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Hermans LE, Centner CM, Morel CM, Mbamalu O, Bonaconsa C, Ferreyra C, Lindahl O, Mendelson M. Point-of-care diagnostics for infection and antimicrobial resistance in sub-Saharan Africa: A narrative review. Int J Infect Dis 2024; 142:106907. [PMID: 38141961 DOI: 10.1016/j.ijid.2023.11.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 12/25/2023] Open
Abstract
OBJECTIVES Sub-Saharan African (SSA) countries are severely impacted by antimicrobial resistance (AMR). Due to gaps in access to diagnostics in SSA, the true extent of AMR remains unknown. This diagnostic gap affects patient management and leads to significant antimicrobial overuse. This review explores how point-of-care (POC) testing for pathogen identification and AMR may be used to close the diagnostic gap in SSA countries. METHODS A narrative review exploring current clinical practice and novel developments in the field of POC testing for infectious diseases and AMR. RESULTS POC assays for identification of various pathogens have been successfully rolled out in SSA countries. While implementation studies have mostly highlighted impressive test performance of POC assays, there is limited data on the impact of implementation on clinical outcomes and cost-effectiveness. We did not encounter local studies of host-directed POC assays relevant to AMR. Novel POC assays using real-time polymerase chain reaction, isothermal amplification, microfluidics, and other technologies are in various stages of development. CONCLUSIONS Available literature shows that POC testing for AMR applications is implementable in SSA and holds the potential to reduce the diagnostic gap. Implementation will require effective regulatory pathways, incorporation of POC testing in clinical and laboratory guidelines, and adequate value capture in existing health financing models.
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Affiliation(s)
- Lucas Etienne Hermans
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, University of Cape Town, Cape Town, South Africa.
| | - Chad M Centner
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa
| | - Chantal M Morel
- Department of Business Studies, Uppsala University, Uppsala, Sweden; Institute for Hygiene and Public Health, Bonn University Hospital, Bonn, Germany; University of Bern, KPM Center for Public Management, Bern, Switzerland
| | - Oluchi Mbamalu
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Candice Bonaconsa
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Cecilia Ferreyra
- Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland
| | - Olof Lindahl
- Department of Business Studies, Uppsala University, Uppsala, Sweden
| | - Marc Mendelson
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, University of Cape Town, Cape Town, South Africa
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Takem EN, Coox C, Shang J, Ndongmo C, Dokubo EK. The association between HIV pretreatment drug resistance and virological outcomes in children and adults in sub-Saharan Africa: A systematic review and meta-analysis. PLoS One 2024; 19:e0300456. [PMID: 38626183 PMCID: PMC11020706 DOI: 10.1371/journal.pone.0300456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 02/27/2024] [Indexed: 04/18/2024] Open
Abstract
INTRODUCTION Pretreatment drug resistance (PDR) could occur in antiretroviral treatment (ART) naïve individuals, those previously exposed to ART, or individuals re-initiating ARV after a long period of interruption. Few studies have shown its association with virological outcomes, although inconsistent. The objective of this review was to provide a synthesis of the association between PDR and virological outcomes (virological failure or suppression). METHODS This report is presented following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The method was subdivided into three main phases: record identification, screening, and report inclusion. Record identification consisted of an initial search with search term "HIV pretreatment drug resistance". Another search was done using terms "Pretreatment drug resistance OR pre-treatment drug resistance OR Pretreatment drug resist* OR pre-treatment drug resist* OR pretreatment antiretroviral resistance OR pretreatment medic* OR pretreatment medic* resist*" and a list of all the countries in sub-Saharan Africa. After the electronic search, studies were screened from full list based on their title and abstract and then full articles retrieved and studies were assessed based on set criteria. Inclusion criteria involved observational studies that report the association between PDR and virological failure. Data from trials that reported the association were also included. Published articles like modelling studies and reviews, and studies with data that had been previously included in the review were excluded. The Mantel Haenszel method with odds ratios was used for synthesis (meta-analyses) with the weights of each study which depends on the number of events and totals. RESULTS A total of 733 records(studies) were obtained from all database search of which 74 reported on PDR, virological outcomes in sub-Saharan Africa (SSA). Out of the 74 articles, 11 were excluded and 26 did not explicitly report data needed, and 5 did not meet the inclusion criteria. Of the remaining 32 studies, 19 studies that had complete data on the number of participants with PDR and no PDR according to virological failure (VF) were included in the metanalyses. The pooled results from eleven (13) of these studies showed those with PDR had higher odds of virological failure compared to those without PDR OR 3.64[95% CI 2.93, 4.52]. The result was similar when stratified in adults and in children. In six (6) studies that had Virological suppression (VS) as outcome, there was a reduction in the odds of VS in those with PDR compared to those without PDR, OR 0.42 (95% CI 0.30, 0.58). CONCLUSION In conclusion, this systematic review indicates that PDR increases the risk of virological failure in sub-Saharan Africa. The risk could be reduced by PDR monitoring for NNRTIs and INSTIs.
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Affiliation(s)
| | | | - Judith Shang
- Centers for Disease Control and Prevention (CDC), Cameroon
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Ouyang F, Yuan D, Zhai W, Liu S, Zhou Y, Yang H. HIV-1 Drug Resistance Detected by Next-Generation Sequencing among ART-Naïve Individuals: A Systematic Review and Meta-Analysis. Viruses 2024; 16:239. [PMID: 38400015 PMCID: PMC10893194 DOI: 10.3390/v16020239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/31/2023] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND There are an increasing number of articles focused on the prevalence and clinical impact of pretreatment HIV drug resistance (PDR) detected by Sanger sequencing (SGS). PDR may contribute to the increased likelihood of virologic failure and the emergence of new resistance mutations. As SGS is gradually replaced by next-generation sequencing (NGS), it is necessary to assess the levels of PDR using NGS in ART-naïve patients systematically. NGS can detect the viral variants (low-abundance drug-resistant HIV-1 variants (LA-DRVs)) of virus quasi-species at levels below 20% that SGS may fail to detect. NGS has the potential to optimize current HIV drug resistance surveillance methods and inform future research directions. As the NGS technique has high sensitivity, it is highly likely that the level of pretreatment resistance would be underestimated using conventional techniques. METHODS For the systematic review and meta-analysis, we searched for original studies published in PubMed, Web of Science, Scopus, and Embase before 30 March 2023 that focused exclusively on the application of NGS in the detection of HIV drug resistance. Pooled prevalence estimates were calculated using a random effects model using the 'meta' package in R (version 4.2.3). We described drug resistance detected at five thresholds (>1%, 2%, 5%, 10%, and 20% of virus quasi-species). Chi-squared tests were used to analyze differences between the overall prevalence of PDR reported by SGS and NGS. RESULTS A total of 39 eligible studies were selected. The studies included a total of 15,242 ART-naïve individuals living with HIV. The prevalence of PDR was inversely correlated with the mutation detection threshold. The overall prevalence of PDR was 29.74% at the 1% threshold, 22.43% at the 2% threshold, 15.47% at the 5% threshold, 12.95% at the 10% threshold, and 11.08% at the 20% threshold. The prevalence of PDR to INSTIs was 1.22% (95%CI: 0.58-2.57), which is the lowest among the values for all antiretroviral drugs. The prevalence of LA-DRVs was 9.45%. At the 2% and 20% detection threshold, the prevalence of PDR was 22.43% and 11.08%, respectively. Resistance to PIs and INSTIs increased 5.52-fold and 7.08-fold, respectively, in those with a PDR threshold of 2% compared with those with PDR at 20%. However, resistance to NRTIs and NNRTIs increased 2.50-fold and 2.37-fold, respectively. There was a significant difference between the 2% and 5% threshold for detecting HIV drug resistance. There was no statistically significant difference between the results reported by SGS and NGS when using the 20% threshold for reporting resistance mutations. CONCLUSION In this study, we found that next-generation sequencing facilitates a more sensitive detection of HIV-1 drug resistance than SGS. The high prevalence of PDR emphasizes the importance of baseline resistance and assessing the threshold for optimal clinical detection using NGS.
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Affiliation(s)
- Fei Ouyang
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing 210009, China; (F.O.); (D.Y.); (W.Z.); (S.L.)
| | - Defu Yuan
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing 210009, China; (F.O.); (D.Y.); (W.Z.); (S.L.)
| | - Wenjing Zhai
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing 210009, China; (F.O.); (D.Y.); (W.Z.); (S.L.)
| | - Shanshan Liu
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing 210009, China; (F.O.); (D.Y.); (W.Z.); (S.L.)
| | - Ying Zhou
- Department of HIV/STD Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - Haitao Yang
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing 210009, China; (F.O.); (D.Y.); (W.Z.); (S.L.)
- Jiangsu Health Development Research Center, Nanjing 210029, China
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Mirzaei H, Eybpoosh S, Mehrabi F, Shojaei MR, Mirzazadeh A, Khezri M, Nasiri N, Sharifi H. Prevalence of acquired and transmitted HIV drug resistance in Iran: a systematic review and meta-analysis. BMC Infect Dis 2024; 24:29. [PMID: 38166733 PMCID: PMC10763184 DOI: 10.1186/s12879-023-08916-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND There is no systematic review on the prevalence of HIV drug resistance (HIVDR) in Iran. We aimed to estimate the prevalence of HIVDR among people living with HIV (PLHIV) in Iran. We assessed HIVDR prevalence in antiretroviral therapy (ART) naïve PLHIV (i.e., those without a history of ART) and PLHIV receiving ART. METHOD We systematically searched Scopus, PubMed, Web of Science, Embase, Iranian databases (Iranian Medical Research Information System, Magiran, and Scientific Information Database), the references of studies, and Google Scholar until March 2023. A random-effects model was used to calculate a point estimate and 95% confidence interval (95% CI) for the prevalence of HIVDR in PLHIV. RESULTS Among 461 potential publications, 22 studies were included in the meta-analysis. The pooled prevalence of acquired HIVDR in PLHIV receiving ART was 34% (95% CI: 19, 50) for nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs), 27% (95% CI: 15, 41) for non-nucleoside reverse transcriptase inhibitors (NNRTIs), and 9% (95% CI: 3, 18) for protease inhibitors (PIs). The pooled prevalence of acquired HIVDR in treatment failure PLHIV was 50% (95% CI: 31, 69) for NRTIs, 49% (95% CI: 29, 69) for NNRTIs, 11% (95% CI: 2, 24) for PIs, and 1% (95% CI: 0, 4) for integrase inhibitors (INIs). The pooled prevalence of transmitted HIVDR in ART-naïve people was 3% (95% CI; 1, 6) for NRTIs, 5% (95% CI: 2, 9) for NNRTIs, and 0 for PIs and INIs. CONCLUSION The prevalence of HIVDR was relatively high in both ART-naïve PLHIV and those receiving ART. Without universal pretreatment HIVDR testing and more frequent routine HIV viral load testing among PLHIV who are on ART, the HIVDR prevalence might increase in PLHIV in Iran.
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Affiliation(s)
- Hossein Mirzaei
- HIV/STI Surveillance Research Center, and WHO Collaborating Center for HIV Surveillance, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, 7616911320, Iran
| | - Sana Eybpoosh
- Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Fatemeh Mehrabi
- HIV/STI Surveillance Research Center, and WHO Collaborating Center for HIV Surveillance, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, 7616911320, Iran
| | - Mohammad Reza Shojaei
- Department of Microbiology and Virology, Kerman University of Medical Science, Kerman, Iran
| | - Ali Mirzazadeh
- HIV/STI Surveillance Research Center, and WHO Collaborating Center for HIV Surveillance, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, 7616911320, Iran
- Department of Epidemiology and Biostatistics, Institute for Global Health Sciences, University of California, San Francisco, USA
| | - Mehrdad Khezri
- HIV/STI Surveillance Research Center, and WHO Collaborating Center for HIV Surveillance, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, 7616911320, Iran
- Department of Epidemiology, New York University School of Global Public Health, New York, NY, USA
| | - Naser Nasiri
- School of Health, Jiroft University of Medical Sciences, Jiroft, Iran
| | - Hamid Sharifi
- HIV/STI Surveillance Research Center, and WHO Collaborating Center for HIV Surveillance, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, 7616911320, Iran.
- Affiliate, Institute for Global Health Sciences, University of California San Francisco, San Francisco, CA, USA.
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Chu C, Armenia D, Walworth C, Santoro MM, Shafer RW. Genotypic Resistance Testing of HIV-1 DNA in Peripheral Blood Mononuclear Cells. Clin Microbiol Rev 2022; 35:e0005222. [PMID: 36102816 PMCID: PMC9769561 DOI: 10.1128/cmr.00052-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
HIV-1 DNA exists in nonintegrated linear and circular episomal forms and as integrated proviruses. In patients with plasma viremia, most peripheral blood mononuclear cell (PBMC) HIV-1 DNA consists of recently produced nonintegrated virus DNA while in patients with prolonged virological suppression (VS) on antiretroviral therapy (ART), most PBMC HIV-1 DNA consists of proviral DNA produced months to years earlier. Drug-resistance mutations (DRMs) in PBMCs are more likely to coexist with ancestral wild-type virus populations than they are in plasma, explaining why next-generation sequencing is particularly useful for the detection of PBMC-associated DRMs. In patients with ongoing high levels of active virus replication, the DRMs detected in PBMCs and in plasma are usually highly concordant. However, in patients with lower levels of virus replication, it may take several months for plasma virus DRMs to reach detectable levels in PBMCs. This time lag explains why, in patients with VS, PBMC genotypic resistance testing (GRT) is less sensitive than historical plasma virus GRT, if previous episodes of virological failure and emergent DRMs were either not prolonged or not associated with high levels of plasma viremia. Despite the increasing use of PBMC GRT in patients with VS, few studies have examined the predictive value of DRMs on the response to a simplified ART regimen. In this review, we summarize what is known about PBMC HIV-1 DNA dynamics, particularly in patients with suppressed plasma viremia, the methods used for PBMC HIV-1 GRT, and the scenarios in which PBMC GRT has been used clinically.
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Affiliation(s)
- Carolyn Chu
- Department of Family and Community Medicine, University of California San Francisco, San Francisco, California, USA
| | - Daniele Armenia
- UniCamillus, Saint Camillus International University of Health Sciences, Rome, Italy
| | - Charles Walworth
- LabCorp-Monogram Biosciences, South San Francisco, California, USA
| | - Maria M. Santoro
- Department of Experimental Medicine, University of Rome “Tor Vergata”, Rome, Italy
| | - Robert W. Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California, USA
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MILNE RS, BECK IA, LEVINE M, SO I, ANDERSEN N, DENG W, PANPRADIST N, KINGOO J, KIPTINNESS C, YATICH N, KIARIE JN, SAKR SR, CHUNG MH, FRENKEL LM. Low-frequency pre-treatment HIV drug resistance: effects on 2-year outcome of first-line efavirenz-based antiretroviral therapy. AIDS 2022; 36:1949-1958. [PMID: 36305180 PMCID: PMC9623471 DOI: 10.1097/qad.0000000000003361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVES Assess the impact of pre-treatment high-frequency and low-frequency drug-resistant HIV variants on long-term outcomes of first-line efavirenz-based antiretroviral therapy (ART). DESIGN Prospective observational study. METHODS Participants' pre-treatment plasma RNA had two sections of HIV pol encoding reverse transcriptase sequenced (Illumina, MiSeq) using unique molecular identifiers to detect wild-type (pre-treatment drug-resistant variants less than 1% of viral quasispecies), low-frequency (1-9%) or high-frequency drug-resistant variants (10-100%). Associations between pre-treatment drug resistance and virologic outcomes over 24 months of efavirenz-based ART were assessed for the number and frequency of mutations by drug class and other resistance parameters. RESULTS Virologic failure was detected in 30 of 352 (9%) and pre-treatment drug-resistant variants were detected in the viral quasispecies of 31 of 352 (9%) participants prescribed efavirenz-based ART. Survival analyses revealed statistically significant associations between pre-treatment drug resistance at low (P < 0.0001) and high (P < 0.001) frequencies, at oligonucleotide ligation assay (OLA) (P < 0.00001) and non-OLA (P < 0.01) codons, to a single-antiretroviral class (P < 0.00001), and a shorter time to virologic failure of efavirenz-based ART. Regression analyses detected independent effects across resistance categories, including both low-frequency (P < 0.01) and high-frequency (P < 0.001) drug-resistant variants. CONCLUSION We observed that pre-treatment HIV drug resistance detected at low frequencies increased the risk of virologic failure over 24 months of efavirenz-based ART, but that most failures, regardless of drug-resistant variants' frequencies, were detected within a year of ART initiation. These observations suggest that when efavirenz-based ART is prescribed, screening for pre-treatment drug resistance by an assay capable of detecting low-frequency variants, including OLA, may guide clinicians to prescribe more effective ART.
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Affiliation(s)
- Ross S. MILNE
- Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Ingrid A. BECK
- Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Molly LEVINE
- Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Isaac SO
- Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Nina ANDERSEN
- Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Wenjie DENG
- University of Washington, Seattle, Washington, USA
| | | | - James KINGOO
- University of Washington, Seattle, Washington, USA
- Coptic Hospital, Nairobi, Kenya
| | | | - Nelly YATICH
- University of Washington, Seattle, Washington, USA
| | | | | | | | - Lisa M. FRENKEL
- Seattle Children’s Research Institute, Seattle, Washington, USA
- University of Washington, Seattle, Washington, USA
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Abstract
PURPOSE OF REVIEW HIV-1 drug resistance (HIV DR) testing is routinely performed by genotyping plasma viruses using Sanger population sequencing. Next-generation sequencing (NGS) is increasingly replacing standardized Sanger sequencing. This opens up new opportunities, but also brings challenges. RECENT FINDINGS The number of NGS applications and protocols for HIV DR testing is increasing. All of them are noninferior to Sanger sequencing when comparing NGS-derived consensus sequences to Sanger sequencing-derived sequences. In addition, NGS enables high-throughput sequencing of near full-length HIV-1 genomes and detection of low-abundance drug-resistant HIV-1 variants, although their clinical implications need further investigation. Several groups have defined remaining challenges in implementing NGS protocols for HIV-1 resistance testing. Some of them are already being addressed. One of the most important needs is quality management and consequently, if possible, standardization. SUMMARY The use of NGS technologies on HIV DR testing will allow unprecedented insights into genomic structures of virus populations that may be of immediate relevance to both clinical and research areas such as personalized antiretroviral treatment. Efforts continue to tackle the remaining challenges in NGS-based HIV DR testing.
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Point-of-Care Tests for HIV Drug Resistance Monitoring: Advances and Potentials. Pathogens 2022; 11:pathogens11070724. [PMID: 35889970 PMCID: PMC9321160 DOI: 10.3390/pathogens11070724] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 01/25/2023] Open
Abstract
HIV/AIDS is a global public health crisis that is yet to be contained. Effective management of HIV drug resistance (HIVDR) supported by close resistance monitoring is essential in achieving the WHO 95-95-95 targets, aiming to end the AIDS epidemic by 2030. Point-of-care tests (POCT) enable decentralized HIVDR testing with a short turnaround time and minimal instrumental requirement, allowing timely initiation of effective antiretroviral therapy (ART) and regimen adjustment as needed. HIVDR POCT is of particular significance in an era when ART access is scaling up at a global level and enhanced HIVDR monitoring is urgently needed, especially for low-to-middle-income countries. This article provides an overview of the currently available technologies that have been applied or potentially used in HIVDR POCT. It may also benefit the continued research and development efforts toward more innovative HIVDR diagnostics.
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Reduced efficacy of HIV-1 integrase inhibitors in patients with drug resistance mutations in reverse transcriptase. Nat Commun 2020; 11:5922. [PMID: 33262331 PMCID: PMC7708638 DOI: 10.1038/s41467-020-19801-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 10/28/2020] [Indexed: 12/05/2022] Open
Abstract
Little is known about the impact of pretreatment drug resistance (PDR) on the efficacy of second generation integrase inhibitors. We sequenced pretreatment plasma specimens from the ADVANCE trial (NCT03122262). Our primary outcome was 96-week virologic success, defined as a sustained viral load <1000 copies/mL from 12 weeks onwards, <200 copies/mL from 24 weeks onwards, and <50 copies/mL after 48 weeks. Here we report how this outcome was impacted by PDR, defined by the World Health Organization (WHO) mutation list. Of 1053 trial participants, 874 (83%) have successful sequencing, including 289 (33%) randomized to EFV-based therapy and 585 (67%) randomized to DTG-based therapy. Fourteen percent (122/874) have ≥1 WHO-defined mutation, of which 98% (120/122) are NNRTI mutations. Rates of virologic suppression are lower in the total cohort among those with PDR 65% (73/112) compared to those without PDR (85% [605/713], P < 0.001), and for those on EFV-based treatment (60% [12/20] vs 86% [214/248], P = 0.002) and for those on DTG-based treatment (61/92 [66%] vs 84% [391/465] P < 0.001, P for interaction by regimen 0.49). Results are similar in multivariable models adjusted for clinical characteristics and adherence. NNRTI resistance prior to treatment is associated with long-term failure of integrase inhibitor-containing first-line regimens, and portends high rates of first-line failure in sub Saharan Africa. Here the authors combine next generation sequencing on plasma from participants of the ADVANCE clinical trial with virological and follow-up data to investigate the impact of pre-treatment drug resistance (PDR) to non-nucleoside reverse transcriptase inhibitors (NNRTIs) on the efficacy of second-generation integrase inhibitors and find an association between NNRTI resistance prior to treatment and long-term treatment.
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10
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Bertagnolio S, Hermans L, Jordan MR, Avila-Rios S, Iwuji C, Derache A, Delaporte E, Wensing A, Aves T, Borhan ASM, Leenus A, Parkin N, Doherty M, Inzaule S, Mbuagbaw L. Clinical Impact of Pretreatment Human Immunodeficiency Virus Drug Resistance in People Initiating Nonnucleoside Reverse Transcriptase Inhibitor-Containing Antiretroviral Therapy: A Systematic Review and Meta-analysis. J Infect Dis 2020; 224:377-388. [PMID: 33202025 PMCID: PMC8328216 DOI: 10.1093/infdis/jiaa683] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 11/16/2020] [Indexed: 01/15/2023] Open
Abstract
Background Increased access to antiretroviral therapy (ART) has resulted in rising levels of pretreatment human immunodeficiency virus drug resistance (PDR). This is the first systematic review and meta-analysis to assess the impact of PDR on treatment outcomes among people initiating nonnucleoside reverse transcriptase inhibitor (NNRTI)–based ART, including the combination of efavirenz (EFV), tenofovir (TDF), and lamivudine or emtricitabine (XTC). Methods We systematically reviewed studies and conference proceedings comparing treatment outcomes in populations initiating NNRTI-based ART with and without PDR. We conducted subgroup analyses by regimen: (1) NNRTIs + 2 nucleoside reverse transcriptase inhibitors (NRTIs), (2) EFV + 2 NRTIs, or (3) EFV/TDF/XTC; by population (children vs adults); and by definition of resistance (PDR vs NNRTI PDR). Results Among 6197 studies screened, 32 were analyzed (31 441 patients). We found that individuals with PDR initiating NNRTIs across all the subgroups had increased risk of virological failure compared to those without PDR. Risk of acquisition of new resistance mutations and ART switch was also higher in people with PDR. Conclusions This review shows poorer treatment outcomes in the presence of PDR, supporting the World Health Organization’s recommendation to avoid using NNRTIs in countries where levels of PDR are high.
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Affiliation(s)
- Silvia Bertagnolio
- Global HIV, Hepatitis and STI Programmes, World Health Organization, Geneva, Switzerland
| | - Lucas Hermans
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.,Wits Reproductive Health and HIV Institute, University of the Witwatersrand, Johannesburg, South Africa
| | - Michael R Jordan
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, Massachusetts, USA.,Division of Geographic Medicine and Infectious Disease, Tufts Medical Center, Boston, Massachusetts, USA.,Tufts Center for Integrated Management of Antimicrobial Resistance, Boston, Massachusetts, USA
| | - Santiago Avila-Rios
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Collins Iwuji
- Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Falmer, United Kingdom
| | - Anne Derache
- Africa Health Research Institute, KwaZulu-Natal, South Africa
| | - Eric Delaporte
- TransVIHMI, University of Montpellier, Institut de Recherche pour le Développement, Institut national de la santé et de la recherche médicale, Montpellier, France
| | - Annemarie Wensing
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.,Wits Reproductive Health and HIV Institute, University of the Witwatersrand, Johannesburg, South Africa
| | - Theresa Aves
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
| | - A S M Borhan
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
| | - Alvin Leenus
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
| | - Neil Parkin
- Data First Consulting, Sebastopol, California, USA
| | - Meg Doherty
- Global HIV, Hepatitis and STI Programmes, World Health Organization, Geneva, Switzerland
| | - Seth Inzaule
- Global HIV, Hepatitis and STI Programmes, World Health Organization, Geneva, Switzerland
| | - Lawrence Mbuagbaw
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
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Gupta-Wright A, Fielding K, van Oosterhout JJ, Alufandika M, Grint DJ, Chimbayo E, Heaney J, Byott M, Nastouli E, Mwandumba HC, Corbett EL, Gupta RK. Virological failure, HIV-1 drug resistance, and early mortality in adults admitted to hospital in Malawi: an observational cohort study. Lancet HIV 2020; 7:e620-e628. [PMID: 32890497 PMCID: PMC7487765 DOI: 10.1016/s2352-3018(20)30172-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 06/03/2020] [Accepted: 06/12/2020] [Indexed: 01/19/2023]
Abstract
BACKGROUND Antiretroviral therapy (ART) scale-up in sub-Saharan Africa combined with weak routine virological monitoring has driven increasing HIV drug resistance. We investigated ART failure, drug resistance, and early mortality among patients with HIV admitted to hospital in Malawi. METHODS This observational cohort study was nested within the rapid urine-based screening for tuberculosis to reduce AIDS-related mortality in hospitalised patients in Africa (STAMP) trial, which recruited unselected (ie, irrespective of clinical presentation) adult (aged ≥18 years) patients with HIV-1 at admission to medical wards. Patients were included in our observational cohort study if they were enrolled at the Malawi site (Zomba Central Hospital) and were taking ART for at least 6 months at admission. Patients who met inclusion criteria had frozen plasma samples tested for HIV-1 viral load. Those with HIV-1 RNA of at least 1000 copies per mL had drug resistance testing by ultra-deep sequencing, with drug resistance defined as intermediate or high-level resistance using the Stanford HIVDR program. Mortality risk was calculated 56 days from enrolment. Patients were censored at death, at 56 days, or at last contact if lost to follow-up. The modelling strategy addressed the causal association between HIV multidrug resistance and mortality, excluding factors on the causal pathway (most notably, CD4 cell count, clinical signs of advanced HIV, and poor functional and nutritional status). FINDINGS Of 1316 patients with HIV enrolled in the STAMP trial at the Malawi site between Oct 26, 2015, and Sept 19, 2017, 786 had taken ART for at least 6 months. 252 (32%) of 786 patients had virological failure (viral load ≥1000 copies per mL). Mean age was 41·5 years (SD 11·4) and 528 (67%) of 786 were women. Of 237 patients with HIV drug resistance results available, 195 (82%) had resistance to lamivudine, 128 (54%) to tenofovir, and 219 (92%) to efavirenz. Resistance to at least two drugs was common (196, 83%), and this was associated with increased mortality (adjusted hazard ratio 1·7, 95% CI 1·2-2·4; p=0·0042). INTERPRETATION Interventions are urgently needed and should target ART clinic, hospital, and post-hospital care, including differentiated care focusing on patients with advanced HIV, rapid viral load testing, and routine access to drug resistance testing. Prompt diagnosis and switching to alternative ART could reduce early mortality among inpatients with HIV. FUNDING Joint Global Health Trials Scheme of the Medical Research Council, UK Department for International Development, and Wellcome Trust.
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Affiliation(s)
- Ankur Gupta-Wright
- Department of Infection and Immunity, University College London, London UK; Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK; Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi.
| | - Katherine Fielding
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK; School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Joep J van Oosterhout
- Department of Medicine, University of Malawi College of Medicine, Blantyre, Malawi; Dignitas International, Zomba, Malawi
| | - Melanie Alufandika
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi; Dignitas International, Zomba, Malawi
| | - Daniel J Grint
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Elizabeth Chimbayo
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Judith Heaney
- Advanced Pathogen Diagnostics Unit, University College London Hospitals NHS Foundation Trust, London, UK
| | - Matthew Byott
- Advanced Pathogen Diagnostics Unit, University College London Hospitals NHS Foundation Trust, London, UK
| | - Eleni Nastouli
- Advanced Pathogen Diagnostics Unit, University College London Hospitals NHS Foundation Trust, London, UK
| | - Henry C Mwandumba
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi; Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Elizabeth L Corbett
- Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK; Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Ravindra K Gupta
- Department of Medicine, University of Cambridge, Cambridge, UK; Africa Health Research Institute, Durban, KwaZulu-Natal, South Africa
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Inzaule SC, Hamers RL, Bertagnolio S. Is increasing pretreatment HIV drug resistance a real menace or minor detail? Lancet HIV 2020; 7:e316-e317. [PMID: 32386718 DOI: 10.1016/s2352-3018(20)30048-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 02/10/2020] [Indexed: 11/25/2022]
Affiliation(s)
- Seth C Inzaule
- Department of HIV/AIDS, World Health Organization, Geneva, Switzerland.
| | - Raph L Hamers
- Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia; Centre for Tropical Medicine and Global Health, Nuffield Dept of Medicine, University of Oxford, Oxford, UK
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13
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Chung MH, McGrath CJ, Beck IA, Boyce C, Frenkel LM. Is increasing pretreatment HIV drug resistance a real menace or minor detail? - Authors' reply. Lancet HIV 2020; 7:e317-e318. [PMID: 32386719 DOI: 10.1016/s2352-3018(20)30049-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 02/10/2020] [Indexed: 11/15/2022]
Affiliation(s)
- Michael H Chung
- Department of Global Health, University of Washington, Seattle, WA, USA
| | | | - Ingrid A Beck
- Center for Global Infectious Diseases Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Ceejay Boyce
- Center for Global Infectious Diseases Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Lisa M Frenkel
- Center for Global Infectious Diseases Research, Seattle Children's Research Institute, Seattle, WA 98109, USA; Department of Laboratory Medicine and Department of Paediatrics, University of Washington, Seattle, WA, USA.
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14
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van de Vijver DAMC, Nichols BE. Pre-treatment HIV drug resistance testing cost-effectiveness. EClinicalMedicine 2020; 22:100381. [PMID: 32478315 PMCID: PMC7251652 DOI: 10.1016/j.eclinm.2020.100381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 04/30/2020] [Indexed: 11/28/2022] Open
Affiliation(s)
| | - Brooke E Nichols
- Department of Global Health, Boston University School of Public Health, Boston, United States
- Health Economics and Epidemiology Research Office, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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15
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Duarte HA, Babigumira JB, Enns EA, Stauffer DC, Shafer RW, Beck IA, Garrison LP, Chung MH, Frenkel LM, Bendavid E. Cost-effectiveness analysis of pre-ART HIV drug resistance testing in Kenyan women. EClinicalMedicine 2020; 22:100355. [PMID: 32490370 PMCID: PMC7256304 DOI: 10.1016/j.eclinm.2020.100355] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 04/13/2020] [Accepted: 04/14/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The prevalence of pre-treatment drug resistance (PDR) to non-nucleoside reverse-transcriptase inhibitor (NNRTI) agents is increasing in sub-Saharan Africa, which may decrease the effectiveness of efavirenz-based antiretroviral therapy (ART) programs. However, due to recent safety concerns, there has been hesitancy to replace efavirenz-based ART with dolutegravir in women of reproductive potential. Our objective was to evaluate whether PDR testing for women not initiating dolutegravir-based ART would be a cost-effective strategy to address the challenges posed by PDR. METHODS We developed an HIV drug resistance model that simulates the emergence and transmission of resistance mutations, calibrated to the Kenyan epidemic. We modeled three care strategies for PDR testing among women not initiating dolutegravir-based ART: no PDR testing, PDR testing with a low-cost point mutation assay, known as oligonucleotide ligation assay (OLA), and PDR testing with consensus sequencing. Using a health sector perspective, this model was used to evaluate the health outcomes, lifetime costs, and cost-effectiveness under each strategy over a 15-year time horizon starting in 2019. FINDINGS OLA and CS PDR testing were projected to have incremental cost-effectiveness ratios (ICER) of $10,741/QALY gained and $134,396/QALY gained, respectively, which are not cost-effective by national income standards. Viral suppression rates among women at 12 months after ART initiation were 87·8%, 89·0%, and 89·3% with no testing, OLA testing, and CS testing, respectively. PDR testing with OLA and CS were associated with a 0.5% and 0.6% reduction in incidence rate compared to no PDR testing. Initial PDR prevalence among women was 13.1% in 2019. By 2034, this prevalence was 17·6%, 17·4%, and 17·3% with no testing, OLA testing, and CS testing, respectively. INTERPRETATION PDR testing for women is unlikely to be cost-effective in Kenya whether one uses a low-cost assay, such as OLA, or consensus sequencing. FUNDING National Institutes of Health, Gilead Sciences.
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Affiliation(s)
- Horacio A Duarte
- Department of Pediatrics, Division of Infectious Diseases, University of Washington, Seattle, WA, United States
- Seattle Children's Research Institute, Seattle, WA, United States
| | - Joseph B Babigumira
- Department of Global Health, University of Washington, Seattle, WA, United States
| | - Eva A Enns
- School of Public Health, Division of Health Policy and Management, University of Minnesota, Minneapolis, MN, United States
| | - David C Stauffer
- Department of Pediatrics, Division of Infectious Diseases, University of Washington, Seattle, WA, United States
| | - Robert W Shafer
- Department of Medicine, Stanford University, Stanford, CA, United States
| | - Ingrid A Beck
- Seattle Children's Research Institute, Seattle, WA, United States
| | - Louis P Garrison
- The Comparative Health Outcomes, Policy, and Economics (CHOICE) Institute, University of Washington, Seattle, WA, United States
| | | | - Lisa M Frenkel
- Department of Pediatrics, Division of Infectious Diseases, University of Washington, Seattle, WA, United States
- Seattle Children's Research Institute, Seattle, WA, United States
- Department of Global Health, University of Washington, Seattle, WA, United States
- Department of Laboratory Medicine, University of Washington, Seattle, WA, United States
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - Eran Bendavid
- Department of Medicine, Stanford University, Stanford, CA, United States
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Beck IA, Levine M, McGrath CJ, Bii S, Milne RS, Kingoo JM, So I, Andersen N, Dross S, Coombs RW, Kiarie J, Chohan B, Sakr SR, Chung MH, Frenkel LM. Pre-treatment HIV-drug resistance associated with virologic outcome of first-line NNRTI-antiretroviral therapy: A cohort study in Kenya. EClinicalMedicine 2020; 18:100239. [PMID: 31956856 PMCID: PMC6962698 DOI: 10.1016/j.eclinm.2019.100239] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 12/05/2019] [Accepted: 12/09/2019] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Pre-treatment HIV-drug-resistance (PDR) to WHO-recommended 1st-line non-nucleoside reverse transcriptase inhibitors (NNRTI)-based antiretroviral treatment (ART) is increasing in low-resource communities. We evaluated the risk of PDR on treatment failure if detected at single or multiple codons, at minority (2-9%) or higher (≥10%) frequencies during efavirenz- vs. nevirapine-ART. METHODS We conducted a pooled analysis across three cohorts of Kenyans initiating 1st-line NNRTI-ART between 2006 and 2014. Mutations K103N, Y181C, G190A, M184V and K65R were detected by an oligonucleotide ligation assay (OLA) and confirmed by Sanger and next-generation sequencing (NGS). PDR was defined as detection of any mutation by OLA when confirmed by NGS. Treatment failure, defined as plasma HIV RNA ≥400 copies/mL at month-12 of ART, was compared by PDR genotypes. FINDINGS PDR was detected in 59/1231 (4·8%) participants. Compared to wild-type genotypes, PDR in participants prescribed nevirapine-ART was associated with increased treatment failure [PDR 69·2% (27/39) vs. wild-type 10·4% (70/674); p = 0·0001], whether detected as minority [66·7% (4/6)] or higher [69·7% (23/33)] frequencies in an individual's HIV quasispecies (p = 0·002 and p < 0·0001, respectively), or mutations at single [50·0% (12/24)] or multiple [100·0% (15/15)] codons (p < 0·0001). During efavirenz-ART, PDR was also associated with increased virologic failure [PDR 25·0% (5/20) vs. wild-type 5·0% (25/498); p = 0·005], but only if detected at multiple drug-resistant codons [50·0% (3/6); p = 0·003] or high frequencies PDR [33·3% (5/15); p = 0·001]. INTERPRETATION The risk that PDR confers for treatment failure varies by number of mutant codons and their frequency in the quasispecies, with a lower risk for efavirenz- compared to nevirapine-based regimens. PDR detection and management could extend the effective use of efavirenz-ART in low-resource settings. FUNDING NIH, PEPFAR.
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Affiliation(s)
- Ingrid A. Beck
- Center for Infectious Diseases Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Molly Levine
- Center for Infectious Diseases Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Christine J. McGrath
- Department of Global Health, University of Washington, Seattle, WA, United States
| | - Steve Bii
- Center for Infectious Diseases Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Ross S. Milne
- Center for Infectious Diseases Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - James M. Kingoo
- Department of Global Health, University of Washington, Seattle, WA, United States
- Coptic Hope Center for Infectious Diseases, Coptic Hospital, Nairobi, Kenya
| | - Isaac So
- Center for Infectious Diseases Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Nina Andersen
- Center for Infectious Diseases Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Sandra Dross
- Center for Infectious Diseases Research, Seattle Children's Research Institute, Seattle, WA, United States
- Department of Global Health, University of Washington, Seattle, WA, United States
| | - Robert W. Coombs
- Department of Medicine, University of Washington, Seattle, WA, United States
- Department of Laboratory Medicine, University of Washington, Seattle, WA, United States
| | - James Kiarie
- Department of Obstetrics and Gynecology, University of Nairobi, Nairobi, Kenya
| | - Bhavna Chohan
- Department of Global Health, University of Washington, Seattle, WA, United States
- Kenya Medical Research Institute, Nairobi, Kenya
| | - Samah R. Sakr
- Coptic Hope Center for Infectious Diseases, Coptic Hospital, Nairobi, Kenya
| | - Michael H. Chung
- Department of Global Health, University of Washington, Seattle, WA, United States
- Department of Medicine, Aga Khan University, Nairobi, Kenya
| | - Lisa M. Frenkel
- Center for Infectious Diseases Research, Seattle Children's Research Institute, Seattle, WA, United States
- Department of Global Health, University of Washington, Seattle, WA, United States
- Department of Medicine, University of Washington, Seattle, WA, United States
- Department of Laboratory Medicine, University of Washington, Seattle, WA, United States
- Department of Pediatrics, University of Washington, Seattle, WA, United States
- Corresponding author at: Seattle Children's Research Institute, 307 Westlake Ave N, Seattle, WA 98109, United States.
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