23 Result(s)
within
Sergei L. Kosakovsky Pond
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Article
Open AccessThe complete sequence and comparative analysis of ape sex chromosomes
Apes possess two sex chromosomes—the male-specific Y chromosome and the X chromosome, which is present in both males and females. The Y chromosome is crucial for male reproduction, with deletions being linked ...
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Article
Open AccessThe genomic evolutionary dynamics and global circulation patterns of respiratory syncytial virus
Respiratory syncytial virus (RSV) is a leading cause of acute lower respiratory tract infection in young children and the second leading cause of infant death worldwide. While global circulation has been exten...
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Article
Open AccessEmergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa
Three lineages (BA.1, BA.2 and BA.3) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant of concern predominantly drove South Africa’s fourth Coronavirus Disease 2019 (COVID-19)...
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Article
Open AccessHuman HspB1, HspB3, HspB5 and HspB8: Sha** these disease factors during vertebrate evolution
Small heat shock proteins (sHSPs) emerged early in evolution and occur in all domains of life and nearly in all species, including humans. Mutations in four sHSPs (HspB1, HspB3, HspB5, HspB8) are associated wi...
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Article
Open AccessDetection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City
Recombination is an evolutionary process by which many pathogens generate diversity and acquire novel functions. Although a common occurrence during coronavirus replication, detection of recombination is only ...
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Article
Open AccessThe evolution of BDNF is defined by strict purifying selection and prodomain spatial coevolution, but what does it mean for human brain disease?
Brain-Derived Neurotrophic Factor (BDNF) is an essential mediator of brain assembly, development, and maturation. BDNF has been implicated in a variety of brain disorders such as neurodevelopmental disorders (...
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Article
Open AccessRapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa
The SARS-CoV-2 epidemic in southern Africa has been characterized by three distinct waves. The first was associated with a mix of SARS-CoV-2 lineages, while the second and third waves were driven by the Beta (...
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Article
The biological and clinical significance of emerging SARS-CoV-2 variants
The past several months have witnessed the emergence of SARS-CoV-2 variants with novel spike protein mutations that are influencing the epidemiological and clinical aspects of the COVID-19 pandemic. These vari...
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Article
Ready-to-use public infrastructure for global SARS-CoV-2 monitoring
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Article
Detection of a SARS-CoV-2 variant of concern in South Africa
Continued uncontrolled transmission of SARS-CoV-2 in many parts of the world is creating conditions for substantial evolutionary changes to the virus1,2. Here we describe a newly arisen lineage of SARS-CoV-2 (des...
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Protocol
Evolution of Viral Genomes: Interplay Between Selection, Recombination, and Other Forces
Natural selection is a fundamental force sha** organismal evolution, as it both maintains function and enables adaptation and innovation. Viruses, with their typically short and largely coding genomes, exper...
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Article
Open Accessphylotree.js - a JavaScript library for application development and interactive data visualization in phylogenetics
While several JavaScript packages for visualizing phylogenetic trees exist, most are best characterized as frameworks that are designed with a specific set of tasks in mind. Extending such packages to use case...
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Article
Open AccessSelection analyses of paired HIV-1 gag and gp41 sequences obtained before and after antiretroviral therapy
Most HIV-1-infected individuals with virological failure on a pharmacologically-boosted protease inhibitor (PI) regimen do not develop PI-resistance protease mutations. One proposed explanation is that HIV-1 gag ...
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Article
Lorenzo-Redondo et al. reply
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Article
Open AccessEvolution of gag and gp41 in Patients Receiving Ritonavir-Boosted Protease Inhibitors
Several groups have proposed that genotypic determinants in gag and the gp41 cytoplasmic domain (gp41-CD) reduce protease inhibitor (PI) susceptibility without PI-resistance mutations in protease. However, no gag
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Protocol
Unbiased RACE-Based Massive Parallel Surveys of Human IgA Antibody Repertoires
For investigations of human B-cell receptor (BCR) repertoires, we have developed a protocol for large-scale surveys of human antibody heavy chain (VH) rearrangements. Here we study IgA repertoires, as more IgA...
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Article
Open AccessViral Evolution and Cytotoxic T Cell Restricted Selection in Acute Infant HIV-1 Infection
Antiretroviral therapy-naive HIV-1 infected infants experience poor viral containment and rapid disease progression compared to adults. Viral factors (e.g. transmitted cytotoxic T- lymphocyte (CTL) escape muta...
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Article
Persistent HIV-1 replication maintains the tissue reservoir during therapy
Lymphoid tissue is a key reservoir established by HIV-1 during acute infection. It is a site associated with viral production, storage of viral particles in immune complexes, and viral persistence. Although co...
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Protocol
Evolution of Viral Genomes: Interplay Between Selection, Recombination, and Other Forces
RNA viruses evolve very rapidly, often recombine, and are subject to strong host (immune response) and anthropogenic (antiretroviral drugs) selective forces. Given their compact and extensively sequenced genom...
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Protocol
Detecting Signatures of Selection from DNA Sequences Using Datamonkey
Natural selection is a fundamental process affecting all evolving populations. In the simplest case, positive selection increases the frequency of alleles that confer a fitness advantage relative to the rest o...
