Brian Thomas Foley

Brian Thomas Foley
Los Alamos National Laboratory | LANL · Theoretical Biology and Biophysics Group

PhD

About

303
Publications
239,666
Reads
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Introduction
I study the molecular epidemiology and evolution of HIV and other lentiviruses. I am interested in evolution and phylogenetic analysis in general. I have studied the evolution of several other viruses, bacteria and the vertebrate hosts of viruses to gain some perspective on how lentivirus evolution is similar and different from the evolution of other organisms.
Additional affiliations
August 1995 - present
Independent Researcher
Independent Researcher
Position
  • HIV Databases
August 1995 - present
Los Alamos National Laboratory
Position
  • Researcher
Education
August 1990 - April 1995
University of Vermont
Field of study
  • Molecular Genetics
August 1979 - May 1982
Montana State University, Bozeman MT
Field of study
  • Microbiology

Publications

Publications (303)
Article
Prospective molecular studies of HIV-1 pol region (2253–5250 in HXB2 genome) sequences from sequenced samples of 269 HIV-1-infected patients in Cyprus (2017–2021) revealed a transmission cluster of 14 unknown HIV-1 recombinants that were not classified as previously established CRFs. The earliest recombinant was collected in September 2017, and the...
Article
Viral pathogens can rapidly evolve, adapt to novel hosts, and evade human immunity. The early detection of emerging viral pathogens through biosurveillance coupled with rapid and accurate diagnostics are required to mitigate global pandemics. However, RNA viruses can mutate rapidly, hampering biosurveillance and diagnostic efforts. Here, we present...
Article
Full-text available
A total of 1155 partial pol gene sequences of human immunodeficiency virus (HIV)-1 CRF07_BC were sampled between 1997 and 2015, spanning 13 provinces in Mainland China and risk groups [heterosexual, injecting drug users (IDU), and men who have sex with men (MSM)] to investigate the evolution, adaptation, spatiotemporal and risk group dynamics, migr...
Article
Full-text available
HIV consensus sequences are used in various bioinformatic, evolutionary, and vaccine related research. Since the previous HIV-1 subtype and CRF consensus sequences were constructed in 2002, the number of publicly available HIV-1 sequences have grown exponentially, especially from non-EU and US countries. Here, we reconstruct 90 new HIV-1 subtype an...
Article
Full-text available
Background HIV outbreaks in the Former Soviet Union (FSU) countries were characterized by repeated transmission of the HIV variant AFSU, which is now classified as a distinct subtype A sub-subtype called A6. The current study used phylogenetic/phylodynamic and signature mutation analyses to determine likely evolutionary relationship between subtype...
Article
Full-text available
Detection methods that do not require nucleic acid amplification are advantageous for viral diagnostics due to their rapid results. These platforms could provide information for both accurate diagnoses and pandemic surveillance. Influenza virus is prone to pandemic-inducing genetic mutations, so there is a need to apply these detection platforms to...
Article
Full-text available
Background Fostemsavir, a prodrug of the gp120-directed attachment inhibitor temsavir, is indicated for use in heavily treatment-experienced individuals with MDR HIV-1. Reduced susceptibility to temsavir in the clinic maps to discrete changes at amino acid positions in gp160: S375, M426, M434 and M475. Objectives To query the Los Alamos National L...
Article
Full-text available
Humanity is currently facing the challenge of two devastating pandemics, caused by two very different RNA viruses: HIV-1, which has been with us for decades, and SARS-CoV-2, which has swept the world in the course of a single year. The same evolutionary strategies that drive HIV-1 evolution are at play in SARS-CoV-2. Single nucleotide mutations, mu...
Preprint
Full-text available
Viral pathogen can rapidly evolve, adapt to novel hosts and evade human immunity. The early detection of emerging viral pathogens through biosurveillance coupled with rapid and accurate diagnostics are required to mitigate global pandemics. However, RNA viruses can mutate rapidly, hampering biosurveillance and diagnostic efforts. Here, we present a...
Article
Full-text available
We aimed to investigate whether the sequence length of HIV-1 increases over time. We performed a longitudinal analysis of full-length coding region sequences (FLs) during an HIV-1 outbreak among patients with hemophilia and local controls infected with the Korean subclade B of HIV-1 (KSB). Genes were amplified by overlapping RT-PCR or nested PCR an...
Preprint
We aimed to investigate whether the sequence length of HIV-1 increases over time. A longitudinal analysis of full-length coding region sequences (FLs) during an HIV-1 outbreak among pa-tients with hemophilia and local controls infected with the Korean subclade B of HIV-1 (KSB) was performed. Genes were amplified by overlapping RT-PCR or nested PCR...
Preprint
Full-text available
Objective: To compare long-read nanopore DNA sequencing (DNA-seq) with short-read sequencing-by-synthesis for sequencing a full-length (e.g., non-deletion, nor reporter) HIV-1 model provirus in plasmid pHXB2_D. Design: We sequenced pHXB2_D and a control plasmid pNL4-3_gag-pol(Δ1443-4553)_EGFP with long- and short-read DNA-seq, evaluating sample var...
Preprint
The objective of this study is to investigate whether the sequence length of HIV-1 increases over time. A longitudinal analysis of full-length coding region sequences (FLs) in an outbreak of HIV-1 infection among patients with hemophilia and local controls identified as infected with the Korean subclade B of HIV-1 (KSB). Genes amplified by overlapp...
Article
Full-text available
Objective: Dolutegravir (DTG) is now a preferred component of first-line antiretroviral therapy (ART). However, prevalence data on natural resistance to integrase inhibitors (INSTIs) in circulating non-subtype B HIV-1 in sub-Saharan Africa is scarce. Our objective is to report prevalence of pre-treatment integrase polymorphisms associated with res...
Article
Full-text available
To assess the HIV -1subtypes distribution in HIV-1 positive migrants living in Milan we studied 77 HIV-1 patients followed at the San Raffaele Hospital of Milan. Twenty subjects were born in Europe, 43 in the Americas, 10 in Africa and 4 in Asia. Unsafe heterosexual activity prevailed in migrants born in Africa and male homosexuality in those born...
Article
Full-text available
A SARS-CoV-2 variant carrying the Spike protein amino acid change D614G has become the most prevalent form in the global pandemic. Dynamic tracking of variant frequencies revealed a recurrent pattern of G614 increase at multiple geographic levels: national, regional and municipal. The shift occurred even in local epidemics where the original D614 f...
Article
Full-text available
A SARS-CoV-2 variant carrying the Spike protein amino acid change D614G has become the most prevalent form in the global pandemic. Dynamic tracking of variant frequencies revealed a recurrent pattern of G614 increase at multiple geographic levels: national, regional, and municipal. The shift occurred even in local epidemics where the original D614...
Research
Full-text available
A SARS-CoV-2 variant carrying the Spike protein amino acid change D614G has become the most prevalent form in the global pandemic. Dynamic tracking of variant frequencies revealed a recurrent pattern of G614 increase at multiple geographic levels: national, regional and municipal. The shift occurred even in local epidemics where the original D614 f...
Article
Full-text available
COVID-19 has become a global pandemic caused by the novel coronavirus SARS-CoV-2. Understanding the origins of SARS-CoV-2 is critical for deterring future zoonosis, discovering new drugs, and developing a vaccine. We show evidence of strong purifying selection around the receptor binding motif (RBM) in the spike and other genes among bat, pangolin,...
Preprint
Full-text available
We have developed an analysis pipeline to facilitate real-time mutation tracking in SARS-CoV-2, focusing initially on the Spike (S) protein because it mediates infection of human cells and is the target of most vaccine strategies and antibody-based therapeutics. To date we have identified fourteen mutations in Spike that are accumulating. Mutations...
Preprint
Full-text available
COVID-19 has become a global pandemic caused by a novel coronavirus SARS-CoV-2. Understanding the origins of SARS-CoV-2 is critical for deterring future zoonosis and for drug discovery and vaccine development. We show evidence of strong purifying selection around the receptor binding motif (RBM) in the spike gene and in other genes among bat, pango...
Article
Full-text available
To investigate the evolutionary history of the recent outbreak of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) in China, a total of 70 genomes of virus strains from China and elsewhere with sampling dates between 24 December 2019 and 3 February 2020 were analyzed. To explore the potential intermediate animal host of the SARS‐CoV‐2 v...
Experiment Findings
Full-text available
Article
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Deep phylogeny involving arthropod lineages is difficult to recover because the erosion of phylogenetic signals over time leads to unreliable multiple sequence alignment (MSA) and subsequent phylogenetic reconstruction. One way to alleviate the problem is to assemble a large number of gene sequences to compensate for the weakness in each individual...
Article
There is scarce data on circulation of genetic subtypes of HIV-1 in South Sudan due to decades of civil war. In this study, phylogenetic analysis of 10 strains collected from HIV-1-infected South Sudanese patients was performed. Partial pol and env viral gene analysis classified sequences as subtype C (n = 4), subtype D (n = 4), and partially uncla...
Article
Full-text available
We determined the earliest full-length HIV-1 gag gene sequences in 110 patients with HIV-1, including 20 hemophiliacs (HPs) and 90 local controls (LCs). The gag gene from stored sera was amplified using RT-PCR, and was subjected to direct sequencing. Phylogenetic analysis indicated that 94 and 16 sequences belonged to the Korean subclade of HIV-1 s...
Presentation
Full-text available
Workshop explaining uses of the Los Alamos National Lab HIV-1 Genetic Sequences Databases and tools for studying the epidemiology and global diversity of HIV-1. Manoy of the tools can be used in the study of any virus or any type of gene sequences from any organism.
Article
The detection of antisense RNA is hampered by reverse transcription (RT) non-specific priming, due to the ability of RNA secondary structures to prime RT in the absence of specific primers. The detection of antisense RNA by conventional RT-PCR does not allow assessment of the polarity of the initial RNA template, causing the amplification of non-sp...
Article
Full-text available
Understanding HIV latent reservoirs in tissues is essential for the development of new strategies targeting these sites for eradication. Here, we assessed the size of latent reservoirs and the source of residual viruses in multiple lymphoid tissues of SIV-infected and fully suppressed rhesus macaques of Chinese-origin (cRMs). Eight cRMs were infect...
Article
Full-text available
Background To date, no study has described disease progression in Asian patients infected with HIV-1 subtype D. Methods To determine whether the disease progression differs in patients infected with subtypes D and B prior to starting combination antiretroviral therapy, the annual decline (AD) in CD4⁺ T cell counts over 96 ± 59 months was retrospec...
Article
Human immunodeficiency virus type 2 (HIV-2) infection prevalence is increasing in some European countries. The increasing migratory flow from countries where HIV-2 is endemic has facilitated the spread of the virus into Europe and other regions. We describe a case of HIV-2 infection in a migrant individual in the Asylum Seeker Centre (ASC) in Italy...
Article
Full-text available
While in other parts of the world it is on decline, incidence of HIV infection continues to rise in the former Soviet Union (FSU) countries. The present study was conducted to investigate the patterns and modes of HIV transmission in FSU countries. We performed phylogenetic analysis of publicly available 2705 HIV-1 subtype A pol sequences from thir...
Data
A and B. Full-scale version of the trees in Fig 1 with accession numbers and bootstrap values indicated. Bootstrap values between 50–70 and ≤70 are shown, respectively, by red and black dots. (TIF)
Data
For easy reference and analysis clusters in Fig 2 are shown at high resolution and with accessions numbers included in the labels. In the full version of the tree (left), bootstrap values between 50–70 and ≤70 are shown, respectively, by red and black dots. (TIF)
Article
Full-text available
There have been no studies related to groups at the highest risk for HIV-1 infection in Korea before 1993. Here, for the first time, we report the distribution of HIV subtypes in overseas sailors (OSs), and prostitutes who worked in brothels near US military bases in Korea. We retrospectively determined the sequences of nef in 131 patients using RT...
Article
Human Immunodeficiency Virus (HIV) was originally introduced in Bulgaria through heterosexual transmission (HET) and later transferred to other vulnerable groups along with numerous more recent introductions from outside Bulgaria. To define the diversity, origins and dynamics of the HIV-1 subtypes prevalent in HET population in Bulgaria we applied...
Preprint
Full-text available
Botulinum neurotoxins (BoNTs) are produced by diverse members of the Clostridia and result in a flaccid paralysis known as botulism. Exploring the diversity of BoNTs is important for the development of therapeutics and antitoxins. Here we describe a novel, bont -like gene cluster identified in a draft genome assembly for Enterococcus sp. 3G1_DIV062...
Article
Full-text available
The epidemiological link in the hypervariable env gene between viruses infecting HIV-positive hemophiliacs (HPs) and plasma donors was not studied. We determined full-length env gene sequences in 20 HPs, 3 plasma donors whose plasma was used for domestic clotting factor (DCF) production, and 54 local controls (LCs). Env genes from viruses in frozen...
Article
Persistence of HIV-1 reservoirs in the central nervous system (CNS) is an obstacle to cure strategies. However, little is known about residual viral distribution, viral replication levels, and genetic diversity in different brain regions of HIV-infected individuals on combination antiretroviral therapy (cART). Because myeloid cells particularly mic...
Chapter
It is probable that humans were first infected with HIV in the Kinshasa region of the Democratic Republic of the Congo in the 1950s and yet many decades later we are still studying and discovering how best to control what has become a global epidemic. One of the epicenters of the disease was in Miami when people with symptoms that were inexplicable...
Chapter
HIV-1 and HIV-2 both cause AIDS in humans, and both originated in nonhuman primates in Africa before several cross-species transmission events introduced them into humans. Of more than seven such events, only one, creating the HIV-1 M group of viruses, resulted in the AIDS pandemic. Studying the evolution and epidemiology of the viruses has many us...
Chapter
Injection drug use is a major risk behavior associated with transmission of HIV-1B. Yet, despite its importance there have not been many detailed studies characterizing the transmission of HIV-1B in well-defined injection drug use networks. This preliminary study characterized people who were closely associated and injected drugs together under pri...
Chapter
The first documented cases of HIV/AIDS in the United States bewildered physicians as they presented an unusual disease spectrum. Two young men were diagnosed with Kaposi sarcoma and Pneumocystis carinii pneumonia, which was inexplicable at that time, as these health outcomes were rare among their age, race/ethnicity, and individuals not living in n...
Article
Full-text available
The epidemiological link in the hypervariable env gene between viruses infecting HIV-positive hemophiliacs (HPs) and plasma donors was not studied. We determined full-length env gene sequences in 20 HPs, 3 plasma donors whose plasma was used for domestic clotting factor (DCF) production, and 54 local controls (LCs). Env genes from viruses in frozen...
Article
Full-text available
Botrytis cinerea sporadically infects plants in Mediterranean climates and contributes to a significant crop loss every year. Diseases caused by B. cinerea can affect many crops and are of particular concern to strawberry growers in California, which is the major state for fresh strawberry production in the United States. This study looks at geneti...
Book
This book on NeuroAIDS, a collection of chapters written by experts and specialists from around the world, provides a global perspective on HIV and NeuroAIDS in the field, clinic, and laboratory. The chapters address the comorbidity of HIV and other infectious agents, including Zika virus, Ebola, Chagas disease, TB and HCV. Also discussed are key t...
Article
The International Committee for the Taxonomy and Nomenclature of Viruses does not rule on virus classifications below the species level. The definition of species for viruses cannot be clearly defined for all types of viruses. The complex and interesting epidemiology of Human Immunodeficiency Viruses demands a detailed and informative nomenclature...
Article
Full-text available
Background The p6 region of the HIV-1 structural precursor polyprotein, Gag, contains two motifs, P7TAP11 and L35YPLXSL41, designated as late (L) domain-1 and -2, respectively. These motifs bind the ESCRT-I factor Tsg101 and the ESCRT adaptor Alix, respectively, and are critical for efficient budding of virus particles from the plasma membrane. L d...
Article
Full-text available
The Ebola outbreak of 2013–15 infected more than 28 000 people and claimed more lives than all previous filovirus outbreaks combined. Governmental agencies, clinical teams, and the world scientific community pulled together in a multifaceted response ranging from prevention and disease control, to evaluating vaccines and therapeutics in human trial...
Article
Full-text available
Background Clostridium botulinum is a diverse group of bacteria characterized by the production of botulinum neurotoxin. Botulinum neurotoxins are classified into serotypes (BoNT/A–G), which are produced by six species/Groups of Clostridia, but the genetic background of the bacteria remains poorly understood. The purpose of this study was to use co...
Article
The recent availability of multiple Clostridium botulinum genomic sequences has initiated a new genomics era that strengthens our understanding of the bacterial species that produce botulinum neurotoxins (BoNTs)). Analysis of the genomes has reinforced the historical Group I-VI designations and provided evidence that the bont genes can be located w...
Article
Full-text available
CATNAP (Compile, Analyze and Tally NAb Panels) is a new web server at Los Alamos HIV Database, created to respond to the newest advances in HIV neutralizing antibody research. It is a comprehensive platform focusing on neutralizing antibody potencies in conjunction with viral sequences. CATNAP integrates neutralization and sequence data from publis...
Article
The whole genomes for six botulinum neurotoxin-producing clostridial strains were sequenced to provide references for under-represented toxin types, bivalent strains or unusual toxin complexes associated with a bont gene. The strains include three Clostridium botulinum Group I strains (CDC297, CDC 1436, and Prevot 594), a Group II C. botulinum stra...
Article
Full-text available