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Next-generation sequencing and HIV drug resistance surveillance

LANCET HIV (2016)

Journal

LANCET HIV

Volume 3, Issue 12, Pages E553-E554

Publisher

ELSEVIER INC

DOI: 10.1016/S2352-3018(16)30151-5

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Towards Next-Generation Sequencing for HIV-1 Drug Resistance Testing in a Clinical Setting

Calesta Hui Yi Teo, Nurul Hannah Binte Norhisham, Ogestelli Fabia Lee, Siyu Png, Chean Nee Chai, Gabriel Yan, Julian Wei-Tze Tang, Chun Kiat Lee

Summary: The HIV genotypic resistance test is crucial for managing HIV/AIDS patients, and high-throughput sequencing is a reliable and sensitive alternative method for detecting low-abundance covert mutations and drug resistance.

VIRUSES-BASEL (2022)

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Article Microbiology

Added Value of Next Generation over Sanger Sequencing in Kenyan Youth with Extensive HIV-1 Drug Resistance

V Novitsky, W. Nyandiko, R. Vreeman, A. K. DeLong, A. Manne, M. Scanlon, A. Ngeresa, J. Aluoch, F. Sang, C. Ashimosi, E. Jepkemboi, M. Orido, J. W. Hogan, R. Kantor

Summary: The study assessed the added value of using next-generation sequencing (NGS) compared to Sanger sequencing in detecting HIV-1 drug resistance mutations in Kenyan children and adolescents. It found that NGS detected more drug resistance mutations at lower thresholds, suggesting potential benefits of using NGS over existing technology.

MICROBIOLOGY SPECTRUM (2022)

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Article Microbiology

HIV Drug Resistance Mutations Detection by Next-Generation Sequencing during Antiretroviral Therapy Interruption in China

Miaomiao Li, Shujia Liang, Chao Zhou, Min Chen, Shu Liang, Chunhua Liu, Zhongbao Zuo, Lei Liu, Yi Feng, Chang Song, Hui Xing, Yuhua Ruan, Yiming Shao, Lingjie Liao

Summary: A study conducted in China found that patients with antiretroviral therapy interruption are at risk of HIV drug resistance. Next-generation sequencing technology can detect more minority drug resistance variants, with a sharp increase in their numbers when the detection threshold is below 5%.

PATHOGENS (2021)

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Article Public, Environmental & Occupational Health

Surveillance of carbapenem-resistant organisms using next-generation sequencing

Katelin V. Gali, Rachael M. M. St Jacques, Cheyanne I. D. Daniels, Allison O'Rourke, Lauren Turner

Summary: The genomic data generated from next-generation sequencing (NGS) provides nucleotide-level resolution of bacterial genomes which is critical for disease surveillance and the implementation of prevention strategies to interrupt the spread of antimicrobial resistance (AMR) bacteria. Through phylogenetic tools that assess the single nucleotide polymorphisms (SNPs) within a pathogen genome dataset, public health scientists can estimate the genetic identity between isolates. This information is used as an epidemiologic proxy of a putative outbreak.

FRONTIERS IN PUBLIC HEALTH (2023)

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Article Infectious Diseases

HIV-1 Genotypic Resistance Testing Using Sanger and Next-Generation Sequencing in Adults with Low-Level Viremia in China

Qun Li, Fengting Yu, Chuan Song, Hongxin Zhao, Qing Xiao, Xiaojie Lao, Siyuan Yang, Yunxia Tang, Fujie Zhang

Summary: In this study, the performance of next-generation sequencing (NGS) in detecting HIV drug-resistance mutations (DRMs) in patients with low-level viremia (LLV) was explored. The results showed the presence of drug-resistance mutations in LLV patients and suggested the need for genotyping resistance testing to guide antiretroviral therapy optimization.

INFECTION AND DRUG RESISTANCE (2022)

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Review Microbiology

Application of Next Generation Sequencing for Diagnosis and Clinical Management of Drug-Resistant Tuberculosis: Updates on Recent Developments in the Field

Navisha Dookie, Azraa Khan, Nesri Padayatchi, Kogieleum Naidoo

Summary: This review discusses the potential of next generation whole genome sequencing (WGS) in accelerating individualized care for tuberculosis (TB), as well as the challenges and mechanisms of drug resistance and its implications on diagnosis and treatment.

FRONTIERS IN MICROBIOLOGY (2022)

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Article Virology

Added Value of Next Generation Sequencing in Characterizing the Evolution of HIV-1 Drug Resistance in Kenyan Youth

Vlad Novitsky, Winstone Nyandiko, Rachel Vreeman, Allison K. DeLong, Mark Howison, Akarsh Manne, Josephine Aluoch, Ashley Chory, Festus Sang, Celestine Ashimosi, Eslyne Jepkemboi, Millicent Orido, Joseph W. Hogan, Rami Kantor

Summary: Drug resistance is still a global challenge for children and adolescents living with HIV. Next generation sequencing can provide information about resistance evolution and potentially improve care for ART-experienced CALWH in resource-limited settings. A study conducted in Kenya found that resistance evolution was detected in 93% of participants, and minority resistance variants also evolved under drug selection pressure. The study suggests that NGS can help us better understand the dynamics of drug resistance evolution and improve care.

VIRUSES-BASEL (2023)

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Article Engineering, Environmental

Detection of multiple human astroviruses in sewage by next generation sequencing

Zexin Tao, Xiaojuan Lin, Yao Liu, Feng Ji, Suting Wang, Ping Xiong, Li Zhang, Qing Xu, Aiqiang Xu, Ning Cui

Summary: This study collected sewage samples from Jinan, China from 2018 to 2019, and analyzed classic and novel HAstVs using real-time quantitative PCR and next generation sequencing. The results showed that sewage contains a high diversity of astroviruses, and there are multiple co-circulating lineages within each local HAstV genotype.

WATER RESEARCH (2022)

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Article Microbiology

FLASH-TB: an Application of Next-Generation CRISPR to Detect Drug Resistant Tuberculosis from Direct Sputum

Trinh Thi Bich Tram, Vu Thi Ngoc Ha, Le Pham Tien Trieu, Philip M. Ashton, Emily D. Crawford, Do Dang Anh Thu, Nguyen Le Quang, Guy E. Thwaites, Timothy M. Walker, Catherine Anscombe, Nguyen Thuy Thuong Thuong

Summary: FLASH technique allows for rapid detection of Mycobacterium tuberculosis (Mtb) drug resistance from clinical samples, enabling optimal and timely treatment for tuberculosis (TB) patients.

JOURNAL OF CLINICAL MICROBIOLOGY (2023)

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Article Microbiology

HIV-1 Drug Resistance Assay Using Ion Torrent Next Generation Sequencing and On-Instrument End-to-End Analysis Software

Michael T. Pyne, Keith E. Simmon, Melanie A. Mallory, Weston C. Hymas, Jeffery Stevenson, Adam P. Barker, David R. Hillyard

Summary: HIV-1 antiretroviral therapy management requires sequencing of different portions of the HIV-1 pol gene. Traditional Sanger sequencing has limited ability to detect minor variants. Next generation sequencing enables detection of variants at frequencies as low as 1%, allowing for earlier detection of resistance. However, implementation of NGS in the clinical laboratory is hindered by complicated design and analysis.

JOURNAL OF CLINICAL MICROBIOLOGY (2022)

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Article Microbiology

Use of next-generation sequencing to detect mutations associated with antiviral drug resistance in cytomegalovirus

Nicholas T. Streck, Mark J. Espy, Matthew J. Ferber, Eric W. Klee, Raymund R. Razonable, Dimitri Gonzalez, Chalom Sayada, Phillip R. Heaton, Sunwen Chou, Matthew J. Binnicker

Summary: A novel next-generation sequencing (NGS) method was developed and validated in this study to accurately detect mutations in CMV genes associated with antiviral resistance. Compared to traditional Sanger sequencing, the NGS method demonstrated higher consistency and can assist in providing personalized antiviral therapy.

JOURNAL OF CLINICAL MICROBIOLOGY (2023)

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Article Immunology

Near Real-Time Identification of Recent Human Immunodeficiency Virus Transmissions, Transmitted Drug Resistance Mutations, and Transmission Networks by Multiplexed Primer ID-Next-Generation Sequencing in North Carolina

Shuntai Zhou, Sabrina Sizemore, Matt Moeser, Scott Zimmerman, Erika Samoff, Victoria Mobley, Simon Frost, Andy Cressman, Michael Clark, Tara Skelly, Hemant Kelkar, Umadevi Veluvolu, Corbin Jones, Joseph Eron, Myron Cohen, Julie A. E. Nelson, Ronald Swanstrom, Ann M. Dennis

Summary: The study introduces a multiplexed Primer ID-next-generation sequencing approach to identify recent HIV-1 infections among newly diagnosed patients, finding a significant portion of recent infections and certain trends, such as higher likelihood of recent infection in younger individuals and drug users. The rapid identification of recent infections and drug resistance mutations through this approach allows for prioritization of care and intervention efforts towards high-risk individuals.

JOURNAL OF INFECTIOUS DISEASES (2021)

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Article Infectious Diseases

Metagenomic next-generation sequencing of rectal swabs for the surveillance of antimicrobial-resistant organisms on the Illumina Miseq and Oxford MinION platforms

Rebecca Yee, Florian P. Breitwieser, Stephanie Hao, Belita N. A. Opene, Rachael E. Workman, Pranita D. Tamma, Jennifer Dien-Bard, Winston Timp, Patricia J. Simner

Summary: Antimicrobial resistance poses a threat to public health, necessitating efficient surveillance methods like metagenomic next-generation sequencing (mNGS). This approach showed promise in detecting multidrug-resistant organisms and provides a rapid and unbiased diagnostic tool for microbiome and resistome investigations.

EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES (2021)

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Article Engineering, Biomedical

Next generation 3D-printed intravaginal ring for prevention of HIV and unintended pregnancy

Isabella C. Young, Priya Srinivasan, Roopali Shrivastava, Rima Janusziewicz, Allison Thorson, Mackenzie L. Cottrell, Rani S. Sellers, Craig Sykes, Amanda Schauer, Dawn Little, Kristen Kelley, Angela D. M. Kashuba, David Katz, Richard B. Pyles, J. Gerardo Garcia-Lerma, Kathleen L. Vincent, James Smith, S. Rahima Benhabbour

Summary: The article introduces a 3D printed multipurpose prevention technology (MPT) intravaginal ring (IVR) which can be used for HIV prevention and contraception. The MPT IVR offers a sustained release of drugs for up to 150 days in vitro and 14 days in sheep. It has been found to be safe and well tolerated in macaques, making it a potential option for young women and girls.

BIOMATERIALS (2023)

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Review Biochemical Research Methods

Epidemiological data analysis of viral quasispecies in the next-generation sequencing era

Sergey Knyazev, Lauren Hughes, Pavel Skums, Alexander Zelikovsky

Summary: Advancements in next-generation sequencing have enabled detailed assessment of viral population complexity within hosts, extracting crucial epidemiological and biomedical information. However, the complex analysis of NGS data is required to handle the rapidly mutating viral populations.

BRIEFINGS IN BIOINFORMATICS (2021)

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Article Immunology

The relative contributions of HIV drug resistance, nonadherence and low-level viremia to viremic episodes on antiretroviral therapy in sub-Saharan Africa

Seth C. Inzaule, Silvia Bertagnolio, Cissy M. Kityo, Margaret Siwale, Sulaimon Akanmu, Maureen Wellington, Marleen de Jager, Prudence Ive, Kishor Mandaliya, Wendy Stevens, Tamara S. Boender, Pascale Ondoa, Kim C. E. Sigaloff, Tobias F. Rinke de Wit, Raph L. Hamers

AIDS (2020)

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Article Immunology

Xpert MTB/RIF Ultra for the Diagnosis of Tuberculous Meningitis: A Small Step Forward

Joseph Donovan, Fiona Cresswell, Nguyen Thuy Thuong Thuong, David R. Boulware, Guy E. Thwaites, Nathan C. Bahr

CLINICAL INFECTIOUS DISEASES (2020)

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Article Virology

Country Level Diversity of the HIV-1 Pandemic between 1990 and 2015

Joris Hemelaar, Shanghavie Loganathan, Ramyiadarsini Elangovan, Jason Yun, Leslie Dickson-Tetteh, Shona Kirtley

Summary: The research revealed that there is extremely wide variation in the complexity of country level HIV diversity worldwide. Central African countries have the most diverse HIV epidemics, while Western Europe and North America have the greatest number of distinct HIV-1 subtypes and recombinants. The highest proportion of HIV-1 infections due to recombinants was found in Southeast Asia, China, and West and Central Africa.

JOURNAL OF VIROLOGY (2021)

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Article Multidisciplinary Sciences

The impact of HIV-1 subtypes on virologic and immunologic treatment outcomes at the Lagos University Teaching Hospital: A longitudinal evaluation

Ann Abiola Ogbenna, Seema Meloni, Seth Inzaule, Raph L. Hamers, Kim Sigaloff, Akin Osibogun, Titilope Adenike Adeyemo, Prosper Okonkwo, Jay Osi Samuels, Phyllis J. Kanki, Tobias F. Rinke de Wit, Alani Sulaimon Akanmu

PLOS ONE (2020)

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Article Immunology

Plasma Inflammatory Biomarkers Predict CD4+ T-cell Recovery and Viral Rebound in HIV-1 Infected Africans on Suppressive Antiretroviral Therapy

Stefanie Kroeze, Theresa M. Rossouw, Helen C. Steel, Ferdinand W. Wit, Cissy M. Kityo, Margaret Siwale, Sulaimon Akanmu, Kishor Mandaliya, Marleen De Jager, Pascale Ondoa, Peter Reiss, Tobias F. Rinke De Wit, Neeltje A. Kootstra, Raph L. Hamers

Summary: Persistent systemic inflammation, as indicated by plasma biomarkers, during suppressive antiretroviral therapy in HIV-1-infected individuals, may impact CD4(+) T-cell recovery and viral rebound during long-term treatment. Changes in biomarker concentrations could affect viral replication and immune recovery in patients. Further research is needed to understand these potential mechanisms in order to improve clinical outcomes.

JOURNAL OF INFECTIOUS DISEASES (2021)

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Article Infectious Diseases

2021 update to HIV-TRePS: a highly flexible and accurate system for the prediction of treatment response from incomplete baseline information in different healthcare settings

Andrew D. Revell, Dechao Wang, Maria-Jesus Perez-Elias, Robin Wood, Dolphina Cogill, Hugo Tempelman, Raph L. Hamers, Peter Reiss, Ard van Sighem, Catherine A. Rehm, Brian Agan, Gerardo Alvarez-Uria, Julio S. G. Montaner, H. Clifford Lane, Brendan A. Larder

Summary: Novel computational models were developed to accurately predict treatment responses in HIV therapy, even in the absence of baseline data. These models showed strong performance in predicting virological response and absolute changes, offering potential benefits in resource-limited settings.

JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY (2021)

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Article Immunology

Improving host-directed therapy for tuberculous meningitis by linking clinical and multi-omics data

Reinout van Crevel

Summary: There is a clear need to improve host-directed therapy for tuberculous meningitis (TBM), as the current therapy options are limited. The ULTIMATE project aims to address unanswered questions about tryptophan metabolism during TBM and identify novel therapeutic targets for TBM patients. Through integrating data from large patient studies and clinical trials, ULTIMATE seeks to determine which TBM patients benefit from corticosteroids and explore the potential of targeting the tryptophan pathway for treatment.

TUBERCULOSIS (2021)

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Review Infectious Diseases

Surveillance strategies using routine microbiology for antimicrobial resistance in low- and middle-income countries

Cherry Lim, Elizabeth A. Ashley, Raph L. Hamers, Paul Turner, Thomas Kesteman, Samuel Akech, Alejandra Corso, Mayfong Mayxay, Iruka N. Okeke, Direk Limmathurotsakul, H. Rogier van Doorn

Summary: This article reviews the strategies for AMR surveillance using routine microbiology results in LMICs, emphasizing the need for support in certain areas. Different surveillance strategies need to be thoroughly understood in terms of their limitations and potential biases to ensure maximum utilization and interpretation of local routine microbiology data.

CLINICAL MICROBIOLOGY AND INFECTION (2021)

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Review Pharmacology & Pharmacy

Safety and Pharmacokinetic Profiles of Long-Acting Injectable Antiretroviral Drugs for HIV-1 Pre-Exposure Prophylaxis: A Systematic Review and Meta-analysis of Randomized Trials

Gilbert Lazarus, Vincent Kharisma Wangsaputra, Christianto, Melva Louisa, Vivian Soetikno, Raph L. Hamers

Summary: This study investigated the safety and pharmacokinetic profiles of long-acting injectable pre-exposure prophylaxis (LAI PrEP) for HIV-1 prevention, specifically focusing on cabotegravir (CAB-LA) and rilpivirine (RPV-LA). Results showed that both CAB-LA and RPV-LA were generally well-tolerated with favorable prospects in viral inhibitory activity. Further research is needed to confirm the findings on RPV-LA due to limited current evidence.

FRONTIERS IN PHARMACOLOGY (2021)

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Article Medicine, General & Internal

Aspirin in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial

Peter W. Horby, Guilherme Pessoa-Amorim, Natalie Staplin, Jonathan R. Emberson, Mark Campbell, Enti Spata, Leon Peto, Nigel J. Brunskill, Simon Tiberi, Victor Chew, Thomas Brown, Hasan Tahir, Beate Ebert, David Chadwick, Tony Whitehouse, Rahuldeb Sarkar, Clive Graham, J. Kenneth Baillie, Buddha Basnyat, Maya H. Buch, Lucy C. Chappell, Jeremy Day, Saul N. Faust, Raph L. Hamers, Thomas Jaki, Edmund Juszczak, Katie Jeffery, Wei Shen Lim, Alan Montgomery, Andrew Mumford, Kathryn Rowan, Guy Thwaites, Marion Mafham, Richard Haynes, Martin J. Landray

Summary: In patients hospitalized with COVID-19, aspirin was not associated with reductions in 28-day mortality or in the risk of progressing to invasive mechanical ventilation or death, but was associated with a small increase in the rate of being discharged alive within 28 days.

LANCET (2022)

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Editorial Material Infectious Diseases

The value of open-source clinical science in pandemic response: lessons from ISARIC

LANCET INFECTIOUS DISEASES (2021)

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Article Medicine, General & Internal

Casirivimab and imdevimab in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial

Peter W. Horby, Marion Mafham, Leon Peto, Mark Campbell, Guilherme Pessoa-Amorim, Enti Spata, Natalie Staplin, Jonathan R. Emberson, Benjamin Prudon, Paul Hine, Thomas Brown, Christopher A. Green, Rahuldeb Sarkar, Purav Desai, Bryan Yates, Tom Bewick, Simon Tiberi, Tim Felton, J. Kenneth Baillie, Maya H. Bitch, Lucy C. Chappell, Saul N. Faust, Thomas Jaki, Katie Jeffery, Edmund Juszczak, Wei Shen Lim, Alan Montgomery, Andrew Mumford, Kathryn Rowan, David M. Weinreich, Richard Haynes, Martin J. Landray

Summary: This study evaluated the efficacy and safety of the combination therapy of casirivimab and imdevimab in patients hospitalized with COVID-19. The results showed that this combination therapy reduced the 28-day mortality rate in patients without detectable antibodies to SARS-CoV-2 infection at baseline, but not in those with detectable antibodies.

LANCET (2022)

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Letter Infectious Diseases

Transaminases and serum albumin as early predictors of severe dengue

Gilbert Lazarus, Erni J. Nelwan, Raph L. Hamers

LANCET INFECTIOUS DISEASES (2021)

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Article Health Care Sciences & Services

Clinical characteristics and mortality associated with COVID-19 in Jakarta, Indonesia: A hospital-based retrospective cohort study

Henry Surendra, Iqbal R. F. Elyazar, Bimandra A. Djaafara, Lenny L. Ekawati, Kartika Saraswati, Verry Adrian, Widyastuti, Dwi Oktavia, Ngabila Salama, Rosa N. Lina, Adhi Andrianto, Karina D. Lestari, Erlina Burhan, Anuraj H. Shankar, Guy Thwaites, J. Kevin Baird, Raph L. Hamers

Summary: This study investigated the in-hospital mortality of COVID-19 patients in Jakarta, Indonesia from March to July 2020. The results showed that the risk of death was associated with factors such as age, gender, comorbidities, clinical diagnosis, and treatment methods. Patients with more comorbidities had a higher risk of mortality across all age groups.

LANCET REGIONAL HEALTH-WESTERN PACIFIC (2021)

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Review Immunology

Global and regional epidemiology of HIV-1 recombinants in 1990-2015: a systematic review and global survey

Joris Hemelaar, Ramyiadarsini Elangovan, Jason Yun, Leslie Dickson-Tetteh, Shona Kirtley, Eleanor Gouws-Williams, Peter D. Ghys

LANCET HIV (2020)

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Next-generation sequencing and HIV drug resistance surveillance

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ELSEVIER INC

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