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

Social evolution of innate immunity evasion in a virus

(2019) Pilar Domingo-Calap et al.   Nature Microbiology

Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis

(2019) Oliver Ratmann et al.   Nature Communications

Viral diversity from next-generation sequencing of HIV-1 samples provides precise estimates of infection recency and time since infection

(2019) Louisa A Carlisle et al.   JOURNAL OF INFECTIOUS DISEASES

Next-Generation Sequencing of Infectious Pathogens

(2019) Marta Gwinn et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Validation of publicly-available software used in analyzing NGS data for HIV-1 drug resistance mutations and transmission networks in a Washington, DC, Cohort

(2019) Kamwing Jair et al.   PLoS One

PANGEA-HIV 2

(2019) Lucie Abeler-Dörner et al.   Current Opinion in HIV and AIDS

Outbreak analytics: a developing data science for informing the response to emerging pathogens

(2019) Jonathan A. Polonsky et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

SiNPle: Fast and Sensitive Variant Calling for Deep Sequencing Data

(2019) Luca Ferretti et al.   Genes

HIV drug resistance testing – The quest for Point-of-Care

(2019) Marc Noguera-Julian   EBioMedicine

De novo haplotype reconstruction in viral quasispecies using paired-end read guided path finding

(2018) Jiao Chen et al.   BIOINFORMATICS

Nextstrain: real-time tracking of pathogen evolution

(2018) James Hadfield et al.   BIOINFORMATICS

Large Outbreak of Hepatitis C Virus Associated With Drug Diversion by a Healthcare Technician

(2018) Sharon Alroy-Preis et al.   CLINICAL INFECTIOUS DISEASES

Comparison of an In Vitro Diagnostic Next-Generation Sequencing Assay with Sanger Sequencing for HIV-1 Genotypic Resistance Testing

(2018) Philip L. Tzou et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Next-generation sequencing provides an added value in determining drug resistance and viral tropism in Cameroonian HIV-1 vertically infected children

(2018) Joseph Fokam et al.   MEDICINE

HIV-TRACE (TRAnsmission Cluster Engine): a Tool for Large Scale Molecular Epidemiology of HIV-1 and Other Rapidly Evolving Pathogens

(2018) Sergei L Kosakovsky Pond et al.   MOLECULAR BIOLOGY AND EVOLUTION

geno2pheno[ngs-freq]: a genotypic interpretation system for identifying viral drug resistance using next-generation sequencing data

(2018) Matthias Döring et al.   NUCLEIC ACIDS RESEARCH

Identifying Clusters of Recent and Rapid HIV Transmission Through Analysis of Molecular Surveillance Data

(2018) Alexandra M. Oster et al.   JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES

Sanger and Next Generation Sequencing Approaches to Evaluate HIV-1 Virus in Blood Compartments

(2018) Andrea Arias et al.   International Journal of Environmental Research and Public Health

Analysis of drug resistance in HIV protease

(2018) Shrikant D. Pawar et al.   BMC BIOINFORMATICS

Fast estimation of genetic relatedness between members of heterogeneous populations of closely related genomic variants

(2018) Viachaslau Tsyvina et al.   BMC BIOINFORMATICS

Impact of Next-generation Sequencing Defined Human Immunodeficiency Virus Pretreatment Drug Resistance on Virological Outcomes in the ANRS 12249 Treatment-as-Prevention Trial

(2018) Anne Derache et al.   CLINICAL INFECTIOUS DISEASES

Predicted antiviral activity of tenofovir versus abacavir in combination with a cytosine analogue and the integrase inhibitor dolutegravir in HIV-1-infected South African patients initiating or failing first-line ART

(2018) Anne Derache et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

A large HCV transmission network enabled a fast-growing HIV outbreak in rural Indiana, 2015

(2018) Sumathi Ramachandran et al.   EBioMedicine

De novo assembly of viral quasispecies using overlap graphs

(2017) Jasmijn A. Baaijens et al.   GENOME RESEARCH

RNA and DNA Sanger sequencing versus next-generation sequencing for HIV-1 drug resistance testing in treatment-naive patients

(2017) E K Alidjinou et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Corrigendum to “Next generation sequencing for whole genome analysis and surveillance of influenza A viruses” [J. Clin. Virol. 79 (2016) 44–50]

(2017) Jana McGinnis et al.   JOURNAL OF CLINICAL VIROLOGY

Long Single-Molecule Reads Can Resolve the Complexity of the Influenza Virus Composed of Rare, Closely Related Mutant Variants

(2017) Alexander Artyomenko et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Global epidemiology of HCV subtypes and resistance-associated substitutions evaluated by sequencing-based subtype analyses

(2017) Tania M. Welzel et al.   JOURNAL OF HEPATOLOGY

Detailed Transmission Network Analysis of a Large Opiate-Driven Outbreak of HIV Infection in the United States

(2017) Ellsworth M Campbell et al.   JOURNAL OF INFECTIOUS DISEASES

MinVar: A rapid and versatile tool for HIV-1 drug resistance genotyping by deep sequencing

(2017) Michael Huber et al.   JOURNAL OF VIROLOGICAL METHODS

PHYLOSCANNER: Inferring Transmission from Within- and Between-Host Pathogen Genetic Diversity

(2017) Chris Wymant et al.   MOLECULAR BIOLOGY AND EVOLUTION

Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples

(2017) Joshua Quick et al.   Nature Protocols

HIV Drug Resistance — An Emerging Threat to Epidemic Control

(2017) Chris Beyrer et al.   NEW ENGLAND JOURNAL OF MEDICINE

From clinical sample to complete genome: Comparing methods for the extraction of HIV-1 RNA for high-throughput deep sequencing

(2017) Marion Cornelissen et al.   VIRUS RESEARCH

Recent advances in inferring viral diversity from high-throughput sequencing data

(2017) Susana Posada-Cespedes et al.   VIRUS RESEARCH

Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks

(2017) Don Klinkenberg et al.   PLoS Computational Biology

Second-line antiretroviral therapy: so much to be done

(2017) Yibeltal Assefa et al.   Lancet HIV

A random forest classifier for detecting rare variants in NGS data from viral populations

(2017) Raunaq Malhotra et al.   Computational and Structural Biotechnology Journal

Current Approaches in Computational Drug Resistance Prediction in HIV

(2016) Mona Riemenschneider et al.   CURRENT HIV RESEARCH

Comparison of Next-Generation Sequencing Technologies for Comprehensive Assessment of Full-Length Hepatitis C Viral Genomes

(2016) Emma Thomson et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Deep Sequencing of Influenza A Virus from a Human Challenge Study Reveals a Selective Bottleneck and Only Limited Intrahost Genetic Diversification

(2016) Ashley Sobel Leonard et al.   JOURNAL OF VIROLOGY

Real-time, portable genome sequencing for Ebola surveillance

(2016) Joshua Quick et al.   NATURE

HIV Infection Linked to Injection Use of Oxymorphone in Indiana, 2014–2015

(2016) Philip J. Peters et al.   NEW ENGLAND JOURNAL OF MEDICINE

Phylogenetically resolving epidemiologic linkage

(2016) Ethan O. Romero-Severson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ultrasensitive single-genome sequencing: accurate, targeted, next generation sequencing of HIV-1 RNA

(2016) Valerie F. Boltz et al.   Retrovirology

Current Approaches for Diagnosis of Influenza Virus Infections in Humans

(2016) Sai Vemula et al.   Viruses-Basel

SCOTTI: Efficient Reconstruction of Transmission within Outbreaks with the Structured Coalescent

(2016) Nicola De Maio et al.   PLoS Computational Biology

Next-generation sequencing and HIV drug resistance surveillance

(2016) Raph L Hamers et al.   Lancet HIV

Deep sequencing analysis of viral infection and evolution allows rapid and detailed characterization of viral mutant spectrum

(2015) Ofer Isakov et al.   BIOINFORMATICS

IVA: accuratede novoassembly of RNA virus genomes

(2015) Martin Hunt et al.   BIOINFORMATICS

ViVaMBC: estimating viral sequence variation in complex populations from illumina deep-sequencing data using model-based clustering

(2015) Bie Verbist et al.   BMC BIOINFORMATICS

Differentiation of acute from chronic hepatitis C virus infection by nonstructural 5B deep sequencing: A population-level tool for incidence estimation

(2015) Vincent Montoya et al.   HEPATOLOGY

Hepatitis C virus drug resistance-associated substitutions: State of the art summary

(2015) Erik Lontok et al.   HEPATOLOGY

Evaluation of Unbiased Next-Generation Sequencing of RNA (RNA-seq) as a Diagnostic Method in Influenza Virus-Positive Respiratory Samples

(2015) Nicole Fischer et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Next generation sequencing improves detection of drug resistance mutations in infants after PMTCT failure

(2015) Randall G. Fisher et al.   JOURNAL OF CLINICAL VIROLOGY

Accurate Genetic Detection of Hepatitis C Virus Transmissions in Outbreak Settings

(2015) David S. Campo et al.   JOURNAL OF INFECTIOUS DISEASES

CoVaMa: Co-Variation Mapper for disequilibrium analysis of mutant loci in viral populations using next-generation sequence data

(2015) Andrew Routh et al.   METHODS

Virologic Tools for HCV Drug Resistance Testing

(2015) Slim Fourati et al.   Viruses-Basel

Deep Sequencing of Protease Inhibitor Resistant HIV Patient Isolates Reveals Patterns of Correlated Mutations in Gag and Protease

(2015) William F. Flynn et al.   PLoS Computational Biology

Deep Sequencing of HIV: Clinical and Research Applications

(2014) Shiven B. Chabria et al.   Annual Review of Genomics and Human Genetics

VirVarSeq: a low-frequency virus variant detection pipeline for Illumina sequencing using adaptive base-calling accuracy filtering

(2014) Bie M.P. Verbist et al.   BIOINFORMATICS

ViQuaS: an improved reconstruction pipeline for viral quasispecies spectra generated by next-generation sequencing

(2014) Duleepa Jayasundara et al.   BIOINFORMATICS

Accurate viral population assembly from ultra-deep sequencing data

(2014) S. Mangul et al.   BIOINFORMATICS

Next-generation sequencing reveals large connected networks of intra-host HCV variants

(2014) David S Campo et al.   BMC GENOMICS

A Bayesian approach for inferring the dynamics of partially observed endemic infectious diseases from space-time-genetic data

(2014) N. Mollentze et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Phylodynamic Inference for Structured Epidemiological Models

(2014) David A. Rasmussen et al.   PLoS Computational Biology

Viral Quasispecies Assembly via Maximal Clique Enumeration

(2014) Armin Töpfer et al.   PLoS Computational Biology

Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data

(2014) Thibaut Jombart et al.   PLoS Computational Biology

Detection of Low-Frequency HIV Type 1 Reverse Transcriptase Drug Resistance Mutations by Ultradeep Sequencing in Naive HIV Type 1-Infected individuals

(2013) Pantxika Bellecave et al.   AIDS RESEARCH AND HUMAN RETROVIRUSES

Reconstruction of viral population structure from next-generation sequencing data using multicommodity flows

(2013) Pavel Skums et al.   BMC BIOINFORMATICS

V-Phaser 2: variant inference for viral populations

(2013) Xiao Yang et al.   BMC GENOMICS

Relating Phylogenetic Trees to Transmission Trees of Infectious Disease Outbreaks

(2013) Rolf J. F. Ypma et al.   GENETICS

HIV Haplotype Inference Using a Propagating Dirichlet Process Mixture Model

(2013) Sandhya Prabhakaran et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Molecular epidemiology of viral diseases in the era of next generation sequencing

(2013) Mayra Cruz-Rivera et al.   JOURNAL OF CLINICAL VIROLOGY

Probabilistic Inference of Viral Quasispecies Subject to Recombination

(2013) Armin Töpfer et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Simultaneous and complete genome sequencing of influenza A and B with high coverage by Illumina MiSeq Platform

(2013) Wiriya Rutvisuttinunt et al.   JOURNAL OF VIROLOGICAL METHODS

Dynamic changes in viral population structure and compartmentalization during chronic hepatitis C virus infection in children

(2013) María Inés Gismondi et al.   VIROLOGY

Viral Phylodynamics

(2013) Erik M. Volz et al.   PLoS Computational Biology

Efficient error correction for next-generation sequencing of viral amplicons

(2012) Pavel Skums et al.   BMC BIOINFORMATICS

De novo assembly of highly diverse viral populations

(2012) Xiao Yang et al.   BMC GENOMICS

Next-generation sequencing technology in clinical virology

(2012) M.R. Capobianchi et al.   CLINICAL MICROBIOLOGY AND INFECTION

HIV-GRADE: A Publicly Available, Rules-Based Drug Resistance Interpretation Algorithm Integrating Bioinformatic Knowledge

(2012) Martin Obermeier et al.   INTERVIROLOGY

Automating HIV Drug Resistance Genotyping with RECall, a Freely Accessible Sequence Analysis Tool

(2012) Conan K. Woods et al.   JOURNAL OF CLINICAL MICROBIOLOGY

LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets

(2012) Andreas Wilm et al.   NUCLEIC ACIDS RESEARCH

Human viruses: discovery and emergence

(2012) M. Woolhouse et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Bayesian Inference Framework to Reconstruct Transmission Trees Using Epidemiological and Genetic Data

(2012) Marco J. Morelli et al.   PLoS Computational Biology

Highly Sensitive and Specific Detection of Rare Variants in Mixed Viral Populations from Massively Parallel Sequence Data

(2012) Alexander R. Macalalad et al.   PLoS Computational Biology

Whole Genome Deep Sequencing of HIV-1 Reveals the Impact of Early Minor Variants Upon Immune Recognition During Acute Infection

(2012) Matthew R. Henn et al.   PLoS Pathogens

QuRe: software for viral quasispecies reconstruction from next-generation sequencing data

(2011) Mattia C. F. Prosperi et al.   BIOINFORMATICS

Inferring viral quasispecies spectra from 454 pyrosequencing reads

(2011) Irina Astrovskaya et al.   BMC BIOINFORMATICS

ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data

(2011) Osvaldo Zagordi et al.   BMC BIOINFORMATICS

The relationship between social network factors, HIV, and Hepatitis C among injection drug users in Chennai, India

(2011) Carl Latkin et al.   DRUG AND ALCOHOL DEPENDENCE

Temporal Variations in the Hepatitis C Virus Intrahost Population during Chronic Infection

(2011) S. Ramachandran et al.   JOURNAL OF VIROLOGY

Influenza Drug Resistance

(2011) Andrés Pizzorno et al.   SEMINARS IN RESPIRATORY AND CRITICAL CARE MEDICINE

Reconstructing disease outbreaks from genetic data: a graph approach

(2010) T Jombart et al.   HEREDITY

Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction

(2010) Osvaldo Zagordi et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Transmission of Single HIV-1 Genomes and Dynamics of Early Immune Escape Revealed by Ultra-Deep Sequencing

(2010) Will Fischer et al.   PLoS One

VarScan: variant detection in massively parallel sequencing of individual and pooled samples

(2009) Daniel C. Koboldt et al.   BIOINFORMATICS

Viral Population Estimation Using Pyrosequencing

(2008) Nicholas Eriksson et al.   PLoS Computational Biology

Minority HIV-1 Drug Resistance Mutations Are Present in Antiretroviral Treatment–Naïve Populations and Associate with Reduced Treatment Efficacy

(2008) Jeffrey A Johnson et al.   PLOS MEDICINE