ArticleJournal of clinical microbiology2016
A Pan-HIV Strategy for Complete Genome Sequencing.
Article in Journal of clinical microbiology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
28 citing papers in PubMed.
- Article
- First Evidence of Spillover ofTransboundary and emerging diseases · 2025Article
- Preexisting inter-serotype immunity drives antigenic evolution of dengue virus serotype 2.Virology · 2024Article
- Article
- Replication in the presence of dengue convalescent serum impacts Zika virus neutralization sensitivity and fitness.Frontiers in cellular and infection microbiology · 2023Article
- Probe Capture Enrichment Methods for HIV and HCV Genome Sequencing and Drug Resistance Genotyping.Pathogens (Basel, Switzerland) · 2022Review
- A high prevalence of potential HIV elite controllers identified over 30 years in Democratic Republic of Congo.EBioMedicine · 2021Article
- Evaluation of Phylogenetic Methods for Inferring the Direction of Human Immunodeficiency Virus (HIV) Transmission: HIV Prevention Trials Network (HPTN) 052.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2021Article
- Article
- Validation of Variant Assembly Using HAPHPIPE with Next-Generation Sequence Data from Viruses.Viruses · 2020Article
- Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance.Nature microbiology · 2020Article
- Brief Report: Complete Genome Sequence of CG-0018a-01 Establishes HIV-1 Subtype L.Journal of acquired immune deficiency syndromes (1999) · 2020Article
- A cross-sectional study to characterize local HIV-1 dynamics in Washington, DC using next-generation sequencing.Scientific reports · 2020Article
- Advanced molecular surveillance approaches for characterization of blood borne hepatitis viruses.PloS one · 2020Article
- HIV Silencing and Inducibility Are Heterogeneous and Are Affected by Factors Intrinsic to the Virus.mBio · 2019Article
- Article
- Low-Bias RNA Sequencing of the HIV-2 Genome from Blood Plasma.Journal of virology · 2019Article
- Lowering the Barriers to Routine Whole-Genome Sequencing of Bacteria in the Clinical Microbiology Laboratory.Journal of clinical microbiology · 2018Article
- ARCHITECT HIV Combo Ag/Ab and RealTime HIV-1 Assays Detect Diverse HIV Strains in Clinical Specimens.AIDS research and human retroviruses · 2018Article
- Universal Target Capture of HIV Sequences From NGS Libraries.Frontiers in microbiology · 2018Article
Corrections and comments
- Commented on by
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Molecular surveillance is essential to monitor HIV diversity and track emerging strains. We have developed a universal library preparation method (HIV-SMART [i.e.,switchingmechanismat 5' end ofRNAtranscript]) for next-generation sequencing that harnesses the specificity of HIV-directed priming to enable full genome characterization of all HIV-1 groups (M, N, O, and P) and HIV-2. Broad application of the HIV-SMART approach was demonstrated using a panel of diverse cell-cultured virus isolates. HIV-1 non-subtype B-infected clinical specimens from Cameroon were then used to optimize the protocol to sequence directly from plasma. When multiplexing 8 or more libraries per MiSeq run, full genome coverage at a median ∼2,000× depth was routinely obtained for either sample type. The method reproducibly generated the same consensus sequence, consistently identified viral sequence heterogeneity present in specimens, and at viral loads of ≤4.5 log copies/ml yielded sufficient coverage to permit strain classification. HIV-SMART provides an unparalleled opportunity to identify diverse HIV strains in patient specimens and to determine phylogenetic classification based on the entire viral genome. Easily adapted to sequence any RNA virus, this technology illustrates the utility of next-generation sequencing (NGS) for viral characterization and surveillance.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.