19 vaccine doses, particularly in older adults.
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Affiliation(s)
| | | | - Peter K. Cheung
- Faculty of Health Sciences, Simon Fraser University, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Canada
| | - Yurou Sang
- Faculty of Health Sciences, Simon Fraser University, Canada
| | - Fatima Yaseen
- Faculty of Health Sciences, Simon Fraser University, Canada
| | | | | | - Sneha Datwani
- Faculty of Health Sciences, Simon Fraser University, Canada
| | - F. Harrison Omondi
- Faculty of Health Sciences, Simon Fraser University, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Canada
| | - Laura Burns
- Division of Medical Microbiology and Virology, St. Paul’s Hospital, Canada
| | - Landon Young
- Division of Medical Microbiology and Virology, St. Paul’s Hospital, Canada
| | - Victor Leung
- Department of Medicine, University of British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Canada
| | - Olga Agafitei
- Faculty of Health Sciences, Simon Fraser University, Canada
| | - Siobhan Ennis
- Faculty of Health Sciences, Simon Fraser University, Canada
| | - Winnie Dong
- British Columbia Centre for Excellence in HIV/AIDS, Canada
| | - Simran Basra
- Faculty of Health Sciences, Simon Fraser University, Canada
| | - Li Yi Lim
- Faculty of Health Sciences, Simon Fraser University, Canada
| | - Kurtis Ng
- Faculty of Health Sciences, Simon Fraser University, Canada
| | | | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Canada
- Department of Medicine, University of British Columbia, Canada
| | - Julio S.G. Montaner
- British Columbia Centre for Excellence in HIV/AIDS, Canada
- Department of Medicine, University of British Columbia, Canada
| | - Natalie Prystajecky
- Department of Pathology and Laboratory Medicine, University of British Columbia, Canada
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, Canada
| | - Christopher F. Lowe
- Division of Medical Microbiology and Virology, St. Paul’s Hospital, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Canada
| | - Mari L. DeMarco
- Division of Medical Microbiology and Virology, St. Paul’s Hospital, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Canada
| | - Daniel T. Holmes
- Division of Medical Microbiology and Virology, St. Paul’s Hospital, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Canada
| | - Janet Simons
- Division of Medical Microbiology and Virology, St. Paul’s Hospital, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Canada
| | | | - Marc G. Romney
- Division of Medical Microbiology and Virology, St. Paul’s Hospital, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Canada
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Canada
| | - Mark A. Brockman
- Faculty of Health Sciences, Simon Fraser University, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Canada
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14
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Miller RL, McLaughlin A, Liang RH, Harding J, Wong J, Le AQ, Brumme CJ, Montaner JSG, Joy JB. Phylogenetic prioritization of HIV-1 transmission clusters with viral lineage-level diversification rates. Evol Med Public Health 2022; 10:305-315. [PMID: 35899097 PMCID: PMC9311310 DOI: 10.1093/emph/eoac026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 07/07/2022] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background and objectives
Public health officials faced with a large number of transmission clusters require a rapid, scalable and unbiased way to prioritize distribution of limited resources to maximize benefits. We hypothesize that transmission cluster prioritization based on phylogenetically derived lineage-level diversification rates will perform as well as or better than commonly used growth-based prioritization measures, without need for historical data or subjective interpretation.
Methodology
9822 HIV pol sequences collected during routine drug resistance genotyping were used alongside simulated sequence data to infer sets of phylogenetic transmission clusters via patristic distance threshold. Prioritized clusters inferred from empirical data were compared to those prioritized by the current public health protocols. Prioritization of simulated clusters was evaluated based on correlation of a given prioritization measure with future cluster growth, as well as the number of direct downstream transmissions from cluster members.
Results
Empirical data suggest diversification rate-based measures perform comparably to growth-based measures in recreating public heath prioritization choices. However, unbiased simulated data reveals phylogenetic diversification rate-based measures perform better in predicting future cluster growth relative to growth-based measures, particularly long-term growth. Diversification rate-based measures also display advantages over growth-based measures in highlighting groups with greater future transmission events compared to random groups of the same size. Furthermore, diversification rate measures were notably more robust to effects of decreased sampling proportion.
Conclusions and implications
Our findings indicate diversification rate-based measures frequently outperform growth-based measures in predicting future cluster growth and offer several additional advantages beneficial to optimizing the public health prioritization process.
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Affiliation(s)
- Rachel L Miller
- Molecular Epidemiology and Evolutionary Genetics, British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Bioinformatics Program, University of British Columbia, Vancouver, Canada
| | - Angela McLaughlin
- Molecular Epidemiology and Evolutionary Genetics, British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Bioinformatics Program, University of British Columbia, Vancouver, Canada
| | - Richard H Liang
- Laboratory Program, British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | | | - Jason Wong
- Clinical Prevention Services, British Columbia Centre for Disease Control, Vancouver, Canada
| | - Anh Q Le
- Laboratory Program, British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Chanson J Brumme
- Laboratory Program, British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Julio S G Montaner
- Department of Medicine, University of British Columbia, Vancouver, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Jeffrey B Joy
- Corresponding author. Molecular Epidemiology and Evolutionary Genetics, BC Centre for Excellence in HIV/AIDS, 615-1033 Davie St, Vancouver, BC, V6E 1M5, Canada. Tel: +1-(604)-368-5569; E-mail:
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15
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McLaughlin A, Sereda P, Brumme CJ, Brumme ZL, Barrios R, Montaner JSG, Joy JB. Concordance of HIV transmission risk factors elucidated using viral diversification rate and phylogenetic clustering. Evol Med Public Health 2021; 9:338-348. [PMID: 34754454 PMCID: PMC8573190 DOI: 10.1093/emph/eoab028] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 09/14/2021] [Indexed: 11/22/2022]
Abstract
Background and objectives Although HIV sequence clustering is routinely used to identify subpopulations experiencing elevated transmission, it over-simplifies transmission dynamics and is sensitive to methodology. Complementarily, viral diversification rates can be used to approximate historical transmission rates. Here, we investigated the concordance and sensitivity of HIV transmission risk factors identified by phylogenetic clustering, viral diversification rate, changes in viral diversification rate and a combined approach. Methodology Viral sequences from 9848 people living with HIV in British Columbia, Canada, sampled between 1996 and February 2019, were used to infer phylogenetic trees, from which clusters were identified and viral diversification rates of each tip were calculated. Factors associated with heightened transmission risk were compared across models of cluster membership, viral diversification rate, changes in diversification rate, and viral diversification rate among clusters. Results Viruses within larger clusters had higher diversification rates and lower changes in diversification rate than those within smaller clusters; however, rates within individual clusters, independent of size, varied widely. Risk factors for both cluster membership and elevated viral diversification rate included being male, young, a resident of health authority E, previous injection drug use, previous hepatitis C virus infection or a high recent viral load. In a sensitivity analysis, models based on cluster membership had wider confidence intervals and lower concordance of significant effects than viral diversification rate for lower sampling rates. Conclusions and implications Viral diversification rate complements phylogenetic clustering, offering a means of evaluating transmission dynamics to guide provision of treatment and prevention services. Lay Summary Understanding HIV transmission dynamics within clusters can help prioritize public health resource allocation. We compared socio-demographic and clinical risk factors associated with phylogenetic cluster membership and viral diversification rate, a historical branching rate, in order to assess their relative concordance and sampling sensitivity.
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Affiliation(s)
- Angela McLaughlin
- British Columbia Centre for Excellence in HIV/AIDS, St. Paul's Hospital, 608-1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada.,Department of Bioinformatics, University of British Columbia, Genome Sciences Centre, British Columbia Cancer Agency, 100-570 West 7th Avenue, Vancouver, BC V5Z 4S6, Canada
| | - Paul Sereda
- British Columbia Centre for Excellence in HIV/AIDS, St. Paul's Hospital, 608-1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, St. Paul's Hospital, 608-1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada.,Division of Infectious Diseases, Department of Medicine, University of British Columbia, 452D, Heather Pavilion East, Vancouver General Hospital, 2733 Heather Street, Vancouver, BC V5Z 3J5, Canada
| | - Zabrina L Brumme
- British Columbia Centre for Excellence in HIV/AIDS, St. Paul's Hospital, 608-1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada.,Faculty of Health Sciences, Simon Fraser University, Blusson Hall, Room 11300, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Rolando Barrios
- British Columbia Centre for Excellence in HIV/AIDS, St. Paul's Hospital, 608-1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada
| | - Julio S G Montaner
- British Columbia Centre for Excellence in HIV/AIDS, St. Paul's Hospital, 608-1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada.,Division of Infectious Diseases, Department of Medicine, University of British Columbia, 452D, Heather Pavilion East, Vancouver General Hospital, 2733 Heather Street, Vancouver, BC V5Z 3J5, Canada
| | - Jeffrey B Joy
- British Columbia Centre for Excellence in HIV/AIDS, St. Paul's Hospital, 608-1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada.,Department of Bioinformatics, University of British Columbia, Genome Sciences Centre, British Columbia Cancer Agency, 100-570 West 7th Avenue, Vancouver, BC V5Z 4S6, Canada.,Division of Infectious Diseases, Department of Medicine, University of British Columbia, 452D, Heather Pavilion East, Vancouver General Hospital, 2733 Heather Street, Vancouver, BC V5Z 3J5, Canada
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16
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Brumme ZL, Mwimanzi F, Lapointe HR, Cheung P, Sang Y, Duncan MC, Yaseen F, Agafitei O, Ennis S, Ng K, Basra S, Lim LY, Kalikawe R, Speckmaier S, Moran-Garcia N, Young L, Ali H, Ganase B, Umviligihozo G, Omondi FH, Atkinson K, Sudderuddin H, Toy J, Sereda P, Burns L, Costiniuk CT, Cooper C, Anis AH, Leung V, Holmes D, DeMarco ML, Simons J, Hedgcock M, Romney MG, Barrios R, Guillemi S, Brumme CJ, Pantophlet R, Montaner JS, Niikura M, Harris M, Hull M, Brockman MA. Humoral immune responses to COVID-19 vaccination in people living with HIV receiving suppressive antiretroviral therapy. medRxiv 2021:2021.10.03.21264320. [PMID: 34671779 PMCID: PMC8528088 DOI: 10.1101/2021.10.03.21264320] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Humoral responses to COVID-19 vaccines in people living with HIV (PLWH) remain incompletely understood. We measured circulating antibodies against the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein, ACE2 displacement and live viral neutralization activities one month following the first and second COVID-19 vaccine doses in 100 adult PLWH and 152 controls. All PLWH were receiving suppressive antiretroviral therapy, with median CD4+ T-cell counts of 710 (IQR 525-935) cells/mm 3 . Nadir CD4+ T-cell counts ranged as low as <10 (median 280; IQR 120-490) cells/mm 3 . After adjustment for sociodemographic, health and vaccine-related variables, HIV infection was significantly associated with 0.2 log 10 lower anti-RBD antibody concentrations (p=0.03) and ∼11% lower ACE2 displacement activity (p=0.02), but not lower viral neutralization (p=0.1) after one vaccine dose. Following two doses however, HIV was no longer significantly associated with the magnitude of any response measured. Rather, older age, a higher burden of chronic health conditions, and having received two ChAdOx1 doses (versus a heterologous or dual mRNA vaccine regimen) were independently associated with lower responses. After two vaccine doses, no significant correlation was observed between the most recent or nadir CD4+ T-cell counts and vaccine responses in PLWH. These results suggest that PLWH with well-controlled viral loads on antiretroviral therapy and CD4+ T-cell counts in a healthy range will generally not require a third COVID-19 vaccine dose as part of their initial immunization series, though other factors such as older age, co-morbidities, vaccine regimen type, and durability of vaccine responses will influence when this group may benefit from additional doses. Further studies of PLWH who are not receiving antiretroviral treatment and/or who have low CD4+ T-cell counts are needed.
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Affiliation(s)
- Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Francis Mwimanzi
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Hope R. Lapointe
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Peter Cheung
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Yurou Sang
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Maggie C. Duncan
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Fatima Yaseen
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Olga Agafitei
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Siobhan Ennis
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Kurtis Ng
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Simran Basra
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
- Department of Chemistry, Simon Fraser University, Burnaby, Canada
| | - Li Yi Lim
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Rebecca Kalikawe
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Sarah Speckmaier
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | | | - Landon Young
- Division of Medical Microbiology and Virology, St. Paul’s Hospital, Vancouver, Canada
| | - Hesham Ali
- John Ruedy Clinic, St, Paul’s Hospital, Vancouver, Canada
| | - Bruce Ganase
- AIDS Research Program, St. Paul’s Hospital, Vancouver, Canada
| | | | - F. Harrison Omondi
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Kieran Atkinson
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Hanwei Sudderuddin
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Junine Toy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Paul Sereda
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Laura Burns
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada
| | - Cecilia T. Costiniuk
- Division of Infectious Diseases and Chronic Viral Illness Service, McGill University Health Centre and Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Curtis Cooper
- Department of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Hospital Research Institute, Ottawa, Canadas
| | - Aslam H. Anis
- School of Population and Public Health, University of British Columbia, Vancouver, Canada
- CIHR Canadian HIV Trials Network, University of British Columbia, Vancouver, Canada
- Centre for Health Evaluation and Outcome Sciences, Vancouver, Canada
| | - Victor Leung
- Division of Medical Microbiology and Virology, St. Paul’s Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Daniel Holmes
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Mari L. DeMarco
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Janet Simons
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | | | - Marc G. Romney
- Division of Medical Microbiology and Virology, St. Paul’s Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Rolando Barrios
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | - Silvia Guillemi
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Family Practice, Faculty of Medicine, University of British Columbia, Canada
| | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Ralph Pantophlet
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Julio S.G. Montaner
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Masahiro Niikura
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Marianne Harris
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Family Practice, Faculty of Medicine, University of British Columbia, Canada
| | - Mark Hull
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Mark A. Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
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17
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Watson BE, Atkinson K, Auyeung K, Baynes KA, Lepik KJ, Toy J, Sereda P, Barrios R, Brumme CJ. Untimed Efavirenz Drug Levels After Switching From Brand to Generic Formulations: A Short Communication. Ther Drug Monit 2021; 43:701-705. [PMID: 33560098 DOI: 10.1097/ftd.0000000000000876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 01/25/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND In British Columbia, antiretrovirals are distributed at no cost to patients via a publicly funded program, using generic formulations if available. A generic efavirenz-emtricitabine-tenofovir DF (EFV-FTC-TDF) combination pill became available in April 2018. The authors compared EFV untimed drug levels in subjects switching from brand to generic EFV-FTC-TDF. METHODS Archived plasma HIV viral load samples were identified for consenting participants who switched from brand to generic EFV-FTC-TDF; 3 preswitch and 2-3 postswitch samples, collected ≥1 month apart were assessed for each subject. "Untimed" EFV concentrations with unknown dosing and collection time were assessed using a validated liquid chromatography-tandem mass spectrometry method. Participants' mean, minimum, and maximum EFV levels were compared using the Wilcoxon signed rank test. Participants with EFV levels in the range associated with lower risks of virologic failure and central nervous system toxicity (1000-4000 ng/mL), preswitch and postswitch, were enumerated. RESULTS EFV levels were assessed in 297 preswitch and 249 postswitch samples from 99 participants, having exposure to brand and generic EFV for a median of 103 (Q1-Q3: 87-116) and 10.3 (Q1-Q3: 8.9-11.7) months, respectively. The final brand sample was collected at a median of 98 days preswitch; the first generic sample was collected at a median of 133 days postswitch. No significant differences were observed in participant mean EFV levels before (median 1968 ng/mL; Q1-Q3: 1534-2878 ng/mL) and after (median 1987 ng/mL; Q1-Q3: 1521-2834 ng/mL) switch (P = 0.85). Eighty participants had mean EFV levels within the 1000-4000 ng/mL range on the brand drug, of which 74 remained within this range postswitch. CONCLUSIONS There were no statistically significant differences between untimed EFV levels in patients switching from the brand to generic EFV combination pill. Given the long elimination half-life of EFV, untimed drug levels may be a convenient way to estimate product bioequivalence.
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Affiliation(s)
| | | | | | | | - Katherine J Lepik
- British Columbia Centre for Excellence in HIV/AIDS
- Pharmacy Department, St. Paul's Hospital; and
| | - Junine Toy
- British Columbia Centre for Excellence in HIV/AIDS
- Pharmacy Department, St. Paul's Hospital; and
| | - Paul Sereda
- British Columbia Centre for Excellence in HIV/AIDS
| | | | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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18
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Brooks K, Omondi FH, Liang RH, Sudderuddin H, Jones BR, Joy JB, Brumme CJ, Hunter E, Brumme ZL. Proviral Turnover During Untreated HIV Infection Is Dynamic and Variable Between Hosts, Impacting Reservoir Composition on ART. Front Microbiol 2021; 12:719153. [PMID: 34489909 PMCID: PMC8417368 DOI: 10.3389/fmicb.2021.719153] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/30/2021] [Indexed: 12/25/2022] Open
Abstract
Human immunodeficiency virus (HIV) can persist as an integrated provirus, in a transcriptionally repressed state, within infected cells. This small yet enduring pool of cellular reservoirs that harbor replication-competent HIV is the main barrier to cure. Entry of viral sequences into cellular reservoirs begins shortly after infection, and cells containing integrated proviral DNA are extremely stable once suppressive antiretroviral therapy (ART) is initiated. During untreated HIV infection however, reservoir turnover is likely to be more dynamic. Understanding these dynamics is important because the longevity of the persisting proviral pool during untreated infection dictates reservoir composition at ART initiation. If the persisting proviral pool turns over slowly pre-ART, then HIV sequences seeded into it during early infection would have a high likelihood of persisting for long periods. However, if pre-ART turnover was rapid, the persisting proviral pool would rapidly shift toward recently circulating HIV sequences. One-way to estimate this turnover rate is from the age distributions of proviruses sampled shortly after therapy initiation: this is because, at the time of sampling, the majority of proviral turnover would have already occurred prior to ART. Recently, methods to estimate a provirus’ age from its sequence have made this possible. Using data from 12 individuals with HIV subtype C for whom proviral ages had been determined phylogenetically, we estimated that the average proviral half-life during untreated infection was 0.78 (range 0.45–2.38) years, which is >15 times faster than that of proviral DNA during suppressive ART. We further show that proviral turnover during untreated infection correlates with both viral setpoint and rate of CD4+ T-cell decline during this period. Overall, our results support dynamic proviral turnover pre-ART in most individuals, which helps explain why many individuals’ reservoirs are skewed toward younger HIV sequences. Broadly, our findings are consistent with the notion that active viral replication creates an environment less favorable to proviral persistence, while viral suppression creates conditions more favorable to persistence, where ART stabilizes the proviral pool by dramatically slowing its rate of decay. Strategies to inhibit this stabilizing effect and/or to enhance reservoir turnover during ART could represent additional strategies to reduce the HIV reservoir.
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Affiliation(s)
- Kelsie Brooks
- Emory Vaccine Center, Emory University, Atlanta, GA, United States
| | - F Harrison Omondi
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Richard H Liang
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Hanwei Sudderuddin
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Bradley R Jones
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.,Bioinformatics Program, University of British Columbia, Vancouver, BC, Canada
| | - Jeffrey B Joy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.,Bioinformatics Program, University of British Columbia, Vancouver, BC, Canada.,Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.,Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Eric Hunter
- Emory Vaccine Center, Emory University, Atlanta, GA, United States.,Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
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19
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Feder AF, Harper KN, Brumme CJ, Pennings PS. Understanding patterns of HIV multi-drug resistance through models of temporal and spatial drug heterogeneity. eLife 2021; 10:e69032. [PMID: 34473060 PMCID: PMC8412921 DOI: 10.7554/elife.69032] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 08/03/2021] [Indexed: 01/09/2023] Open
Abstract
Triple-drug therapies have transformed HIV from a fatal condition to a chronic one. These therapies should prevent HIV drug resistance evolution, because one or more drugs suppress any partially resistant viruses. In practice, such therapies drastically reduced, but did not eliminate, resistance evolution. In this article, we reanalyze published data from an evolutionary perspective and demonstrate several intriguing patterns about HIV resistance evolution - resistance evolves (1) even after years on successful therapy, (2) sequentially, often via one mutation at a time and (3) in a partially predictable order. We describe how these observations might emerge under two models of HIV drugs varying in space or time. Despite decades of work in this area, much opportunity remains to create models with realistic parameters for three drugs, and to match model outcomes to resistance rates and genetic patterns from individuals on triple-drug therapy. Further, lessons from HIV may inform other systems.
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Affiliation(s)
- Alison F Feder
- Department of Integrative Biology, University of California, BerkeleyBerkeleyUnited States
- Department of Genome Sciences, University of WashingtonSeattleUnited States
| | - Kristin N Harper
- Harper Health and Science Communications, LLCSeattleUnited States
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDSVancouverCanada
- Department of Medicine, University of British ColumbiaVancouverCanada
| | - Pleuni S Pennings
- Department of Biology, San Francisco State UniversitySan FranciscoUnited States
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20
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Lapointe HR, Dong W, Dong WWY, Kirkby D, Woods C, Poon AFY, Howe AYM, Harrigan PR, Brumme CJ. Validation of a Genotype-Independent Hepatitis C Virus Near-Whole Genome Sequencing Assay. Viruses 2021; 13:v13091721. [PMID: 34578305 PMCID: PMC8473162 DOI: 10.3390/v13091721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/17/2021] [Accepted: 08/26/2021] [Indexed: 11/16/2022] Open
Abstract
Despite the effectiveness of direct-acting antiviral agents in treating hepatitis C virus (HCV), cases of treatment failure have been associated with the emergence of resistance-associated substitutions. To better guide clinical decision-making, we developed and validated a near-whole-genome HCV genotype-independent next-generation sequencing strategy. HCV genotype 1-6 samples from direct-acting antiviral agent treatment-naïve and -treated HCV-infected individuals were included. Viral RNA was extracted using a NucliSens easyMAG and amplified using nested reverse transcription-polymerase chain reaction. Libraries were prepared using Nextera XT and sequenced on the Illumina MiSeq sequencing platform. Data were processed by an in-house pipeline (MiCall). Nucleotide consensus sequences were aligned to reference strain sequences for resistance-associated substitution identification and compared to NS3, NS5a, and NS5b sequence data obtained from a validated in-house assay optimized for HCV genotype 1. Sequencing success rates (defined as achieving >100-fold read coverage) approaching 90% were observed for most genotypes in samples with a viral load >5 log10 IU/mL. This genotype-independent sequencing method resulted in >99.8% nucleotide concordance with the genotype 1-optimized method, and 100% agreement in genotype assignment with paired line probe assay-based genotypes. The assay demonstrated high intra-run repeatability and inter-run reproducibility at detecting substitutions above 2% prevalence. This study highlights the performance of a freely available laboratory and bioinformatic approach for reliable HCV genotyping and resistance-associated substitution detection regardless of genotype.
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Affiliation(s)
- Hope R. Lapointe
- Department of Medicine, Division of Social Medicine, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; (H.R.L.); (P.R.H.)
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada; (W.D.); (W.W.Y.D.); (D.K.); (C.W.)
| | - Weiyan Dong
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada; (W.D.); (W.W.Y.D.); (D.K.); (C.W.)
| | - Winnie W. Y. Dong
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada; (W.D.); (W.W.Y.D.); (D.K.); (C.W.)
| | - Don Kirkby
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada; (W.D.); (W.W.Y.D.); (D.K.); (C.W.)
| | - Conan Woods
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada; (W.D.); (W.W.Y.D.); (D.K.); (C.W.)
| | - Art F. Y. Poon
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada;
| | - Anita Y. M. Howe
- British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4, Canada;
| | - P. Richard Harrigan
- Department of Medicine, Division of Social Medicine, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; (H.R.L.); (P.R.H.)
| | - Chanson J. Brumme
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada; (W.D.); (W.W.Y.D.); (D.K.); (C.W.)
- Department of Medicine, Division of Infectious Diseases, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Correspondence:
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21
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Matic N, Lowe CF, Ritchie G, Stefanovic A, Lawson T, Jang W, Young M, Dong W, Brumme ZL, Brumme CJ, Leung V, Romney MG. Rapid Detection of SARS-CoV-2 Variants of Concern, Including B.1.1.28/P.1, British Columbia, Canada. Emerg Infect Dis 2021; 27:1673-1676. [PMID: 33784237 PMCID: PMC8153894 DOI: 10.3201/eid2706.210532] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
To screen all severe acute respiratory syndrome coronavirus 2-positive samples in Vancouver, British Columbia, Canada, and determine whether they represented variants of concern, we implemented a real-time reverse transcription PCR-based algorithm. We rapidly identified 77 samples with variants: 57 with B.1.1.7, 7 with B.1.351, and an epidemiologic cluster of 13 with B.1.1.28/P.1.
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22
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Kinloch NN, Ritchie G, Brumme CJ, Dong W, Dong W, Lawson T, Jones RB, Montaner JSG, Leung V, Romney MG, Stefanovic A, Matic N, Lowe CF, Brumme ZL. Corrigendum to: Suboptimal Biological Sampling as a Probable Cause of False-Negative COVID-19 Diagnostic Test Results. J Infect Dis 2021; 224:184. [PMID: 34057182 PMCID: PMC8195218 DOI: 10.1093/infdis/jiab230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Affiliation(s)
- Natalie N Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Gordon Ritchie
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada.,Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Winnie Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Weiyan Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Tanya Lawson
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
| | - R Brad Jones
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, USA
| | - Julio S G Montaner
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada.,Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Victor Leung
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Marc G Romney
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Aleksandra Stefanovic
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Nancy Matic
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Christopher F Lowe
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
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23
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McCann CD, van Dorp CH, Danesh A, Ward AR, Dilling TR, Mota TM, Zale E, Stevenson EM, Patel S, Brumme CJ, Dong W, Jones DS, Andresen TL, Walker BD, Brumme ZL, Bollard CM, Perelson AS, Irvine DJ, Jones RB. A participant-derived xenograft model of HIV enables long-term evaluation of autologous immunotherapies. J Exp Med 2021; 218:212105. [PMID: 33988715 PMCID: PMC8129803 DOI: 10.1084/jem.20201908] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 02/15/2021] [Accepted: 04/12/2021] [Indexed: 12/13/2022] Open
Abstract
HIV-specific CD8+ T cells partially control viral replication and delay disease progression, but they rarely provide lasting protection, largely due to immune escape. Here, we show that engrafting mice with memory CD4+ T cells from HIV+ donors uniquely allows for the in vivo evaluation of autologous T cell responses while avoiding graft-versus-host disease and the need for human fetal tissues that limit other models. Treating HIV-infected mice with clinically relevant HIV-specific T cell products resulted in substantial reductions in viremia. In vivo activity was significantly enhanced when T cells were engineered with surface-conjugated nanogels carrying an IL-15 superagonist, but it was ultimately limited by the pervasive selection of a diverse array of escape mutations, recapitulating patterns seen in humans. By applying mathematical modeling, we show that the kinetics of the CD8+ T cell response have a profound impact on the emergence and persistence of escape mutations. This “participant-derived xenograft” model of HIV provides a powerful tool for studying HIV-specific immunological responses and facilitating the development of effective cell-based therapies.
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Affiliation(s)
- Chase D McCann
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY.,Immunology & Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, NY
| | | | - Ali Danesh
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Adam R Ward
- Department of Microbiology, Immunology & Tropical Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC.,PhD Program in Epidemiology, Milken Institute School of Public Health, The George Washington University, Washington, DC
| | - Thomas R Dilling
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Talia M Mota
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Elizabeth Zale
- Immunology & Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, NY
| | - Eva M Stevenson
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Shabnum Patel
- Center for Cancer and Immunology Research, Children's National Health System, Washington, DC.,George Washington University Cancer Center, George Washington University, Washington, DC
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Winnie Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | | | | | - Bruce D Walker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Boston, MA.,Institute for Medical and Engineering Sciences, Massachusetts Institute of Technology, Cambridge, MA.,Howard Hughes Medical Institute, Chevy Chase, MD
| | - Zabrina L Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada.,Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Catherine M Bollard
- Center for Cancer and Immunology Research, Children's National Health System, Washington, DC.,George Washington University Cancer Center, George Washington University, Washington, DC
| | - Alan S Perelson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM
| | - Darrell J Irvine
- Howard Hughes Medical Institute, Chevy Chase, MD.,Department of Material Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA
| | - R Brad Jones
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY.,Immunology & Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, NY
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24
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Akahoshi T, Gatanaga H, Kuse N, Chikata T, Koyanagi M, Ishizuka N, Brumme CJ, Murakoshi H, Brumme ZL, Oka S, Takiguchi M. T-cell responses to sequentially emerging viral escape mutants shape long-term HIV-1 population dynamics. PLoS Pathog 2020; 16:e1009177. [PMID: 33370400 PMCID: PMC7833229 DOI: 10.1371/journal.ppat.1009177] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 01/25/2021] [Accepted: 11/18/2020] [Indexed: 11/18/2022] Open
Abstract
HIV-1 strains harboring immune escape mutations can persist in circulation, but the impact of selection by multiple HLA alleles on population HIV-1 dynamics remains unclear. In Japan, HIV-1 Reverse Transcriptase codon 135 (RT135) is under strong immune pressure by HLA-B*51:01-restricted and HLA-B*52:01-restricted T cells that target a key epitope in this region (TI8; spanning RT codons 128-135). Major population-level shifts have occurred at HIV-1 RT135 during the Japanese epidemic, which first affected hemophiliacs (via imported contaminated blood products) and subsequently non-hemophiliacs (via domestic transmission). Specifically, threonine accumulated at RT135 (RT135T) in hemophiliac and non-hemophiliac HLA-B*51:01+ individuals diagnosed before 1997, but since then RT135T has markedly declined while RT135L has increased among non-hemophiliac individuals. We demonstrated that RT135V selection by HLA-B*52:01-restricted TI8-specific T-cells led to the creation of a new HLA-C*12:02-restricted epitope TN9-8V. We further showed that TN9-8V-specific HLA-C*12:02-restricted T cells selected RT135L while TN9-8T-specific HLA-C*12:02-restricted T cells suppressed replication of the RT135T variant. Thus, population-level accumulation of the RT135L mutation over time in Japan can be explained by initial targeting of the TI8 epitope by HLA-B*52:01-restricted T-cells, followed by targeting of the resulting escape mutant by HLA-C*12:02-restricted T-cells. We further demonstrate that this phenomenon is particular to Japan, where the HLA-B*52:01-C*12:02 haplotype is common: RT135L did not accumulate over a 15-year longitudinal analysis of HIV sequences in British Columbia, Canada, where this haplotype is rare. Together, our observations reveal that T-cell responses to sequentially emerging viral escape mutants can shape long-term HIV-1 population dynamics in a host population-specific manner.
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Affiliation(s)
| | - Hiroyuki Gatanaga
- Division of International Collaboration Research, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Tokyo, Japan
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Nozomi Kuse
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
- Division of International Collaboration Research, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Tokyo, Japan
| | - Takayuki Chikata
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
- Division of International Collaboration Research, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Tokyo, Japan
| | - Madoka Koyanagi
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | | | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Hayato Murakoshi
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
- Division of International Collaboration Research, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Tokyo, Japan
| | - Zabrina L. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Shinichi Oka
- Division of International Collaboration Research, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Tokyo, Japan
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Masafumi Takiguchi
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
- Division of International Collaboration Research, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Tokyo, Japan
- * E-mail:
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25
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Kinloch NN, Shahid A, Ritchie G, Dong W, Lawson T, Montaner JSG, Romney MG, Stefanovic A, Matic N, Brumme CJ, Lowe CF, Brumme ZL, Leung V. Evaluation of Nasopharyngeal Swab Collection Techniques for Nucleic Acid Recovery and Participant Experience: Recommendations for COVID-19 Diagnostics. Open Forum Infect Dis 2020; 7:ofaa488. [PMID: 33235889 PMCID: PMC7665666 DOI: 10.1093/ofid/ofaa488] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 10/09/2020] [Indexed: 12/23/2022] Open
Abstract
Nasopharyngeal swabs are critical to the diagnosis of respiratory infections including coronavirus disease 2019, but collection techniques vary. We compared 2 recommended nasopharyngeal swab collection techniques in adult volunteers and found that swab rotation following nasopharyngeal contact did not recover additional nucleic acid (as measured by human DNA/RNA copy number). Rotation was also less tolerable for participants. Notably, both discomfort and nucleic acid recovery were significantly higher in Asian participants, consistent with nasal anatomy differences. Our results suggest that it is unnecessary to rotate the swab in place following contact with the nasopharynx and reveal that procedural discomfort levels can differ by ethnicity.
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Affiliation(s)
- Natalie N Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Gordon Ritchie
- Division of Medical Microbiology and Virology, St Paul's Hospital, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Winnie Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Tanya Lawson
- Division of Medical Microbiology and Virology, St Paul's Hospital, Vancouver, British Columbia, Canada
| | - Julio S G Montaner
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada.,Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marc G Romney
- Division of Medical Microbiology and Virology, St Paul's Hospital, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Aleksandra Stefanovic
- Division of Medical Microbiology and Virology, St Paul's Hospital, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nancy Matic
- Division of Medical Microbiology and Virology, St Paul's Hospital, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada.,Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Christopher F Lowe
- Division of Medical Microbiology and Virology, St Paul's Hospital, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Victor Leung
- Division of Medical Microbiology and Virology, St Paul's Hospital, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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26
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Jin SW, Mwimanzi FM, Mann JK, Bwana MB, Lee GQ, Brumme CJ, Hunt PW, Martin JN, Bangsberg DR, Ndung’u T, Brumme ZL, Brockman MA. Variation in HIV-1 Nef function within and among viral subtypes reveals genetically separable antagonism of SERINC3 and SERINC5. PLoS Pathog 2020; 16:e1008813. [PMID: 32925973 PMCID: PMC7515180 DOI: 10.1371/journal.ppat.1008813] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 09/24/2020] [Accepted: 07/15/2020] [Indexed: 12/14/2022] Open
Abstract
HIV Nef counteracts cellular host restriction factors SERINC3 and SERINC5, but our understanding of how naturally occurring global Nef sequence diversity impacts these activities is limited. Here, we quantify SERINC3 and SERINC5 internalization function for 339 Nef clones, representing the major pandemic HIV-1 group M subtypes A, B, C and D. We describe distinct subtype-associated hierarchies for Nef-mediated internalization of SERINC5, for which subtype B clones display the highest activities on average, and of SERINC3, for which subtype B clones display the lowest activities on average. We further identify Nef polymorphisms that modulate its ability to counteract SERINC proteins, including substitutions in the N-terminal domain that selectively impair SERINC3 internalization. Our findings demonstrate that the SERINC antagonism activities of HIV Nef differ markedly among major viral subtypes and between individual isolates within a subtype, suggesting that variation in these functions may contribute to global differences in viral pathogenesis.
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Affiliation(s)
- Steven W. Jin
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | | | - Jaclyn K. Mann
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Mwebesa Bosco Bwana
- Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Guinevere Q. Lee
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Peter W. Hunt
- School of Medicine, University of California, San Francisco, United States of America
| | - Jeff N. Martin
- School of Medicine, University of California, San Francisco, United States of America
| | - David R. Bangsberg
- School of Public Health, Oregon Health Science University, Portland, United States of America
| | - Thumbi Ndung’u
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
- Africa Health Research Institute, Durban, South Africa
- Ragon Institute of MGH, MIT, and Harvard University, Cambridge, United States of America
- Max Planck Institute for Infection Biology, Berlin, Germany
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Mark A. Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
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27
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Kinloch NN, Ritchie G, Brumme CJ, Dong W, Dong W, Lawson T, Jones RB, Montaner JSG, Leung V, Romney MG, Stefanovic A, Matic N, Lowe CF, Brumme ZL. Suboptimal Biological Sampling as a Probable Cause of False-Negative COVID-19 Diagnostic Test Results. J Infect Dis 2020; 222:899-902. [PMID: 32594170 PMCID: PMC7337811 DOI: 10.1093/infdis/jiaa370] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/02/2020] [Indexed: 01/30/2023] Open
Abstract
False-negative severe acute respiratory syndrome coronavirus 2 test results can negatively impact the clinical and public health response to coronavirus disease 2019 (COVID-19). We used droplet digital polymerase chain reaction (ddPCR) to demonstrate that human DNA levels, a stable molecular marker of sampling quality, were significantly lower in samples from 40 confirmed or suspected COVID-19 cases that yielded negative diagnostic test results (ie, suspected false-negative test results) compared with a representative pool of 87 specimens submitted for COVID-19 testing. Our results support suboptimal biological sampling as a contributor to false-negative COVID-19 test results and underscore the importance of proper training and technique in the collection of nasopharyngeal specimens.
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Affiliation(s)
- Natalie N Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Gordon Ritchie
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada.,Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Winnie Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Weiyan Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Tanya Lawson
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
| | - R Brad Jones
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, USA
| | - Julio S G Montaner
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada.,Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Victor Leung
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Marc G Romney
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Aleksandra Stefanovic
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Nancy Matic
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Christopher F Lowe
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
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28
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Umviligihozo G, Cobarrubias KD, Chandrarathna S, Jin SW, Reddy N, Byakwaga H, Muzoora C, Bwana MB, Lee GQ, Hunt PW, Martin JN, Brumme CJ, Bangsberg DR, Karita E, Allen S, Hunter E, Ndung'u T, Brumme ZL, Brockman MA. Differential Vpu-Mediated CD4 and Tetherin Downregulation Functions among Major HIV-1 Group M Subtypes. J Virol 2020; 94:e00293-20. [PMID: 32376625 PMCID: PMC7343213 DOI: 10.1128/jvi.00293-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 04/30/2020] [Indexed: 12/12/2022] Open
Abstract
Downregulation of BST-2/tetherin and CD4 by HIV-1 viral protein U (Vpu) promotes viral egress and allows infected cells to evade host immunity. Little is known however about the natural variability in these Vpu functions among the genetically diverse viral subtypes that contribute to the HIV-1 pandemic. We collected Vpu isolates from 332 treatment-naive individuals living with chronic HIV-1 infection in Uganda, Rwanda, South Africa, and Canada. Together, these Vpu isolates represent four major HIV-1 group M subtypes (A [n = 63], B [n = 84], C [n = 94], and D [n = 59]) plus intersubtype recombinants and uncommon strains (n = 32). The ability of each Vpu clone to downregulate endogenous CD4 and tetherin was quantified using flow cytometry following transfection into an immortalized T-cell line and compared to that of a reference Vpu clone derived from HIV-1 subtype B NL4.3. Overall, the median CD4 downregulation function of natural Vpu isolates was similar to that of NL4.3 (1.01 [interquartile range {IQR}, 0.86 to 1.18]), while the median tetherin downregulation function was moderately lower than that of NL4.3 (0.90 [0.79 to 0.97]). Both Vpu functions varied significantly among HIV-1 subtypes (Kruskal-Wallis P < 0.0001). Specifically, subtype C clones exhibited the lowest CD4 and tetherin downregulation activities, while subtype D and B clones were most functional for both activities. We also identified Vpu polymorphisms associated with CD4 or tetherin downregulation function and validated six of these using site-directed mutagenesis. Our results highlight the marked extent to which Vpu function varies among global HIV-1 strains, raising the possibility that natural variation in this accessory protein may contribute to viral pathogenesis and/or spread.IMPORTANCE The HIV-1 accessory protein Vpu enhances viral spread by downregulating CD4 and BST-2/tetherin on the surface of infected cells. Natural variability in these Vpu functions may contribute to HIV-1 pathogenesis, but this has not been investigated among the diverse viral subtypes that contribute to the HIV-1 pandemic. In this study, we found that Vpu function differs significantly among HIV-1 subtypes A, B, C, and D. On average, subtype C clones displayed the lowest ability to downregulate both CD4 and tetherin, while subtype B and D clones were more functional. We also identified Vpu polymorphisms that associate with functional differences among HIV-1 isolates and subtypes. Our study suggests that genetic diversity in Vpu may play an important role in the differential pathogenesis and/or spread of HIV-1.
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Affiliation(s)
- Gisele Umviligihozo
- Faculty of Health Sciences, Simon Fraser University, Vancouver, British Columbia, Canada
| | - Kyle D Cobarrubias
- Faculty of Health Sciences, Simon Fraser University, Vancouver, British Columbia, Canada
| | - Sandali Chandrarathna
- Faculty of Health Sciences, Simon Fraser University, Vancouver, British Columbia, Canada
| | - Steven W Jin
- Faculty of Health Sciences, Simon Fraser University, Vancouver, British Columbia, Canada
| | - Nicole Reddy
- University of KwaZulu-Natal, Durban, South Africa
- Africa Health Research Institute, Durban, South Africa
| | - Helen Byakwaga
- Mbarara University of Science and Technology, Mbarara, Uganda
- University of California, San Francisco, California, USA
| | - Conrad Muzoora
- Mbarara University of Science and Technology, Mbarara, Uganda
| | - Mwebesa B Bwana
- Mbarara University of Science and Technology, Mbarara, Uganda
| | - Guinevere Q Lee
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Peter W Hunt
- University of California, San Francisco, California, USA
| | - Jeff N Martin
- University of California, San Francisco, California, USA
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- University of British Columbia, Vancouver, British Columbia, Canada
| | - David R Bangsberg
- Oregon Health and Science University-Portland State University School of Public Health, Portland, Oregon, USA
| | - Etienne Karita
- Rwanda Zambia HIV Research Group-Projet San Francisco, Kigali, Rwanda
| | - Susan Allen
- Rwanda Zambia HIV Research Group-Projet San Francisco, Kigali, Rwanda
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, USA
- Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Eric Hunter
- Rwanda Zambia HIV Research Group-Projet San Francisco, Kigali, Rwanda
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Thumbi Ndung'u
- University of KwaZulu-Natal, Durban, South Africa
- Africa Health Research Institute, Durban, South Africa
- Max Planck Institute for Infection Biology, Berlin, Germany
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Vancouver, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Mark A Brockman
- Faculty of Health Sciences, Simon Fraser University, Vancouver, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
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29
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Ji H, Sandstrom P, Paredes R, Harrigan PR, Brumme CJ, Avila Rios S, Noguera-Julian M, Parkin N, Kantor R. Are We Ready for NGS HIV Drug Resistance Testing? The Second "Winnipeg Consensus" Symposium. Viruses 2020; 12:E586. [PMID: 32471096 PMCID: PMC7354487 DOI: 10.3390/v12060586] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/13/2020] [Accepted: 05/25/2020] [Indexed: 12/31/2022] Open
Abstract
HIV drug resistance is a major global challenge to successful and sustainable antiretroviral therapy. Next-generation sequencing (NGS)-based HIV drug resistance (HIVDR) assays enable more sensitive and quantitative detection of drug-resistance-associated mutations (DRMs) and outperform Sanger sequencing approaches in detecting lower abundance resistance mutations. While NGS is likely to become the new standard for routine HIVDR testing, many technical and knowledge gaps remain to be resolved before its generalized adoption in regular clinical care, public health, and research. Recognizing this, we conceived and launched an international symposium series on NGS HIVDR, to bring together leading experts in the field to address these issues through in-depth discussions and brainstorming. Following the first symposium in 2018 (Winnipeg, MB Canada, 21-22 February, 2018), a second "Winnipeg Consensus" symposium was held in September 2019 in Winnipeg, Canada, and was focused on external quality assurance strategies for NGS HIVDR assays. In this paper, we summarize this second symposium's goals and highlights.
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Affiliation(s)
- Hezhao Ji
- National HIV and Retrovirology Laboratories at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada;
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Paul Sandstrom
- National HIV and Retrovirology Laboratories at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada;
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Roger Paredes
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, s/n, 08916 Badalona, Catalonia, Spain; (R.P.); (M.N.-J.)
- Infectious Diseases Department, Hospital Germans Trias i Pujol, 08916 Badalona, Catalonia, Spain
| | - P. Richard Harrigan
- Division of AIDS, Department of Medicine, University of British Columbia, Vancouver, BC V5Z 1M9, Canada;
| | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada;
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Santiago Avila Rios
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City 14080, Mexico;
| | - Marc Noguera-Julian
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, s/n, 08916 Badalona, Catalonia, Spain; (R.P.); (M.N.-J.)
- Chair in AIDS and Related Illnesses, Centre for Health and Social Care Research (CESS), Faculty of Medicine, University of Vic–Central University of Catalonia (UVic–UCC), Can Baumann, Ctra. de Roda, 70, 08500 Vic, Spain
| | - Neil Parkin
- Data First Consulting Inc., Sebastopol, CA 95472, USA;
| | - Rami Kantor
- Division of Infectious Diseases, Brown University Alpert Medical School, Providence, RI 02906, USA;
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30
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Sudderuddin H, Kinloch NN, Jin SW, Miller RL, Jones BR, Brumme CJ, Joy JB, Brockman MA, Brumme ZL. Longitudinal within-host evolution of HIV Nef-mediated CD4, HLA and SERINC5 downregulation activity: a case study. Retrovirology 2020; 17:3. [PMID: 31918727 PMCID: PMC6953280 DOI: 10.1186/s12977-019-0510-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 12/26/2019] [Indexed: 11/29/2022] Open
Abstract
The HIV accessory protein Nef downregulates the viral entry receptor CD4, the Human Leukocyte Antigen (HLA)-A and -B molecules, the Serine incorporator 5 (SERINC5) protein and other molecules from the infected cell surface, thereby promoting viral infectivity, replication and immune evasion. The nef locus also represents one of the most genetically variable regions in the HIV genome, and nef sequences undergo substantial evolution within a single individual over the course of infection. Few studies however have simultaneously characterized the impact of within-host nef sequence evolution on Nef protein function over prolonged timescales. Here, we isolated 50 unique Nef clones by single-genome amplification over an 11-year period from the plasma of an individual who was largely naïve to antiretroviral treatment during this time. Together, these clones harbored nonsynonymous substitutions at 13% of nef’s codons. We assessed their ability to downregulate cell-surface CD4, HLA and SERINC5 and observed that all three Nef functions declined modestly over time, where the reductions in CD4 and HLA downregulation (an average of 0.6% and 2.0% per year, respectively) achieved statistical significance. The results from this case study support all three Nef activities as being important to maintain throughout untreated HIV infection, but nevertheless suggest that, despite nef’s mutational plasticity, within-host viral evolution can compromise Nef function, albeit modestly, over prolonged periods.
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Affiliation(s)
- Hanwei Sudderuddin
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.,BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Natalie N Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.,BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Steven W Jin
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Rachel L Miller
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | | | - Chanson J Brumme
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.,Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Jeffrey B Joy
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.,Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Mark A Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.,BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada. .,BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.
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31
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Kinloch NN, Ren Y, Alberto WC, Dong W, Huang SH, Wilson A, Mota TM, Kikby D, Del Rio Estrada PM, Brumme CJ, Lee GQ, Lynch RM, Brumme ZL, Jones RB. Intra- and inter-individual HIV diversity limits the application of the intact proviral detection assay (IPDA). J Virus Erad 2019. [DOI: 10.1016/s2055-6640(20)30093-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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32
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McLaughlin A, Sereda P, Oliveira N, Barrios R, Brumme CJ, Brumme ZL, Montaner JSG, Joy JB. Detection of HIV transmission hotspots in British Columbia, Canada: A novel framework for the prioritization and allocation of treatment and prevention resources. EBioMedicine 2019; 48:405-413. [PMID: 31628022 PMCID: PMC6838403 DOI: 10.1016/j.ebiom.2019.09.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 09/14/2019] [Indexed: 01/05/2023] Open
Abstract
Background Identifying populations at high risk of HIV transmission is critical for prioritizing treatment and prevention resources and achieving the UNAIDS 90-90-90 Targets. Methods HIV transmission rates can be estimated from phylogenetic trees as viral lineage-level diversification rates. To identify HIV-1 transmission foci in British Columbia, Canada, we inferred diversification rates from phylogenetic trees of 36 271 HIV-1 sequences from 9630 anonymized individuals. Diversification rates were combined with sociodemographic and clinical data, then aggregated by patients’ area of residence to predict the distribution of new HIV cases between 2008 and 2018. The predictive power of the model was compared with a phylogenetically uninformed model. Findings Aggregated diversification rate measures were predictive of new HIV cases in the subsequent year after adjusting for prevalent and incident cases in the previous year. For every one-unit increase in the mean of the top five diversification rates, the number of new HIV cases increased by on average 1·38-fold (95% CI, 1·28–1·49). In a blind prediction of 2018 cases, diversification rate improved the model's specificity by 12%, accuracy by 9%, top 20 agreement by 100%, and correlation of predicted and observed values by 162% relative to a model that incorporated epidemiological data alone. Interpretation By predicting the distribution of future HIV cases, a combined phylogenetic and epidemiological approach identifies hotspots where public health resources are needed most. Funding Canadian Institutes of Health Research, University of British Columbia, Public Health Agency of Canada, Genome Canada, Genome BC, Michael Smith Foundation for Health Research, and BC Centre for Excellence in HIV/AIDS.
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Affiliation(s)
- Angela McLaughlin
- British Columbia Centre for Excellence in HIV/AIDS, University of British Columbia Department of Medicine, 608-1081 Burrard Street, Vancouver, BC, V6Z 1Y6, Canada; School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada; Bioinformatics, University of British Columbia, Vancouver, BC, Canada
| | - Paul Sereda
- British Columbia Centre for Excellence in HIV/AIDS, University of British Columbia Department of Medicine, 608-1081 Burrard Street, Vancouver, BC, V6Z 1Y6, Canada
| | - Natalia Oliveira
- British Columbia Centre for Excellence in HIV/AIDS, University of British Columbia Department of Medicine, 608-1081 Burrard Street, Vancouver, BC, V6Z 1Y6, Canada
| | - Rolando Barrios
- British Columbia Centre for Excellence in HIV/AIDS, University of British Columbia Department of Medicine, 608-1081 Burrard Street, Vancouver, BC, V6Z 1Y6, Canada; School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, University of British Columbia Department of Medicine, 608-1081 Burrard Street, Vancouver, BC, V6Z 1Y6, Canada
| | - Zabrina L Brumme
- British Columbia Centre for Excellence in HIV/AIDS, University of British Columbia Department of Medicine, 608-1081 Burrard Street, Vancouver, BC, V6Z 1Y6, Canada; Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Julio S G Montaner
- British Columbia Centre for Excellence in HIV/AIDS, University of British Columbia Department of Medicine, 608-1081 Burrard Street, Vancouver, BC, V6Z 1Y6, Canada; Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Jeffrey B Joy
- British Columbia Centre for Excellence in HIV/AIDS, University of British Columbia Department of Medicine, 608-1081 Burrard Street, Vancouver, BC, V6Z 1Y6, Canada; Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada.
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33
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Tadesse BT, Chala A, Mukonzo J, Chaka TE, Tadesse S, Makonnen E, Brumme ZL, Brumme CJ, Aklillu E. Rates and Correlates of Short Term Virologic Response among Treatment-Naïve HIV-Infected Children Initiating Antiretroviral Therapy in Ethiopia: A Multi-Center Prospective Cohort Study. Pathogens 2019; 8:pathogens8040161. [PMID: 31554200 PMCID: PMC6963769 DOI: 10.3390/pathogens8040161] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 09/19/2019] [Accepted: 09/20/2019] [Indexed: 01/19/2023] Open
Abstract
There is limited data on virologic outcome and its correlates among HIV-infected children in resource-limited settings. We investigated rate and correlates of virologic outcome among treatment naïve HIV-infected Ethiopian children initiating cART, and were followed prospectively at baseline, 8, 12, 24 and 48 weeks using plasma viral load, clinical examination, laboratory tests and pretreatment HIV drug resistance (PDR) screening. Virologic outcome was assessed using two endpoints–virological suppression defined as having “undetectable” plasma viral load < 150 RNA copies/mL, and rebound defined as viral load ≥150 copies/mL after achieving suppression. Cox Proportional Hazards Regression was employed to assess correlates of outcome. At the end of follow up, virologic outcome was measured for 110 participants. Overall, 94(85.5%) achieved virological suppression, of which 36(38.3%) experienced virologic rebound. At 48 weeks, 9(8.2%) children developed WHO-defined virological treatment failure. Taking tenofovir-containing regimen (Hazard Ratio (HR) 3.1-[95% confidence interval (95%CI) 1.0–9.6], p = 0.049) and absence of pretreatment HIV drug resistance (HR 11.7-[95%CI 1.3–104.2], p = 0.028) were independently associated with earlier virologic suppression. In conclusion, PDR and cART regimen type correlate with rate of virologic suppression which was prominent during the first year of cART initiation. However, the impact of viral rebound in 38.3% of the children needs evaluation.
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Affiliation(s)
- Birkneh Tilahun Tadesse
- Division of Clinical Pharmacology, Department of Laboratory Medicine, Karolinska Institute, Karolinska University Hospital Huddinge, 141 86 Stockholm, Sweden.
- Department of Pediatrics, College of Medicine and Health Sciences, Hawassa University, Hawassa 1560, Ethiopia.
| | - Adugna Chala
- Department of Pharmacology, College of Health Sciences, Addis Ababa University, Addis Ababa 9086, Ethiopia.
| | - Jackson Mukonzo
- Department of Pharmacology, College of Health Sciences, Makerere University, Kampala, Uganda.
| | | | - Sintayehu Tadesse
- Department of Pharmacology, College of Health Sciences, Addis Ababa University, Addis Ababa 9086, Ethiopia.
| | - Eyasu Makonnen
- Department of Pharmacology, College of Health Sciences, Addis Ababa University, Addis Ababa 9086, Ethiopia.
- CDT Africa, College of Health Sciences, Addis Ababa University, Addis Ababa 9086, Ethiopia.
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada.
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada.
- Department of Medicine, University of British Columbia, Vancouver, BC V5Z 1M9, Canada.
| | - Eleni Aklillu
- Division of Clinical Pharmacology, Department of Laboratory Medicine, Karolinska Institute, Karolinska University Hospital Huddinge, 141 86 Stockholm, Sweden.
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34
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Penrose KJ, Brumme CJ, Scoulos-Hanson M, Hamanishi K, Gordon K, Viana RV, Wallis CL, Harrigan PR, Mellors JW, Parikh UM. Frequent cross-resistance to rilpivirine among subtype C HIV-1 from first-line antiretroviral therapy failures in South Africa. Antivir Chem Chemother 2019; 26:2040206618762985. [PMID: 29566538 PMCID: PMC5890541 DOI: 10.1177/2040206618762985] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Background Rilpivirine (TMC278LA) is a promising drug for pre-exposure prophylaxis of HIV-1 because of its sub-nanomolar potency and long-acting formulation; however, increasing transmission of non-nucleoside reverse transcriptase inhibitor-resistant HIV-1 with potential cross-resistance to rilpivirine could reduce its preventive efficacy. This study investigated rilpivirine cross-resistance among recombinant subtype C HIV-1 derived from 100 individuals failing on first-line non-nucleoside reverse transcriptase inhibitor-containing antiretroviral therapy in South Africa whose samples were sent for routine HIV-1 drug resistance testing to Lancet Laboratories (Johannesburg, South Africa). Methods Plasma samples were selected from individuals with HIV-1 RNA > 10,000 copies/ml and ≥1 non-nucleoside reverse transcriptase inhibitor-resistance mutation in reverse transcriptase. Recombinant HIV-1LAI-containing bulk-cloned full-length reverse transcriptase sequences from plasma were assayed for susceptibility to nevirapine (NVP), efavirenz (EFV) and rilpivirine in TZM-bl cells. Fold-change (FC) decreases in drug susceptibility were calculated against a mean IC50 from 12 subtype C HIV-1 samples from treatment-naïve individuals in South Africa. Cross-resistance was evaluated based on biological cutoffs established for rilpivirine (2.5-FC) and the effect of mutation combinations on rilpivirine phenotype. Results Of the 100 samples from individuals on failing antiretroviral therapy, 69 had 2.5- to 75-fold decreased susceptibility to rilpivirine and 11 had >75-fold resistance. Rilpivirine resistance was strongly associated with K103N especially in combination with other rilpivirine-associated mutations. Conclusion The frequently observed cross-resistance of HIV-1 suggests that the preventive efficacy of TMC278LA pre-exposure prophylaxis could be compromised by transmission of HIV-1 from individuals with failure of first-line non-nucleoside reverse transcriptase inhibitor-containing antiretroviral therapy.
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Affiliation(s)
- Kerri J Penrose
- 1 Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Chanson J Brumme
- 2 Laboratory Program, 198129 British Columbia Centre for Excellence in HIV/AIDS , Vancouver, British Columbia, Canada
| | - Maritsa Scoulos-Hanson
- 1 Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Kristen Hamanishi
- 1 Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Kelley Gordon
- 1 Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Raquel V Viana
- 3 Specialty Molecular Division, BARC-SA and Lancet Laboratories, Johannesburg, South Africa
| | - Carole L Wallis
- 3 Specialty Molecular Division, BARC-SA and Lancet Laboratories, Johannesburg, South Africa
| | - P Richard Harrigan
- 2 Laboratory Program, 198129 British Columbia Centre for Excellence in HIV/AIDS , Vancouver, British Columbia, Canada
| | - John W Mellors
- 1 Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Urvi M Parikh
- 1 Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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35
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Olmstead AD, Montoya V, Chui CK, Dong W, Joy JB, Tai V, Poon AFY, Nguyen T, Brumme CJ, Martinello M, Matthews GV, Richard Harrigan P, Dore GJ, Applegate TL, Grebely J, Howe AYM. A systematic, deep sequencing-based methodology for identification of mixed-genotype hepatitis C virus infections. Infect Genet Evol 2019; 69:76-84. [PMID: 30654177 DOI: 10.1016/j.meegid.2019.01.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 01/10/2019] [Accepted: 01/13/2019] [Indexed: 02/06/2023]
Abstract
Hepatitis C virus (HCV) mixed genotype infections can affect treatment outcomes and may have implications for vaccine design and disease progression. Previous studies demonstrate 0-39% of high-risk, HCV-infected individuals harbor mixed genotypes however standardized, sensitive methods of detection are lacking. This study compared PCR amplicon, random primer (RP), and probe enrichment (PE)-based deep sequencing methods coupled with a custom sequence analysis pipeline to detect multiple HCV genotypes. Mixed infection cutoff values, based on HCV read depth and coverage, were identified using receiver operating characteristic curve analysis. The methodology was validated using artificially mixed genotype samples and then applied to two clinical trials of HCV treatment in high-risk individuals (ACTIVATE, 114 samples from 90 individuals; DARE-C II, 26 samples from 18 individuals) and a cohort of HIV/HCV co-infected individuals (Canadian Coinfection Cohort (CCC), 3 samples from 2 individuals with suspected mixed genotype infections). Amplification bias of genotype (G)1b, G2, G3 and G5 was observed in artificially mixed samples using the PCR method while no genotype bias was observed using RP and PE. RP and PE sequencing of 140 ACTIVATE and DARE-C II samples identified the following primary genotypes: 15% (n = 21) G1a, 76% (n = 106) G3, and 9% (n = 13) G2. Sequencing of ACTIVATE and DARE-C II demonstrated, on average, 2% and 1% of HCV reads mapping to a second genotype using RP and PE, respectively, however none passed the mixed infection cutoff criteria and phylogenetics confirmed no mixed infections. From CCC, one mixed infection was confirmed while the other was determined to be a recombinant genotype. This study underlines the risk for false identification of mixed HCV infections and stresses the need for standardized methods to improve prevalence estimates and to understand the impact of mixed infections for management and elimination of HCV.
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Affiliation(s)
| | | | - Celia K Chui
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Winnie Dong
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Jeffrey B Joy
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada; Faculty of Medicine, Department of Medicine, Division of AIDS, University of British Columbia, Vancouver, BC, Canada
| | - Vera Tai
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Art F Y Poon
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Thuy Nguyen
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | | | | | | | - P Richard Harrigan
- Faculty of Medicine, Department of Medicine, Division of AIDS, University of British Columbia, Vancouver, BC, Canada
| | - Gregory J Dore
- UNSW Sydney, The Kirby Institute, Sydney, NSW, Australia
| | | | - Jason Grebely
- UNSW Sydney, The Kirby Institute, Sydney, NSW, Australia
| | - Anita Y M Howe
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
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36
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Ji H, Enns E, Brumme CJ, Parkin N, Howison M, Lee ER, Capina R, Marinier E, Avila‐Rios S, Sandstrom P, Van Domselaar G, Harrigan R, Paredes R, Kantor R, Noguera‐Julian M. Bioinformatic data processing pipelines in support of next-generation sequencing-based HIV drug resistance testing: the Winnipeg Consensus. J Int AIDS Soc 2018; 21:e25193. [PMID: 30350345 PMCID: PMC6198166 DOI: 10.1002/jia2.25193] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 09/26/2018] [Indexed: 11/14/2022] Open
Abstract
INTRODUCTION Next-generation sequencing (NGS) has several advantages over conventional Sanger sequencing for HIV drug resistance (HIVDR) genotyping, including detection and quantitation of low-abundance variants bearing drug resistance mutations (DRMs). However, the high HIV genomic diversity, unprecedented large volume of data, complexity of analysis and potential for error pose significant challenges for data processing. Several NGS analysis pipelines have been developed and used in HIVDR research; however, the absence of uniformity in data processing strategies results in lack of consistency and comparability of outputs from different pipelines. To fill this gap, an international symposium on bioinformatic strategies for NGS-based HIVDR testing was held in February 2018 in Winnipeg, Canada, convening laboratory scientists, bioinformaticians and clinicians involved in four recently developed, publicly available NGS HIVDR pipelines. The goal of this symposium was to establish a consensus on effective bioinformatic strategies for NGS data management and its use for HIVDR reporting. DISCUSSION Essential functionalities of an NGS HIVDR pipeline were divided into five analytic blocks: (1) NGS read quality control (QC)/quality assurance (QA); (2) NGS read alignment and reference mapping; (3) HIV variant calling and variant QC; (4) NGS HIVDR reporting; and (5) extended data applications and additional considerations for data management. The consensuses reached among the participants on all major aspects of these blocks are summarized here. They encompass not only recommended data management and analysis strategies, but also detailed bioinformatic approaches that help ensure accuracy of the derived HIVDR analysis outputs for both research and potential clinical use. CONCLUSIONS While NGS is being adopted more broadly in HIVDR testing laboratories, data processing is often a bottleneck hindering its generalized application. The proposed standardization of NGS read QC/QA, read alignment and reference mapping, variant calling and QC, HIVDR reporting and relevant data management strategies in this "Winnipeg Consensus" may serve as a starting guideline for NGS HIVDR data processing that informs the refinement of existing pipelines and those yet to be developed. Moreover, the bioinformatic strategies presented here may apply more broadly to NGS data analysis of microbes harbouring significant genomic diversity.
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Affiliation(s)
- Hezhao Ji
- National HIV and Retrovirology Laboratories at JC Wilt Infectious Diseases Research CentrePublic Health Agency of CanadaWinnipegMBCanada
- Department of Medical Microbiology and Infectious DiseasesUniversity of ManitobaWinnipegMBCanada
| | - Eric Enns
- Bioinformatics Core at the National Microbiology LaboratoryPublic Health Agency of CanadaWinnipegMBCanada
| | | | | | - Mark Howison
- Watson Institute for International and Public AffairsBrown UniversityProvidenceRIUSA
| | - Emma R. Lee
- National HIV and Retrovirology Laboratories at JC Wilt Infectious Diseases Research CentrePublic Health Agency of CanadaWinnipegMBCanada
| | - Rupert Capina
- National HIV and Retrovirology Laboratories at JC Wilt Infectious Diseases Research CentrePublic Health Agency of CanadaWinnipegMBCanada
| | - Eric Marinier
- Bioinformatics Core at the National Microbiology LaboratoryPublic Health Agency of CanadaWinnipegMBCanada
| | - Santiago Avila‐Rios
- Centre for Research in Infectious DiseasesNational Institute of Respiratory DiseasesMexico CityMexico
| | - Paul Sandstrom
- National HIV and Retrovirology Laboratories at JC Wilt Infectious Diseases Research CentrePublic Health Agency of CanadaWinnipegMBCanada
- Department of Medical Microbiology and Infectious DiseasesUniversity of ManitobaWinnipegMBCanada
| | - Gary Van Domselaar
- Department of Medical Microbiology and Infectious DiseasesUniversity of ManitobaWinnipegMBCanada
- Bioinformatics Core at the National Microbiology LaboratoryPublic Health Agency of CanadaWinnipegMBCanada
| | - Richard Harrigan
- Division of AIDSDepartment of MedicineUniversity of British ColumbiaVancouverBCCanada
| | - Roger Paredes
- IrsiCaixa AIDS Research InstituteBadalonaCataloniaSpain
| | - Rami Kantor
- Division of Infectious DiseasesBrown University Alpert Medical SchoolProvidenceRIUSA
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Valenzuela-Ponce H, Alva-Hernández S, Garrido-Rodríguez D, Soto-Nava M, García-Téllez T, Escamilla-Gómez T, García-Morales C, Quiroz-Morales VS, Tapia-Trejo D, Del Arenal-Sánchez S, Prado-Galbarro FJ, Hernández-Juan R, Rodríguez-Aguirre E, Murakami-Ogasawara A, Mejía-Villatoro C, Escobar-Urias IY, Pinzón-Meza R, Pascale JM, Zaldivar Y, Porras-Cortés G, Quant-Durán C, Lorenzana I, Meza RI, Palou EY, Manzanero M, Cedillos RA, Aláez C, Brockman MA, Harrigan PR, Brumme CJ, Brumme ZL, Ávila-Ríos S, Reyes-Terán G. Novel HLA class I associations with HIV-1 control in a unique genetically admixed population. Sci Rep 2018; 8:6111. [PMID: 29666450 PMCID: PMC5904102 DOI: 10.1038/s41598-018-23849-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 03/21/2018] [Indexed: 12/26/2022] Open
Abstract
Associations between HLA class I alleles and HIV progression in populations exhibiting Amerindian and Caucasian genetic admixture remain understudied. Using univariable and multivariable analyses we evaluated HLA associations with five HIV clinical parameters in 3,213 HIV clade B-infected, ART-naïve individuals from Mexico and Central America (MEX/CAM cohort). A Canadian cohort (HOMER, n = 1622) was used for comparison. As expected, HLA allele frequencies in MEX/CAM and HOMER differed markedly. In MEX/CAM, 13 HLA-A, 24 HLA-B, and 14 HLA-C alleles were significantly associated with at least one clinical parameter. These included previously described protective (e.g. B*27:05, B*57:01/02/03 and B*58:01) and risk (e.g. B*35:02) alleles, as well as novel ones (e.g. A*03:01, B*15:39 and B*39:02 identified as protective, and A*68:03/05, B*15:30, B*35:12/14, B*39:01/06, B*39:05~C*07:02, and B*40:01~C*03:04 identified as risk). Interestingly, both protective (e.g. B*39:02) and risk (e.g. B*39:01/05/06) subtypes were identified within the common and genetically diverse HLA-B*39 allele group, characteristic to Amerindian populations. While HLA-HIV associations identified in MEX and CAM separately were similar overall (Spearman's rho = 0.33, p = 0.03), region-specific associations were also noted. The identification of both canonical and novel HLA/HIV associations provides a first step towards improved understanding of HIV immune control among unique and understudied Mestizo populations.
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Affiliation(s)
- Humberto Valenzuela-Ponce
- National Institute of Respiratory Diseases, CIENI Center for Research in Infectious Diseases, Mexico City, Mexico
| | - Selma Alva-Hernández
- National Institute of Respiratory Diseases, CIENI Center for Research in Infectious Diseases, Mexico City, Mexico
| | - Daniela Garrido-Rodríguez
- National Institute of Respiratory Diseases, CIENI Center for Research in Infectious Diseases, Mexico City, Mexico
| | - Maribel Soto-Nava
- National Institute of Respiratory Diseases, CIENI Center for Research in Infectious Diseases, Mexico City, Mexico
| | - Thalía García-Téllez
- National Institute of Respiratory Diseases, CIENI Center for Research in Infectious Diseases, Mexico City, Mexico.,Institut Pasteur, Unité HIV, Inflammation and Persistence, Paris, France
| | - Tania Escamilla-Gómez
- National Institute of Respiratory Diseases, CIENI Center for Research in Infectious Diseases, Mexico City, Mexico
| | - Claudia García-Morales
- National Institute of Respiratory Diseases, CIENI Center for Research in Infectious Diseases, Mexico City, Mexico
| | | | - Daniela Tapia-Trejo
- National Institute of Respiratory Diseases, CIENI Center for Research in Infectious Diseases, Mexico City, Mexico
| | - Silvia Del Arenal-Sánchez
- National Institute of Respiratory Diseases, CIENI Center for Research in Infectious Diseases, Mexico City, Mexico
| | | | - Ramón Hernández-Juan
- National Institute of Respiratory Diseases, CIENI Center for Research in Infectious Diseases, Mexico City, Mexico
| | - Edna Rodríguez-Aguirre
- National Institute of Respiratory Diseases, CIENI Center for Research in Infectious Diseases, Mexico City, Mexico
| | - Akio Murakami-Ogasawara
- National Institute of Respiratory Diseases, CIENI Center for Research in Infectious Diseases, Mexico City, Mexico
| | | | | | | | | | - Yamitzel Zaldivar
- Instituto Conmemorativo Gorgas de Estudios de la Salud, Panama City, Panama
| | | | | | - Ivette Lorenzana
- Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Rita I Meza
- Honduras HIV National Laboratory, Tegucigalpa, Honduras
| | - Elsa Y Palou
- Hospital Escuela Universitario, Tegucigalpa, Honduras
| | | | | | - Carmen Aláez
- National Institute of Genomic Medicine, Translational Medicine Laboratory, Mexico City, Mexico
| | - Mark A Brockman
- Simon Fraser University, Faculty of Health Sciences, Burnaby, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | | | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Zabrina L Brumme
- Simon Fraser University, Faculty of Health Sciences, Burnaby, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Santiago Ávila-Ríos
- National Institute of Respiratory Diseases, CIENI Center for Research in Infectious Diseases, Mexico City, Mexico.
| | - Gustavo Reyes-Terán
- National Institute of Respiratory Diseases, CIENI Center for Research in Infectious Diseases, Mexico City, Mexico.
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Tadesse BT, Kinloch NN, Baraki B, Lapointe HR, Cobarrubias KD, Brockman MA, Brumme CJ, Foster BA, Jerene D, Makonnen E, Aklillu E, Brumme ZL. High Levels of Dual-Class Drug Resistance in HIV-Infected Children Failing First-Line Antiretroviral Therapy in Southern Ethiopia. Viruses 2018; 10:E60. [PMID: 29389912 PMCID: PMC5850367 DOI: 10.3390/v10020060] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 01/30/2018] [Accepted: 01/30/2018] [Indexed: 11/29/2022] Open
Abstract
Clinical monitoring of pediatric HIV treatment remains a major challenge in settings where drug resistance genotyping is not routinely available. As a result, our understanding of drug resistance, and its impact on subsequent therapeutic regimens available in these settings, remains limited. We investigate the prevalence and correlates of HIV-1 drug resistance among 94 participants of the Ethiopia Pediatric HIV Cohort failing first-line combination antiretroviral therapy (cART) using dried blood spot-based genotyping. Overall, 81% (73/90) of successfully genotyped participants harbored resistance mutations, including 69% (62/90) who harbored resistance to both Nucleoside Reverse Transcriptase Inhibitors (NRTIs) and Non-nucleoside Reverse Transcriptase Inhibitors (NNRTIs). Strikingly, 42% of resistant participants harbored resistance to all four NRTIs recommended for second-line use in this setting, meaning that there are effectively no remaining cART options for these children. Longer cART duration and prior regimen changes were significantly associated with detection of drug resistance mutations. Replicate genotyping increased the breadth of drug resistance detected in 34% of cases, and thus is recommended for consideration when typing from blood spots. Implementation of timely drug resistance testing and access to newer antiretrovirals and drug classes are urgently needed to guide clinical decision-making and improve outcomes for HIV-infected children on first-line cART in Ethiopia.
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Affiliation(s)
| | - Natalie N Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.
| | - Bemuluyigza Baraki
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.
| | - Hope R Lapointe
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada.
| | - Kyle D Cobarrubias
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.
| | - Mark A Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada.
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada.
| | - Byron A Foster
- Departments of Dermatology and Pediatrics, Oregon Health Sciences University, Portland, OR 97239, USA.
| | - Degu Jerene
- Management Sciences for Health, Addis Ababa 1250, Ethiopia.
| | - Eyasu Makonnen
- Department of Pharmacology, College of Health Sciences, Addis Ababa University, Addis Ababa 9086, Ethiopia.
| | - Eleni Aklillu
- Division of Clinical Pharmacology, Department of Laboratory Medicine, Karolinska Institute, Karolinska University Hospital Huddinge C1:68, Stockholm 141 86, Sweden.
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada.
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39
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Rocheleau G, Franco-Villalobos C, Oliveira N, Brumme ZL, Rusch M, Shoveller J, Brumme CJ, Harrigan PR. Sociodemographic correlates of HIV drug resistance and access to drug resistance testing in British Columbia, Canada. PLoS One 2017; 12:e0184848. [PMID: 28937991 PMCID: PMC5609746 DOI: 10.1371/journal.pone.0184848] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 08/31/2017] [Indexed: 01/25/2023] Open
Abstract
Sociodemographic correlates of engagement in human immunodeficiency virus (HIV) care are well studied, however the association with accessing drug resistance testing (DRT) and the development of drug resistance have not been characterized. Between 1996–2014, 11 801 HIV patients accessing therapy in British Columbia were observed longitudinally. A subset of 9456 patients had testable viral load; of these 8398 were linked to census data. Sociodemographic (census tract-level) and clinical (individual-level) correlates of DRT were assessed using multivariable General Estimating Equation logistic regression adjusted odds ratios (aOR). The mean number of tests per patient was 2.1 (Q1-Q3; 0–3). Separately, any drug resistance was determined using IAS-USA (2013) list for 5703 initially treatment naïve patients without baseline resistance; 5175 were census-linked (mean of 1.5 protease-reverse transcriptase sequences/patient, Q1-Q3; 0–2). Correlates of detecting drug resistance in this subset were analyzed using Cox PH regression adjusted hazard ratios (aHR). Our results indicate baseline CD4 <200 cells/μL (aOR: 1.5, 1.3–1.6), nRTI-only baseline regimens (aOR: 1.4, 1.3–1.6), and unknown (therapy initiation before routine pVL in BC) baseline pVL (aOR: 1.8, 1.5–2.1) were among individual-level clinical covariates strongly associated with having accessed DRT; while imperfect adherence (aHR: 2.2, 1.9–2.5), low baseline CD4 count (aHR: 1.9, 1.6–2.3), and high baseline pVL (aHR: 2.0, 1.6–2.6) were associated with a higher likelihood of developing drug resistance. A higher median income (aOR: 0.83, 0.77–0.89) and higher percentage of those with aboriginal ancestry (aOR: 0.85, 0.76–0.95) were census tract-level sociodemographic covariates associated with decreased access to DRT. Similarly, aboriginal ancestry (aHR: 1.2, 1.1–1.5) was associated with development of drug resistance. In conclusion, clinical covariates continue to be the strongest correlates of development of drug resistance and access to DRT for individuals. Regions of high median income and high aboriginal ancestry were weak census-level sociodemographic indicators of reduced DRT uptake, however high aboriginal ancestry was the only sociodemographic indicator for development of drug resistance.
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Affiliation(s)
- Genevieve Rocheleau
- Department of Medicine, University of British Columbia, Vancouver, Canada
- BC Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | | | | | - Zabrina L. Brumme
- BC Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | | | - Jeannie Shoveller
- BC Centre for Excellence in HIV/AIDS, Vancouver, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | | | - P. Richard Harrigan
- Department of Medicine, University of British Columbia, Vancouver, Canada
- BC Centre for Excellence in HIV/AIDS, Vancouver, Canada
- * E-mail:
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40
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Rocheleau G, Brumme CJ, Shoveller J, Lima VD, Harrigan PR. Longitudinal trends of HIV drug resistance in a large Canadian cohort, 1996-2016. Clin Microbiol Infect 2017; 24:185-191. [PMID: 28652115 DOI: 10.1016/j.cmi.2017.06.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 06/13/2017] [Accepted: 06/14/2017] [Indexed: 11/25/2022]
Abstract
OBJECTIVES We aim to identify long-term trends in HIV drug resistance before and after combined antiretroviral therapy (cART) initiation. METHODS IAS-USA (2015) mutations were identified in 23 271 HIV protease-reverse transcriptase sequences from 6543 treatment naïve adults in British Columbia. Participants who started cART between 1996 and 2014 were followed until April 2016. Equality of proportions test was used to compare the percentage of participants with acquired drug resistance (ADR) or transmitted drug resistance (TDR) in 1996, to those in 2014. Kaplan-Meier was used to estimate time to ADR in four drug resistance categories. Multivariable regression odds ratios (OR) of ADR for select clinical variables were determined by 5-year eras of cART initiation. RESULTS The proportion of individuals with ADR declined from 39% (51/132) to 3% (8/322) in 1996-2014 (p <0.0001), while the proportion with TDR increased from 12% (16/132) to 18% (59/322) (p 0.14). The estimated proportions of individuals with ADR rose to 29% (NNRTI), 28% (3TC/FTC), 14% (other nRTI), and 7% (PI) after >16 years of therapy. After 5 years on therapy, participants initiating cART in 1996-2000 had 5.5-times more 3TC/FTC ADR, 5.3-times more other nRTI ADR, 4.7-times more NNRTI ADR, and 24-times more PI ADR than those starting in 2011-2014. The individuals with highest odds of developing ADR in 1996-2010 were adherent to regimens at levels between 60% and 80%, which shifted to <40% adherent in 2011-2014. CONCLUSIONS HIV drug resistance transitioned from being primarily selected de-novo to being driven by TDR. Among those who started treatment in the past 5 years, ADR is rare and observed mostly in the lowest adherence strata.
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Affiliation(s)
- G Rocheleau
- Experimental Medicine, Faculty of Medicine, University of British Columbia, Vancouver, Canada; British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - C J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - J Shoveller
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada; School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | - V D Lima
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada; School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | - P R Harrigan
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada; Division of AIDS, Faculty of Medicine, University of British Columbia, Vancouver, Canada.
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41
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Gonzalez-Serna A, Glas AC, Brumme CJ, Poon AFY, Nohpal De La Rosa A, Mudrikova T, Dias Lima V, Wensing AMJ, Harrigan R. Genotypic susceptibility score (GSS) and CD4+ T cell recovery in HIV-1 patients with suppressed viral load. J Antimicrob Chemother 2016; 72:496-503. [PMID: 27999069 DOI: 10.1093/jac/dkw455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 09/23/2016] [Accepted: 09/23/2016] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES HIV drug resistance, measured by the genotypic susceptibility score (GSS), has a deleterious effect on the virological outcome of HIV-1-infected patients. However, it is not known if GSS retains any predictive value for CD4 recovery in patients with suppressed viral load. METHODS Four hundred and six patients on virological failure (>500 copies/mL) with GSS : <6 months prior to switch therapy who achieved undetectable plasma viral load (<50 copies/mL) within 1 year, remained undetectable >1 year on an unchanged regimen and had CD4 data available during entire follow-up were included. Adjusted and unadjusted analyses of all characteristics at switch related to CD4 recovery were made for three time frames: (i) 'switch-suppression'; (ii) 'suppression-1 year'; and (iii) 'switch-1 year'. RESULTS Higher GSS was associated with a greater CD4 recovery between 'switch' and '1 year' in the unadjusted analysis (P = 0.010); however, the effect of GSS was no longer statistically significant after adjusting for pre-switch clinical (CD4 count and plasma viral load) and demographic variables. Furthermore, only a lower pre-switch CD4 count was associated with increased CD4 recovery in the 'suppression-1 year' period in both unadjusted and adjusted models. The main CD4 recovery occurred in 'switch-suppression' and the variables associated, both unadjusted and adjusted, were CD4 and plasma viral load at switch, maintaining a trend for GSS (P = 0.06). CONCLUSIONS In individuals who re-suppressed HIV viraemia after switching therapy, regimens having a higher GSS were associated with improved CD4 recovery only during the period from switch to virological suppression, but, once viral load is re-suppressed, the GSS of the new regimen has no further effect on subsequent CD4 recovery.
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Affiliation(s)
- Alejandro Gonzalez-Serna
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada .,Laboratory of Molecular Immunobiology, Hospital General Universitario Gregorio Maranon, Madrid, Spain
| | - Arie C Glas
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - C J Brumme
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Art F Y Poon
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | | | - Tania Mudrikova
- Department of Internal Medicine and Infectious Diseases, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Annemarie M J Wensing
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
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Brumme CJ, Poon AFY. Promises and pitfalls of Illumina sequencing for HIV resistance genotyping. Virus Res 2016; 239:97-105. [PMID: 27993623 DOI: 10.1016/j.virusres.2016.12.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 12/15/2016] [Accepted: 12/15/2016] [Indexed: 12/13/2022]
Abstract
Genetic sequencing ("genotyping") plays a critical role in the modern clinical management of HIV infection. This virus evolves rapidly within patients because of its error-prone reverse transcriptase and short generation time. Consequently, HIV variants with mutations that confer resistance to one or more antiretroviral drugs can emerge during sub-optimal treatment. There are now multiple HIV drug resistance interpretation algorithms that take the region of the HIV genome encoding the major drug targets as inputs; expert use of these algorithms can significantly improve to clinical outcomes in HIV treatment. Next-generation sequencing has the potential to revolutionize HIV resistance genotyping by lowering the threshold that rare but clinically significant HIV variants can be detected reproducibly, and by conferring improved cost-effectiveness in high-throughput scenarios. In this review, we discuss the relative merits and challenges of deploying the Illumina MiSeq instrument for clinical HIV genotyping.
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Affiliation(s)
- Chanson J Brumme
- BC Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Art F Y Poon
- Department of Pathology & Laboratory Medicine, Western University, London, Ontario, Canada.
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Sakai K, Chikata T, Brumme ZL, Brumme CJ, Gatanaga H, Oka S, Takiguchi M. Erratum to: Lack of a significant impact of Gag-Protease-mediated HIV-1 replication capacity on clinical parameters in treatment-naive Japanese individuals. Retrovirology 2015; 12:100. [PMID: 26620834 PMCID: PMC4665959 DOI: 10.1186/s12977-015-0227-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Keiko Sakai
- Center for AIDS Research, Kumamoto University, Kumamoto, 860-0811, Japan.
| | - Takayuki Chikata
- Center for AIDS Research, Kumamoto University, Kumamoto, 860-0811, Japan
| | - Zabrina L Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.,Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Hiroyuki Gatanaga
- Center for AIDS Research, Kumamoto University, Kumamoto, 860-0811, Japan.,National Center for Global Health and Medicine, Tokyo, 162-8655, Japan
| | - Shinichi Oka
- Center for AIDS Research, Kumamoto University, Kumamoto, 860-0811, Japan.,National Center for Global Health and Medicine, Tokyo, 162-8655, Japan
| | - Masafumi Takiguchi
- Center for AIDS Research, Kumamoto University, Kumamoto, 860-0811, Japan.,International Research Center for Medical Sciences, Kumamoto University, Kumamoto, 860-0811, Japan.,Nuffield Department of Medicine, University of Oxford, Oxford, UK
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Sakai K, Chikata T, Brumme ZL, Brumme CJ, Gatanaga H, Gatanag H, Oka S, Takiguchi M. Lack of a significant impact of Gag-Protease-mediated HIV-1 replication capacity on clinical parameters in treatment-naive Japanese individuals. Retrovirology 2015; 12:98. [PMID: 26585907 PMCID: PMC4653850 DOI: 10.1186/s12977-015-0223-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 11/08/2015] [Indexed: 01/29/2023] Open
Abstract
Background HLA class I-associated escape mutations in HIV-1 Gag can reduce viral replication, suggesting that associated fitness costs could impact HIV-1 disease progression. Previous studies in North American and African cohorts have reported reduced Gag-Protease mediated viral replication capacity (Gag-Pro RC) in individuals expressing protective HLA class I alleles including HLA-B*57:01, B*27:05, and B*81:01. These studies also reported significant positive associations between Gag-Pro RCs and plasma viral load (pVL). However, these HLA alleles are virtually absent in Japan, and the importance of Gag as an immune target is not clearly defined in this population. Results We generated chimeric NL4-3 viruses carrying patient-derived Gag-Protease from 306 treatment-naive Japanese individuals chronically infected with HIV-1 subtype B. We analyzed associations between Gag-Pro RC and clinical markers of HIV-1 infection and host HLA expression. We observed no significant correlation between Gag-Pro RC and pVL in Japan in the overall cohort. However, upon exclusion of individuals expressing Japanese protective alleles HLA-B*52:01 and B*67:01, Gag-Pro RC correlated positively with pVL and negatively with CD4 T-cell count. Our results thus contrast with studies from other global cohorts reporting significantly lower Gag-Pro RC among persons expressing protective HLA alleles, and positive relationships between Gag-Pro RC and pVL in the overall study populations. We also identified five amino acids in Gag-Protease significantly associated with Gag-Pro RC, whose effects on RC were confirmed by site-directed mutagenesis. However, of the four mutations that decreased Gag-Pro RC, none were associated with reductions in pVL in Japan though two were associated with lower pVL in North America. Conclusions These data indicate that Gag fitness does not affect clinical outcomes in subjects with protective HLA class I alleles as well as the whole Japanese population. Moreover, the impact of Gag fitness costs on HIV-1 clinical parameters in chronic infection is likely low in Japan compared to other global populations. Electronic supplementary material The online version of this article (doi:10.1186/s12977-015-0223-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Keiko Sakai
- Center for AIDS Research, Kumamoto University, Kumamoto, 860-0811, Japan.
| | - Takayuki Chikata
- Center for AIDS Research, Kumamoto University, Kumamoto, 860-0811, Japan.
| | - Zabrina L Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada. .,Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.
| | - Hiroyuki Gatanaga
- Center for AIDS Research, Kumamoto University, Kumamoto, 860-0811, Japan.
| | | | - Shinichi Oka
- Center for AIDS Research, Kumamoto University, Kumamoto, 860-0811, Japan. .,National Center for Global Health and Medicine, Tokyo, 162-8655, Japan.
| | - Masafumi Takiguchi
- Center for AIDS Research, Kumamoto University, Kumamoto, 860-0811, Japan. .,International Research Center for Medical Sciences, Kumamoto University, Kumamoto, 860-0811, Japan. .,Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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45
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Poon AFY, Joy JB, Woods CK, Shurgold S, Colley G, Brumme CJ, Hogg RS, Montaner JSG, Harrigan PR. The impact of clinical, demographic and risk factors on rates of HIV transmission: a population-based phylogenetic analysis in British Columbia, Canada. J Infect Dis 2014; 211:926-35. [PMID: 25312037 DOI: 10.1093/infdis/jiu560] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The diversification of human immunodeficiency virus (HIV) is shaped by its transmission history. We therefore used a population based province wide HIV drug resistance database in British Columbia (BC), Canada, to evaluate the impact of clinical, demographic, and behavioral factors on rates of HIV transmission. METHODS We reconstructed molecular phylogenies from 27,296 anonymized bulk HIV pol sequences representing 7747 individuals in BC-about half the estimated HIV prevalence in BC. Infections were grouped into clusters based on phylogenetic distances, as a proxy for variation in transmission rates. Rates of cluster expansion were reconstructed from estimated dates of HIV seroconversion. RESULTS Our criteria grouped 4431 individuals into 744 clusters largely separated with respect to risk factors, including large established clusters predominated by injection drug users and more-recently emerging clusters comprising men who have sex with men. The mean log10 viral load of an individual's phylogenetic neighborhood (composed of 5 other individuals with shortest phylogenetic distances) increased their odds of appearing in a cluster by >2-fold per log10 viruses per milliliter. CONCLUSIONS Hotspots of ongoing HIV transmission can be characterized in near real time by the secondary analysis of HIV resistance genotypes, providing an important potential resource for targeting public health initiatives for HIV prevention.
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Affiliation(s)
- Art F Y Poon
- BC Centre for Excellence in HIV/AIDS Department of Medicine, University of British Columbia, Vancouver
| | | | | | | | | | | | - Robert S Hogg
- BC Centre for Excellence in HIV/AIDS Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Julio S G Montaner
- BC Centre for Excellence in HIV/AIDS Department of Medicine, University of British Columbia, Vancouver
| | - P Richard Harrigan
- BC Centre for Excellence in HIV/AIDS Department of Medicine, University of British Columbia, Vancouver
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46
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Lee GQ, Carlson J, Brumme CJ, Byakwaga H, Muzoora C, MacMillan D, Kinloch N, Cobarrubias K, Brockman MA, Hunt PW, Martin JN, Carrington M, Bangsberg DR, Harrigan PR, Brumme ZL. Subtype-Specific HIV-1 Adaptation to Host HLA. AIDS Res Hum Retroviruses 2014. [DOI: 10.1089/aid.2014.5475.abstract] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | | | | | - Helen Byakwaga
- Mbarara University of Science and Technology, Mbarara, Uganda
- University of California San Francisco, San Francisco, CA, United States
| | - Conrad Muzoora
- Mbarara University of Science and Technology, Mbarara, Uganda
| | - Daniel MacMillan
- Simon Fraser University, Faculty of Health Sciences, Burnaby, BC, Canada
| | - Natalie Kinloch
- Simon Fraser University, Faculty of Health Sciences, Burnaby, BC, Canada
| | - Kyle Cobarrubias
- Simon Fraser University, Faculty of Health Sciences, Burnaby, BC, Canada
| | - Mark A. Brockman
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
- Simon Fraser University, Faculty of Health Sciences, Burnaby, BC, Canada
| | - Peter W. Hunt
- University of California San Francisco, San Francisco, CA, United States
| | - Jeff N. Martin
- University of California San Francisco, San Francisco, CA, United States
| | - Mary Carrington
- Frederick National Laboratory for Cancer Research, Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC Frederick, Inc., Frederick, MD, United States
| | - David R. Bangsberg
- Massachusetts General Hospital and Harvard University, Boston, MA, United States
| | - P. Richard Harrigan
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
- University of British Columbia, Department of Medicine, Vancouver, BC, Canada
| | - Zabrina L. Brumme
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
- Simon Fraser University, Faculty of Health Sciences, Burnaby, BC, Canada
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47
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Lee GQ, Bangsberg DR, Muzoora C, Boum Y, Oyugi JH, Emenyonu N, Bennett J, Hunt PW, Knapp D, Brumme CJ, Harrigan PR, Martin JN. Prevalence and virologic consequences of transmitted HIV-1 drug resistance in Uganda. AIDS Res Hum Retroviruses 2014; 30:896-906. [PMID: 24960249 DOI: 10.1089/aid.2014.0043] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Few reports have examined the impact of HIV-1 transmitted drug resistance (TDR) in resource-limited settings where there are fewer regimen choices and limited pretherapy/posttherapy resistance testing. In this study, we examined TDR prevalence in Kampala and Mbarara, Uganda and assessed its virologic consequences after antiretroviral therapy initiation. We sequenced the HIV-1 protease/reverse transcriptase from n=81 and n=491 treatment-naive participants of the Uganda AIDS Rural Treatment Outcomes (UARTO) pilot study in Kampala (AMU 2002-2004) and main cohort in Mbarara (MBA 2005-2010). TDR-associated mutations were defined by the WHO 2009 surveillance mutation list. Posttreatment viral load data were available for both populations. Overall TDR prevalence was 7% (Kampala) and 3% (Mbarara) with no significant time trend. There was a slight but statistically nonsignificant trend indicating that the presence of TDR was associated with a worse treatment outcome. Virologic suppression (≤400 copies/ml within 6 months posttherapy initiation) was achieved in 87% and 96% of participants with wildtype viruses versus 67% and 83% of participants with TDR (AMU, MBA p=0.2 and 0.1); time to suppression (log-rank p=0.3 and p=0.05). Overall, 85% and 96% of study participants achieved suppression regardless of TDR status. Surprisingly, among the TDR cases, approximately half still achieved suppression; the presence of pretherapy K103N while on nevirapine and fewer active drugs in the first regimen were most often observed with failures. The majority of patients benefited from the local HIV care system even without resistance monitoring. Overall, TDR prevalence was relatively low and its presence did not always imply treatment failure.
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Affiliation(s)
| | - David R. Bangsberg
- Mbarara University of Science of Technology, Mbarara, Uganda
- Harvard Medical School, Boston, Massachusetts
- Harvard School of Public Health, Boston, Massachusetts
- Massachusetts General Hospital, Boston, Massachusetts
| | - Conrad Muzoora
- Mbarara University of Science of Technology, Mbarara, Uganda
| | - Yap Boum
- Mbarara University of Science of Technology, Mbarara, Uganda
| | - Jessica H. Oyugi
- University of California, San Francisco, California
- Independent consultant
| | - Nneka Emenyonu
- Mbarara University of Science of Technology, Mbarara, Uganda
| | - John Bennett
- University of California, San Francisco, California
| | | | - David Knapp
- B.C. Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
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48
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Liang RH, Mo T, Dong W, Lee GQ, Swenson LC, McCloskey RM, Woods CK, Brumme CJ, Ho CKY, Schinkel J, Joy JB, Harrigan PR, Poon AFY. Theoretical and experimental assessment of degenerate primer tagging in ultra-deep applications of next-generation sequencing. Nucleic Acids Res 2014; 42:e98. [PMID: 24810852 PMCID: PMC4081055 DOI: 10.1093/nar/gku355] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Primer IDs (pIDs) are random oligonucleotide tags used in next-generation sequencing to identify sequences that originate from the same template. These tags are produced by degenerate primers during the reverse transcription of RNA molecules into cDNA. The use of pIDs helps to track the number of RNA molecules carried through amplification and sequencing, and allows resolution of inconsistencies between reads sharing a pID. Three potential issues complicate the above applications. First, multiple cDNAs may share a pID by chance; we found that while preventing any cDNAs from sharing a pID may be unfeasible, it is still practical to limit the number of these collisions. Secondly, a pID must be observed in at least three sequences to allow error correction; as such, pIDs observed only one or two times must be rejected. If the sequencing product contains copies from a high number of RT templates but produces few reads, our findings indicate that rejecting such pIDs will discard a great deal of data. Thirdly, the use of pIDs could influence amplification and sequencing. We examined the effects of several intrinsic and extrinsic factors on sequencing reads at both the individual and ensemble level.
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Affiliation(s)
- Richard H Liang
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, V6Z 1Y6, Canada
| | - Theresa Mo
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, V6Z 1Y6, Canada
| | - Winnie Dong
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, V6Z 1Y6, Canada
| | - Guinevere Q Lee
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, V6Z 1Y6, Canada
| | - Luke C Swenson
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, V6Z 1Y6, Canada
| | | | - Conan K Woods
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, V6Z 1Y6, Canada
| | - Chanson J Brumme
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, V6Z 1Y6, Canada
| | - Cynthia K Y Ho
- Section of Clinical Virology, Department of Medical Microbiology, Academic Medical Center, 1105AZ Amsterdam, The Netherlands
| | - Janke Schinkel
- Section of Clinical Virology, Department of Medical Microbiology, Academic Medical Center, 1105AZ Amsterdam, The Netherlands
| | - Jeffrey B Joy
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, V6Z 1Y6, Canada
| | - P Richard Harrigan
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, V6Z 1Y6, Canada Department of Medicine, University of British Columbia, Vancouver, BC, V5Z 1M9, Canada
| | - Art F Y Poon
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, V6Z 1Y6, Canada Department of Medicine, University of British Columbia, Vancouver, BC, V5Z 1M9, Canada
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49
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Cotton LA, Kuang XT, Le AQ, Carlson JM, Chan B, Chopera DR, Brumme CJ, Markle TJ, Martin E, Shahid A, Anmole G, Mwimanzi P, Nassab P, Penney KA, Rahman MA, Milloy MJ, Schechter MT, Markowitz M, Carrington M, Walker BD, Wagner T, Buchbinder S, Fuchs J, Koblin B, Mayer KH, Harrigan PR, Brockman MA, Poon AFY, Brumme ZL. Genotypic and functional impact of HIV-1 adaptation to its host population during the North American epidemic. PLoS Genet 2014; 10:e1004295. [PMID: 24762668 PMCID: PMC3998893 DOI: 10.1371/journal.pgen.1004295] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 02/21/2014] [Indexed: 11/20/2022] Open
Abstract
HLA-restricted immune escape mutations that persist following HIV transmission could gradually spread through the viral population, thereby compromising host antiviral immunity as the epidemic progresses. To assess the extent and phenotypic impact of this phenomenon in an immunogenetically diverse population, we genotypically and functionally compared linked HLA and HIV (Gag/Nef) sequences from 358 historic (1979–1989) and 382 modern (2000–2011) specimens from four key cities in the North American epidemic (New York, Boston, San Francisco, Vancouver). Inferred HIV phylogenies were star-like, with approximately two-fold greater mean pairwise distances in modern versus historic sequences. The reconstructed epidemic ancestral (founder) HIV sequence was essentially identical to the North American subtype B consensus. Consistent with gradual diversification of a “consensus-like” founder virus, the median “background” frequencies of individual HLA-associated polymorphisms in HIV (in individuals lacking the restricting HLA[s]) were ∼2-fold higher in modern versus historic HIV sequences, though these remained notably low overall (e.g. in Gag, medians were 3.7% in the 2000s versus 2.0% in the 1980s). HIV polymorphisms exhibiting the greatest relative spread were those restricted by protective HLAs. Despite these increases, when HIV sequences were analyzed as a whole, their total average burden of polymorphisms that were “pre-adapted” to the average host HLA profile was only ∼2% greater in modern versus historic eras. Furthermore, HLA-associated polymorphisms identified in historic HIV sequences were consistent with those detectable today, with none identified that could explain the few HIV codons where the inferred epidemic ancestor differed from the modern consensus. Results are therefore consistent with slow HIV adaptation to HLA, but at a rate unlikely to yield imminent negative implications for cellular immunity, at least in North America. Intriguingly, temporal changes in protein activity of patient-derived Nef (though not Gag) sequences were observed, suggesting functional implications of population-level HIV evolution on certain viral proteins. Upon HIV transmission, many – though not all – immune escape mutations selected in the previous host will revert to the consensus residue. The persistence of certain escape mutations following transmission has led to concerns that these could gradually accumulate in circulating HIV sequences over time, thereby undermining host antiviral immune potential as the epidemic progresses. As certain immune-driven mutations reduce viral fitness, their spread through the population could also have consequences for the average replication capacity and/or protein function of circulating HIV sequences. Here, we characterized HIV sequences, linked to host immunogenetic information, from patients enrolled in historic (1979–1989) and modern (2000–2011) HIV cohorts from four key cities in the North American epidemic. We reconstructed the epidemic's ancestral (founder) HIV sequence and assessed the subsequent extent to which known HIV immune escape mutations have spread in the population. Our data support the gradual spread of many - though not all - immune escape mutations in HIV sequences over time, but to an extent that is unlikely to have major immediate immunologic consequences for the North American epidemic. Notably, in vitro assessments of ancestral and patient-derived HIV sequences suggested functional implications of ongoing HIV evolution for certain viral proteins.
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Affiliation(s)
- Laura A. Cotton
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Xiaomei T. Kuang
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Anh Q. Le
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | | | - Benjamin Chan
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Denis R. Chopera
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- KwaZulu-Natal Research Institute for Tuberculosis and HIV, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, KwaZulu-Natal, South Africa
| | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Tristan J. Markle
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Eric Martin
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Gursev Anmole
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Philip Mwimanzi
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Pauline Nassab
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Kali A. Penney
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Manal A. Rahman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - M.-J. Milloy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Martin T. Schechter
- Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Martin Markowitz
- Aaron Diamond AIDS Research Center, The Rockefeller University, New York, New York, United States of America
| | - Mary Carrington
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
- Ragon Institute of MGH, MIT and Harvard University, Cambridge, Massachusetts, United States of America
| | - Bruce D. Walker
- Ragon Institute of MGH, MIT and Harvard University, Cambridge, Massachusetts, United States of America
| | - Theresa Wagner
- San Francisco Department of Public Health, San Francisco, California, United States of America
| | - Susan Buchbinder
- San Francisco Department of Public Health, San Francisco, California, United States of America
| | - Jonathan Fuchs
- San Francisco Department of Public Health, San Francisco, California, United States of America
| | - Beryl Koblin
- New York Blood Center, New York, New York, United States of America
| | - Kenneth H. Mayer
- Fenway Community Health, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - P. Richard Harrigan
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mark A. Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Art F. Y. Poon
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- * E-mail:
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50
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Shimizu A, Kawana-Tachikawa A, Yamagata A, Han C, Zhu D, Sato Y, Nakamura H, Koibuchi T, Carlson J, Martin E, Brumme CJ, Shi Y, Gao GF, Brumme ZL, Fukai S, Iwamoto A. Structure of TCR and antigen complexes at an immunodominant CTL epitope in HIV-1 infection. Sci Rep 2013; 3:3097. [PMID: 24192765 PMCID: PMC3818656 DOI: 10.1038/srep03097] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 10/15/2013] [Indexed: 12/13/2022] Open
Abstract
We investigated the crystal structure of an HLA-A*2402-restricted CTL epitope in the HIV-1 nef gene (Nef134-10) before (pHLA) or after TCR docking. The wild type epitope and two escape mutants were included in the study. Y135F was an early-appearing major mutation, while F139L was a late-appearing mutation which was selected in the patients without Y135F. F139 was an eminent feature of the Nef134-10 epitope. Wild type-specific TCR was less fit to F139L mutant suggesting that F139L is an escape from the CTL against the wild type epitope. Although Y135F mutation disrupted the hydrogen bond to HLA-A*2402 His70, newly formed hydrogen bond between T138 and His70 kept the conformation of the epitope in the reconstituted pMHC. TCR from Y135F- or dually-specific CTL had unique mode of binding to the mutant epitope. Y135F has been reported as a processing mutant but CTL carrying structurally adequate TCR can be found in the patients.
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Affiliation(s)
- Akihisa Shimizu
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, the University of Tokyo. 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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