J. Hackett

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A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples

M. Zaharia, J. Derisi, T. Sittler, 2014, Genome Research.

HCV core antigen as an alternate test to HCV RNA for assessment of virologic responses to all-oral, interferon-free treatment in HCV genotype 1 infected patients.

J. Pawlotsky, J. Rockstroh, C. Sarrazin, 2017, Journal of Virological Methods.

Serologic Prevalence of Ebola Virus in Equatorial Africa

G. Simmons, I. Steffen, Kai Lu, 2019, Emerging infectious diseases.

Search for retrovirus in patients with multiple sclerosis

S. Sato, R. Roos, J. Hackett, 1996, Annals of neurology.

Characterization of antibodies elicited by XMRV infection and development of immunoassays useful for epidemiologic studies

R. Silverman, E. Klein, G. Schochetman, 2010, Retrovirology.

Detection of Individuals With Acute HIV-1 Infection Using the ARCHITECT HIV Ag/Ab Combo Assay

O. Laeyendecker, M. Chesney, L. Khaki, 2009, Journal of acquired immune deficiency syndromes.

Sequencing and Phylogenetic Analysis of Near Full-Length HIV-1 Subtypes A, B, G and Unique Recombinant AC and AD Viral Strains Identified in South Africa

T. de Oliveira, C. Brennan, G. Jacobs, 2015, AIDS research and human retroviruses.

Clinical Utility of HCV Core Antigen Detection and Quantification in the Diagnosis and Management of Patients with Chronic Hepatitis C Receiving an All-Oral, Interferon-Free Regimen

J. Pawlotsky, C. Sarrazin, H. Wedemeyer, 2016, Antiviral therapy.

Chronic Human Pegivirus 2 without Hepatitis C Virus Co-infection

G. Dawson, K. Coller, Jennifer L Evans, 2020, Emerging infectious diseases.

Seroreactivity against Marburg or related filoviruses in West and Central Africa

Nicole A. Hoff, G. Simmons, I. Steffen, 2020, Emerging microbes & infections.

Neutralizing immunity in vaccine breakthrough infections from the SARS-CoV-2 Omicron and Delta variants

R. Andino, J. Doudna, M. Ott, 2022, Cell.

Predominance of antibody-resistant SARS-CoV-2 variants in vaccine breakthrough cases from the San Francisco Bay Area, California

S. Philip, S. Topper, C. Chiu, 2021, Nature Microbiology.

Performance of the automated Abbott RealTime HIV-1 assay on a genetically diverse panel of specimens from London: comparison to VERSANT HIV-1 RNA 3.0, AMPLICOR HIV-1 MONITOR v1.5, and LCx HIV RNA Quantitative assays.

J. Hackett, P. Hay, K. Abravaya, 2006, Journal of virological methods.

In vivo hypermutation of xenotropic murine leukemia virus-related virus DNA in peripheral blood mononuclear cells of rhesus macaque by APOBEC3 proteins.

B. Cullen, R. Silverman, E. Klein, 2011, Virology.

Evaluation of performance across the dynamic range of the Abbott RealTime HIV-1 assay as compared to VERSANT HIV-1 RNA 3.0 and AMPLICOR HIV-1 MONITOR v1.5 using serial dilutions of 39 group M and O viruses.

V. Soriano, J. Hackett, C. de Mendoza, 2007, Journal of virological methods.

Failure to Confirm XMRV/MLVs in the Blood of Patients with Chronic Fatigue Syndrome: A Multi-Laboratory Study

W. Heneine, A. Komaroff, S. Glynn, 2011, Science.

Performance of the automated Abbott RealTime HIV-1 assay on a genetically diverse panel of specimens from Brazil.

R. Badaró, C. Brennan, J. Hackett, 2006, Journal of virological methods.

Role of Serologic and Molecular Diagnostic Assays in Identification and Management of Hepatitis C Virus Infection

G. Dawson, K. Coller, J. Hackett, 2015, Journal of Clinical Microbiology.

Sequence Conservation of the Region Targeted by the Abbott RealTime HCV Viral Load Assay

N. Parkin, J. Hackett, G. Cloherty, 2014, Journal of Clinical Microbiology.

Clinical implications of elevated HIV-1 viral load results obtained from samples stored frozen in vacutainer plasma preparation tubes.

K. Dieckhaus, P. Skolnik, J. Hackett, 2014, Journal of virological methods.

Large-Scale Analysis of the Prevalence and Geographic Distribution of HIV-1 Non-B Variants in the United States

M. T. Pyne, J. Hackett, D. Hillyard, 2013, Journal of Clinical Microbiology.

Toxoplasma gondii That Measure Antibodies to Antibodies as Calibrators in Immunoassays Recombinant Mouse-Human Chimeric

W. Mandecki, M. Klass, J. Hackett, 1998 .

SARS-CoV-2 seroprevalence and neutralizing activity in donor and patient blood

Gregory M. Goldgof, B. Custer, S. Pillai, 2020, Nature Communications.

Neutralizing immunity in vaccine breakthrough infections from the SARS-CoV-2 Omicron and Delta variants

R. Andino, J. Doudna, M. Ott, 2022, Cell.

Analysis of HIV type 1 gp41 sequences in diverse HIV type 1 strains.

M. R. Owens, N. Marlowe, S. Eshleman, 2007, AIDS research and human retroviruses.

Monoclonal antibodies to an HIV-1 group O envelope recombinant.

J. Hackett, R. K. Hickman, J. Scheffel, 1999, Journal of acquired immune deficiency syndromes.

An improved HIV antigen/antibody prototype assay for earlier detection of acute HIV infection.

L. Sokoll, S. Eshleman, J. Hackett, 2021, Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology.

Assays to Estimate HIV Incidence and Detect Acute HIV Infection

J. Kaldor, William Rodriguez, O. Laeyendecker, 2010 .

Minimal sequence variability of the region of HIV-1 integrase targeted by the Abbott RealTime HIV-1 viral load assay in clinical specimens with reduced susceptibility to raltegravir.

N. Parkin, J. Hackett, G. Cloherty, 2013, Journal of virological methods.

Molecular characterization of 39 HIV isolates representing group M (subtypes A-G) and group O: sequence analysis of gag p24, pol integrase, and env gp41.

J. Hackett, P. Swanson, S. Devare, 2003, AIDS research and human retroviruses.

Comparative evaluation of three FDA-approved HIV Ag/Ab combination tests using a genetically diverse HIV panel and diagnostic specimens.

L. Sokoll, G. Dawson, J. Hackett, 2017, Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology.

Near full-length genome characterization of an HIV type 1 CRF25_cpx strain from Cameroon.

C. Brennan, L. Gürtler, K. Luk, 2008, AIDS research and human retroviruses.

Prevalence of XMRV Nucleic Acid and Antibody in HIV-1-Infected Men and in Men at Risk for HIV-1 Infection

Steven Wolinsky, J. Mellors, J. Coffin, 2011, Advances in virology.

Estimation of HIV Incidence in a Large, Community-Based, Randomized Clinical Trial: NIMH Project Accept (HIV Prevention Trials Network 043)

O. Laeyendecker, D. Celentano, L. Richter, 2013, PloS one.

Utility of Metagenomic Next-Generation Sequencing for Characterization of HIV and Human Pegivirus Diversity

C. Chiu, C. Brennan, S. Naccache, 2015, PloS one.

Community Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 Disproportionately Affects the Latinx Population During Shelter-in-Place in San Francisco

E. Crawford, D. Havlir, J. Batson, 2020, Clinical Infectious Diseases.

SARS-CoV-2 Community Transmission disproportionately affects Latinx population during Shelter-in-Place in San Francisco

E. Crawford, J. Derisi, M. Petersen, 2020, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

SARS-CoV-2 antibody magnitude and detectability are driven by disease severity, timing, and assay

M. Peluso, Jeffrey N. Martin, T. Wrin, 2021, Science Advances.

SARS-CoV-2 antibody magnitude and detectability are driven by disease severity, timing, and assay

12, M. Peluso, Jeffrey N. Martin, 2021, medRxiv.

Universal Polymerase Chain Reaction and Antibody Testing Demonstrate Little to No Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 in a Rural Community

M. Peluso, D. Havlir, T. Henrich, 2020, Open forum infectious diseases.

Universal PCR and antibody testing demonstrate little to no transmission of SARS-CoV-2 in a rural community

M. Peluso, D. Havlir, T. Henrich, 2020, medRxiv.

SARS-CoV-2 seroprevalence and neutralizing activity in donor and patient blood from the San Francisco Bay Area

Gregory M. Goldgof, B. Custer, S. Pillai, 2020, medRxiv.

The Perils of Pathogen Discovery: Origin of a Novel Parvovirus-Like Hybrid Genome Traced to Nucleic Acid Extraction Spin Columns

John Hackett, Charles Y. Chiu, Alexander L. Greninger, 2013, Journal of Virology.

Analysis of pol integrase sequences in diverse HIV type 1 strains using a prototype genotyping assay.

N. Marlowe, S. Eshleman, J. Hackett, 2009, AIDS research and human retroviruses.

A RealTime HIV-1 viral load assay for automated quantitation of HIV-1 RNA in genetically diverse group M subtypes A-H, group O and group N samples.

J. Hackett, G. Cloherty, K. Abravaya, 2007, Journal of virological methods.

Thermodynamically modulated partially double-stranded linear DNA probe design for homogeneous real-time PCR

Gavin Cloherty, Klara Abravaya, Shihai Huang, 2007, Nucleic acids research.

Absence of XMRV and Closely Related Viruses in Primary Prostate Cancer Tissues Used to Derive the XMRV-Infected Cell Line 22Rv1

E. Kandel, R. Silverman, E. Klein, 2012, PloS one.

Infection, Viral Dissemination, and Antibody Responses of Rhesus Macaques Exposed to the Human Gammaretrovirus XMRV

R. Silverman, E. Klein, B. Dong, 2011, Journal of Virology.

Failure to Detect XMRV-Specific Antibodies in the Plasma of CFS Patients Using Highly Sensitive Chemiluminescence Immunoassays

B. Huber, J. Hackett, X. Qiu, 2011, Advances in virology.

Use of a multifaceted approach to analyze HIV incidence in a cohort study of women in the United States: HIV Prevention Trials Network 064 Study.

R. Brookmeyer, O. Laeyendecker, J. Justman, 2013, The Journal of infectious diseases.

HIV Surveillance in a Large, Community-Based Study: Results from the Pilot Study of Project Accept (HIV Prevention Trials Network 043)

O. Laeyendecker, T. Coates, L. Richter, 2011, BMC infectious diseases.

ARCHITECT® HIV Ag/Ab Combo assay: correlation of HIV-1 p24 antigen sensitivity and RNA viral load using genetically diverse virus isolates.

C. Brennan, J. Hackett, P. Swanson, 2013, Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology.

Performance of the Celera Diagnostics ViroSeq HIV-1 Genotyping System for Sequence-Based Analysis of Diverse Human Immunodeficiency Virus Type 1 Strains

C. Brennan, N. Marlowe, S. Eshleman, 2004, Journal of Clinical Microbiology.

A Metagenomic Analysis of Pandemic Influenza A (2009 H1N1) Infection in Patients from North America

Steve Miller, John Hackett, Charles Y. Chiu, 2010, PloS one.

Comparative Performance of Three Viral Load Assays on Human Immunodeficiency Virus Type 1 (HIV-1) Isolates Representing Group M (Subtypes A to G) and Group O: LCx HIV RNA Quantitative, AMPLICOR HIV-1 MONITOR Version 1.5, and Quantiplex HIV-1 RNA Version 3.0

V. Soriano, J. Hackett, P. Swanson, 2001, Journal of Clinical Microbiology.

Quantification of HIV-1 group M (subtypes A-G) and group O by the LCx HIV RNA quantitative assay.

G. Schochetman, J. Hackett, P. Swanson, 2000, Journal of virological methods.

HIV-1 strains identified in Brazilian blood donors: significant prevalence of B/F1 recombinants.

R. Badaró, C. Brennan, J. Hackett, 2007, AIDS research and human retroviruses.

The Prevalence of Diverse HIV-1 Strains Was Stable in Cameroonian Blood Donors From 1996 to 2004

C. Brennan, L. Gürtler, G. Schochetman, 2008, Journal of acquired immune deficiency syndromes.

Discovery of a Novel Human Pegivirus in Blood Associated with Hepatitis C Virus Co-Infection

G. Dawson, C. Chiu, K. Coller, 2015, PLoS pathogens.

Development of a high-throughput multiplexed real time RT-PCR assay for detection of human pegivirus 1 and 2.

G. Dawson, K. Coller, J. Hackett, 2017, Journal of virological methods.

Assessment of the Ability of a Fourth-Generation Immunoassay for Human Immunodeficiency Virus (HIV) Antibody and p24 Antigen To Detect both Acute and Recent HIV Infections in a High-Risk Setting

M. Pandori, S. Liska, J. Klausner, 2009, Journal of Clinical Microbiology.

Antibodies to the Novel Human Pegivirus 2 Are Associated with Active and Resolved Infections

G. Dawson, C. Chiu, K. Coller, 2016, Journal of Clinical Microbiology.

SARS-CoV-2 Community Transmission During Shelter-in-Place in San Francisco

E. Crawford, J. Derisi, M. Petersen, 2020, medRxiv.

Concerns over the origin of NIH-CQV, a novel virus discovered in Chinese patients with seronegative hepatitis

E. Delwart, C. Chiu, S. Naccache, 2014, Proceedings of the National Academy of Sciences.

Rapid Assay for Simultaneous Detection and Differentiation of Immunoglobulin G Antibodies to Human Immunodeficiency Virus Type 1 (HIV-1) Group M, HIV-1 Group O, and HIV-2

C. Brennan, J. Hackett, S. Devare, 1998, Journal of Clinical Microbiology.

HIV-1 molecular epidemiology and drug resistance-associated mutations among treatment-naïve blood donors in China

M. Rodgers, J. Hackett, G. Cloherty, 2020, Scientific Reports.

In-Depth Investigation of Archival and Prospectively Collected Samples Reveals No Evidence for XMRV Infection in Prostate Cancer

J. Derisi, R. Silverman, E. Klein, 2012, PloS one.

Genetic analysis of HIV type 1 group O p24gag sequences from Cameroon and Equatorial Guinea.

C. Brennan, L. Gürtler, J. Hackett, 1997, AIDS research and human retroviruses.

Performance of Rapid Point-of-Care and Laboratory Tests for Acute and Established HIV Infection in San Francisco

F. Hecht, M. Pandori, S. Liska, 2013, PloS one.

Failure to Identify HIV-Infected Individuals in a Clinical Trial Using a Single HIV Rapid Test for Screening

Richard D Moore, O. Laeyendecker, J. Blankson, 2014, HIV clinical trials.

Full-length sequence analysis of HIV-1 isolate CM237: a CRF01_AE/B intersubtype recombinant from Thailand.

J. Hackett, P. Swanson, S. Devare, 2003, AIDS research and human retroviruses.

Analysis of insertions and deletions in the gag p6 region of diverse HIV type 1 strains.

N. Marlowe, J. Jackson, S. Eshleman, 2004, AIDS research and human retroviruses.

Naturally occurring sequence polymorphisms within HIV type 1 group O protease.

L. Gürtler, V. Soriano, G. Schochetman, 2001, AIDS research and human retroviruses.

Sequence of gp41env immunodominant region of HIV type 1 group O from west central Africa.

C. Brennan, L. Gürtler, J. Hackett, 1997, AIDS research and human retroviruses.

Performance of the Abbott RealTime HIV-1 Viral Load Assay Is Not Impacted by Integrase Inhibitor Resistance-Associated Mutations

N. Parkin, J. Hackett, G. Cloherty, 2011, Journal of Clinical Microbiology.

Impact of Human Immunodeficiency Virus Type 1 (HIV-1) Genetic Diversity on Performance of Four Commercial Viral Load Assays: LCx HIV RNA Quantitative, AMPLICOR HIV-1 MONITOR v1.5, VERSANT HIV-1 RNA 3.0, and NucliSens HIV-1 QT

V. Soriano, J. Hackett, C. de Mendoza, 2005, Journal of Clinical Microbiology.

Partially double-stranded linear DNA probes: novel design for sensitive detection of genetically polymorphic targets.

K. Luk, J. Hackett, S. Devare, 2007, Journal of virological methods.

Development of sensitive single-round pol or env RT-PCR assays to screen for XMRV in multiple sample types.

M. Busch, G. Leckie, G. Simmons, 2012, Journal of virological methods.

Prevalence of xenotropic murine leukemia virus-related virus infection in different risk populations in Spain.

V. Soriano, J. Hackett, C. de Mendoza, 2012, AIDS research and human retroviruses.

Meeting the challenge of HIV diversity: strategies to mitigate the impact of HIV-1 genetic heterogeneity on performance of nucleic acid testing assays.

J. Hackett, 2012, Clinical laboratory.

Detection and differentiation of HIV-1 group O sera from HIV-1 group M and HIV-2 using recombinant antigens and peptides.

C. Brennan, J. Hackett, S. Devare, 1998, Journal of virological methods.

Analysis of PTAP duplications in the gag p6 region of subtype C HIV type 1.

N. Parkin, N. Marlowe, S. Eshleman, 2005, AIDS research and human retroviruses.

Sexual Transmission of XMRV: A Potential Infection Route

R. Silverman, E. Klein, Prachi Sharma, 2011, Advances in virology.

No Evidence of Murine-Like Gammaretroviruses in CFS Patients Previously Identified as XMRV-Infected

Andreas M. Kogelnik, Yanchen Zhou, John Hackett, 2011, Science.

HIV global surveillance: Foundation for retroviral discovery and assay development

C. Brennan, G. Schochetman, K. Luk, 2006, Journal of medical virology.

HIV Genotypes and Primary Drug Resistance Among HIV-Seropositive Blood Donors in Brazil: Role of Infected Blood Donors as Sentinel Populations for Molecular Surveillance of HIV

C. L. Oliveira, M. Busch, S. Keating, 2013, Journal of acquired immune deficiency syndromes.

Characterization of genetically diverse HIV type 1 from a London cohort: near full-length genomic analysis of a subtype H strain.

J. Hackett, C. Aitken, S. Devare, 2009, AIDS research and human retroviruses.

Near full-length genome characterization of three additional HIV type 1 CRF13_cpx strains from Cameroon.

C. Brennan, L. Gürtler, K. Luk, 2007, AIDS research and human retroviruses.

Genomic characterization of a novel HIV type 1 B/G intersubtype recombinant strain from an injecting drug user in Germany.

H. Schätzl, J. Hackett, S. Devare, 2005, AIDS research and human retroviruses.

Near-full-length genomic sequence of a human immunodeficiency type 1 subtype G strain from Cameroon.

L. Gürtler, J. Hackett, L. Zekeng, 2005, AIDS research and human retroviruses.

Genetic Characterization of a Panel of Diverse HIV-1 Isolates at Seven International Sites

F. Gao, I. Hewlett, Yue Chen, 2016, PloS one.

A SARS-CoV-2 Negative Antigen Rapid Diagnostic in RT-qPCR Positive Samples Correlates With a Low Likelihood of Infectious Viruses in the Nasopharynx

A. Tanuri, M. Rodgers, R. Galliez, 2022, Frontiers in Microbiology.

Performance of the Abbott RealTime HIV-1 Viral Load Assay Is Not Impacted by Integrase Inhibitor Resistance-Associated Mutations

N. Parkin, J. Hackett, G. Cloherty, 2011, Journal of Clinical Microbiology.

A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples

M. Zaharia, J. Derisi, T. Sittler, 2014, Genome research.

Analysis of pol integrase sequences in diverse HIV type 1 strains using a prototype genotyping assay.

N. Marlowe, S. Eshleman, J. Hackett, 2009, AIDS Research and Human Retroviruses.

In vitro selection of a high affinity antibody to oestradiol using a phage display human antibody library.

A Roberts, A Pope, K Pritchard, 1996, Immunotechnology : an international journal of immunological engineering.

Detection of Individuals With Acute HIV-1 Infection Using the ARCHITECT HIV Ag/Ab Combo Assay

O. Laeyendecker, M. Chesney, L. Khaki, 2009, Journal of acquired immune deficiency syndromes.

Large-Scale Analysis of the Prevalence and Geographic Distribution of HIV-1 Non-B Variants in the United States

J. Hackett, D. Hillyard, V. Holzmayer, 2013, Journal of Clinical Microbiology.

Prevalence of XMRV in blood donors, HTLV and HIV cohorts

G. Leckie, G. Schochetman, J. Hackett, 2011, Retrovirology.