Tulio de Oliveira
#88,982
Most Influential Person Now
Brazilian bioinformatics and public health scholar
Tulio de Oliveira's AcademicInfluence.com Rankings
Tulio de Oliveiramedical Degrees
Medical
#1606
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#1963
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Public Health
#319
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#331
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Tulio de Oliveirabiology Degrees
Biology
#7001
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#9835
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Bioinformatics
#91
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#93
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Medical Biology
Tulio de Oliveira's Degrees
- Bachelors Biological Sciences Federal University of Minas Gerais
- Masters Bioinformatics Federal University of Minas Gerais
- PhD Public Health Federal University of Minas Gerais
Why Is Tulio de Oliveira Influential?
(Suggest an Edit or Addition)According to Wikipedia, Tulio de Oliveira is a Brazilian, Portuguese, and South African permanent resident professor of bioinformatics at the University of KwaZulu-Natal and Stellenbosch University, South Africa, and associate professor of global health at the University of Washington. He has studied outbreaks of chikungunya, dengue, hepatitis B and C, HIV, SARS-CoV-2, yellow fever and Zika. During the COVID-19 pandemic he led the team that confirmed the discovery of the Beta variant of the COVID-19 virus in 2020 and the Omicron variant in 2021.
Tulio de Oliveira's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- Efficacy of the ChAdOx1 nCoV-19 Covid-19 Vaccine against the B.1.351 Variant (2021) (937)
- Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa (2021) (860)
- Omicron extensively but incompletely escapes Pfizer BNT162b2 neutralization (2021) (733)
- Detection of a SARS-CoV-2 variant of concern in South Africa (2021) (724)
- Emergence of a SARS-CoV-2 variant of concern with mutations in spike glycoprotein. (2021) (606)
- SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma (2021) (520)
- An automated genotyping system for analysis of HIV-1 and other microbial sequences (2005) (517)
- New SARS-CoV-2 Variants — Clinical, Public Health, and Vaccine Implications (2021) (511)
- The biological and clinical significance of emerging SARS-CoV-2 variants (2021) (510)
- Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma (2021) (472)
- Renewing Felsenstein’s Phylogenetic Bootstrap in the Era of Big Data (2018) (374)
- Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes: performance evaluation of the new REGA version 3 and seven other tools. (2013) (300)
- SARS-CoV-2 Omicron has extensive but incomplete escape of Pfizer BNT162b2 elicited neutralization and requires ACE2 for infection (2021) (298)
- Sixteen novel lineages of SARS-CoV-2 in South Africa (2021) (286)
- T cell responses to SARS-CoV-2 spike cross-recognize Omicron (2022) (284)
- HIV-1 drug resistance before initiation or re-initiation of first-line antiretroviral therapy in low-income and middle-income countries: a systematic review and meta-regression analysis (2017) (239)
- Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa (2022) (237)
- Transmission networks and risk of HIV infection in KwaZulu-Natal, South Africa: a community-wide phylogenetic study. (2017) (227)
- Universal test and treat and the HIV epidemic in rural South Africa: a phase 4, open-label, community cluster randomised trial. (2017) (195)
- Genome Detective: an automated system for virus identification from high-throughput sequencing data (2018) (186)
- Microbial genome-wide association studies: lessons from human GWAS (2016) (181)
- Spread of yellow fever virus outbreak in Angola and the Democratic Republic of the Congo 2015–16: a modelling study (2017) (177)
- SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse (2021) (168)
- A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences (2009) (160)
- Global epidemiology of drug resistance after failure of WHO recommended first-line regimens for adult HIV-1 infection: a multicentre retrospective cohort study (2016) (155)
- Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2 (2021) (146)
- Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2. (2021) (145)
- Molecular Epidemiology: HIV-1 and HCV sequences from Libyan outbreak (2006) (135)
- Molecular Cloning and Functional Analysis of Three Type D Endogenous Retroviruses of Sheep Reveal a Different Cell Tropism from That of the Highly Related Exogenous Jaagsiekte Sheep Retrovirus (2000) (128)
- Escape of SARS-CoV-2 501Y.V2 variants from neutralization by convalescent plasma (2021) (126)
- Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes (2020) (122)
- A specific subtype C of human immunodeficiency virus type 1 circulates in Brazil (2003) (121)
- Concentrated HIV subepidemics in generalized epidemic settings (2014) (119)
- The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages (2021) (116)
- Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus (2022) (111)
- Preliminary Efficacy of the NVX-CoV2373 Covid-19 Vaccine Against the B.1.351 Variant (2021) (105)
- Phylodynamic Analysis of Human Immunodeficiency Virus Type 1 in Distinct Brain Compartments Provides a Model for the Neuropathogenesis of AIDS (2005) (102)
- Recombination Confounds the Early Evolutionary History of Human Immunodeficiency Virus Type 1: Subtype G Is a Circulating Recombinant Form (2007) (100)
- Safety and efficacy of the ChAdOx1 nCoV-19 (AZD1222) Covid-19 vaccine against the B.1.351 variant in South Africa (2021) (96)
- Phylogenetic Surveillance of Viral Genetic Diversity and the Evolving Molecular Epidemiology of Human Immunodeficiency Virus Type 1 (2007) (94)
- Two doses of SARS-CoV-2 vaccination induce robust immune responses to emerging SARS-CoV-2 variants of concern (2021) (93)
- SARS-CoV-2 prolonged infection during advanced HIV disease evolves extensive immune escape (2022) (92)
- Cross-Reactive Neutralizing Antibody Responses Elicited by SARS-CoV-2 501Y.V2 (B.1.351) (2021) (88)
- Variability at Human Immunodeficiency Virus Type 1 Subtype C Protease Cleavage Sites: an Indication of Viral Fitness? (2003) (88)
- The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape (2021) (86)
- Conserved Footprints of APOBEC3G on Hypermutated Human Immunodeficiency Virus Type 1 and Human Endogenous Retrovirus HERV-K(HML2) Sequences (2008) (86)
- Sequential Broadening of CTL Responses in Early HIV-1 Infection Is Associated with Viral Escape (2007) (86)
- Phylogenetic Studies of Transmission Dynamics in Generalized HIV Epidemics: An Essential Tool Where the Burden is Greatest? (2014) (83)
- Track Omicron's spread with molecular data. (2021) (79)
- Molecular Characteristics of Human Immunodeficiency Virus Type 1 Subtype C Viruses from KwaZulu-Natal, South Africa: Implications for Vaccine and Antiretroviral Control Strategies (2003) (79)
- Persistent SARS-CoV-2 infection and intra-host evolution in association with advanced HIV infection (2021) (77)
- HIV-1 Drug Resistance Mutations: Potential Applications for Point-of-Care Genotypic Resistance Testing (2015) (75)
- Trends in Genotypic HIV-1 Antiretroviral Resistance between 2006 and 2012 in South African Patients Receiving First- and Second-Line Antiretroviral Treatment Regimens (2013) (72)
- High-Resolution Molecular Epidemiology and Evolutionary History of HIV-1 Subtypes in Albania (2008) (72)
- Declines in HIV incidence among men and women in a South African population-based cohort (2019) (72)
- Evidence for recombination in natural populations of porcine circovirus type 2 in Hong Kong and mainland China. (2007) (71)
- Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic (2020) (69)
- Tracking the 2022 monkeypox outbreak with epidemiological data in real-time (2022) (67)
- Primary drug resistance in South Africa: data from 10 years of surveys. (2012) (67)
- Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable (2020) (63)
- Dolutegravir for first-line antiretroviral therapy in low-income and middle-income countries: uncertainties and opportunities for implementation and research. (2018) (63)
- High-Levels of Acquired Drug Resistance in Adult Patients Failing First-Line Antiretroviral Therapy in a Rural HIV Treatment Programme in KwaZulu-Natal, South Africa (2013) (61)
- Mapping Sites of Positive Selection and Amino Acid Diversification in the HIV Genome (2004) (60)
- Different Epidemic Potentials of the HIV-1B and C Subtypes (2005) (59)
- Incidence rate estimation, periodic testing and the limitations of the mid-point imputation approach (2017) (58)
- Yellow Fever Virus Reemergence and Spread in Southeast Brazil, 2016–2019 (2019) (57)
- Effect of population viral load on prospective HIV incidence in a hyperendemic rural African community (2017) (55)
- Are subtype differences important in HIV drug resistance? (2012) (55)
- Early transmission of SARS-CoV-2 in South Africa: An epidemiological and phylogenetic report (2020) (54)
- Escape from recognition of SARS-CoV-2 Beta variant spike epitopes but overall preservation of T cell immunity (2021) (54)
- The HIV-1 Subtype C Epidemic in South America Is Linked to the United Kingdom (2010) (53)
- Extensive HIV-1 Intra-Host Recombination Is Common in Tissues with Abnormal Histopathology (2009) (53)
- Evolution and molecular epidemiology of subtype C HIV-1 in Zimbabwe (2009) (53)
- Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch (2021) (53)
- PANGEA-HIV: phylogenetics for generalised epidemics in Africa. (2015) (52)
- Occult HIV-1 drug resistance to thymidine analogues following failure of first-line tenofovir combined with a cytosine analogue and nevirapine or efavirenz in sub Saharan Africa: a retrospective multi-centre cohort study (2016) (49)
- Omicron infection enhances Delta antibody immunity in vaccinated persons (2022) (49)
- Omicron BA.4/BA.5 escape neutralizing immunity elicited by BA.1 infection (2022) (46)
- Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis (2019) (46)
- Impact of Drug Resistance-Associated Amino Acid Changes in HIV-1 Subtype C on Susceptibility to Newer Nonnucleoside Reverse Transcriptase Inhibitors (2014) (45)
- HIV-1 and SARS-CoV-2: Patterns in the evolution of two pandemic pathogens (2021) (45)
- Impact of Next-generation Sequencing Defined Human Immunodeficiency Virus Pretreatment Drug Resistance on Virological Outcomes in the ANRS 12249 Treatment-as-Prevention Trial (2018) (44)
- Current Affairs of Microbial Genome-Wide Association Studies: Approaches, Bottlenecks and Analytical Pitfalls (2020) (42)
- Trends in Pretreatment HIV-1 Drug Resistance in Antiretroviral Therapy-naive Adults in South Africa, 2000–2016: A Pooled Sequence Analysis (2019) (42)
- Reduced efficacy of HIV-1 integrase inhibitors in patients with drug resistance mutations in reverse transcriptase (2020) (42)
- Mosaic Genomes of the Six Major Primate Lentivirus Lineages Revealed by Phylogenetic Analyses (2003) (41)
- Quantifying HIV transmission flow between high-prevalence hotspots and surrounding communities: a population-based study in Rakai, Uganda (2020) (41)
- The ongoing COVID-19 epidemic in Minas Gerais, Brazil: insights from epidemiological data and SARS-CoV-2 whole genome sequencing (2020) (40)
- A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes (2019) (40)
- Rapid replacement of the Beta variant by the Delta variant in South Africa (2021) (40)
- The HIV type 1 epidemic in Bulgaria involves multiple subtypes and is sustained by continuous viral inflow from West and East European countries. (2008) (39)
- Tracing the origin of Brazilian HTLV-1 as determined by analysis of host and viral genes (2006) (38)
- Assessment of automated genotyping protocols as tools for surveillance of HIV-1 genetic diversity (2006) (36)
- Reduced antibody cross-reactivity following infection with B.1.1.7 than with parental SARS-CoV-2 strains (2021) (36)
- A genomics network established to respond rapidly to public health threats in South Africa (2020) (35)
- The continuous evolution of SARS-CoV-2 in South Africa: a new lineage with rapid accumulation of mutations of concern and global detection (2021) (35)
- Prevalence of HIV type-1 drug-associated mutations in pre-therapy patients in the Free State, South Africa (2009) (35)
- Circulating Biomarkers of Immune Activation Distinguish Viral Suppression from Nonsuppression in HAART-Treated Patients with Advanced HIV-1 Subtype C Infection (2014) (35)
- A genomics network established to respond rapidly to public health threats in South Africa (2020) (35)
- Mycobacterium tuberculosis Next-Generation Whole Genome Sequencing: Opportunities and Challenges (2018) (35)
- Modeling HIV-1 Drug Resistance as Episodic Directional Selection (2012) (34)
- Implementing HIV-1 genotypic resistance testing in antiretroviral therapy programs in Africa: needs, opportunities, and challenges. (2013) (34)
- An Affordable HIV-1 Drug Resistance Monitoring Method for Resource Limited Settings (2014) (33)
- Virological Outcomes of Second-line Protease Inhibitor–Based Treatment for Human Immunodeficiency Virus Type 1 in a High-Prevalence Rural South African Setting: A Competing-Risks Prospective Cohort Analysis (2017) (33)
- Sensitive Next-Generation Sequencing Method Reveals Deep Genetic Diversity of HIV-1 in the Democratic Republic of the Congo (2017) (32)
- History and origin of the HIV-1 subtype C epidemic in South Africa and the greater southern African region (2015) (32)
- Genomic and Epidemiological Surveillance of Zika Virus in the Amazon Region. (2020) (32)
- RegaDB: community-driven data management and analysis for infectious diseases (2013) (32)
- Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function (2022) (32)
- Public database for HIV drug resistance in southern Africa (2010) (31)
- Author Correction: Omicron BA.4/BA.5 escape neutralizing immunity elicited by BA.1 infection (2022) (31)
- SARS-CoV-2 501Y.V2 (B.1.351) elicits cross-reactive neutralizing antibodies (2021) (31)
- Increasing HIV-1 Drug Resistance Between 2010 and 2012 in Adults Participating in Population-Based HIV Surveillance in Rural KwaZulu-Natal, South Africa (2016) (31)
- Early transmission of SARS-CoV-2 in South Africa: An epidemiological and phylogenetic report (2020) (31)
- Identifying Recent HIV Infections: From Serological Assays to Genomics (2015) (30)
- Early Genomic Detection of Cosmopolitan Genotype of Dengue Virus Serotype 2, Angola, 2018 (2019) (30)
- Omicron infection of vaccinated individuals enhances neutralizing immunity against the Delta variant (2021) (30)
- Searching for virus phylotypes (2013) (29)
- Determinants of Vaginal Microbiota Composition (2020) (28)
- An outbreak of HIV-1 subtype G among Italian injecting drug users (2007) (28)
- Drug resistance in children at virological failure in a rural KwaZulu-Natal, South Africa, cohort (2014) (28)
- Functional characteristics of HIV-1 subtype C compatible with increased heterosexual transmissibility (2009) (28)
- Genetic variability of human immunodeficiency virus‐1 in Bahia state, Northeast, Brazil: High diversity of HIV genotypes (2009) (27)
- Mutational Correlates of Virological Failure in Individuals Receiving a WHO-Recommended Tenofovir-Containing First-Line Regimen: An International Collaboration (2017) (27)
- Emergence and phenotypic characterization of C.1.2, a globally detected lineage that rapidly accumulated mutations of concern (2021) (26)
- High percentage of undiagnosed HIV cases within a hyperendemic South African community: a population-based study (2017) (26)
- Circulation of chikungunya virus East/Central/South African lineage in Rio de Janeiro, Brazil (2019) (26)
- HIV infection alters SARS-CoV-2 responsive immune parameters but not clinical outcomes in COVID-19 disease (2020) (26)
- Conserved Footprints of APOBEC 3 G on Hypermutated Human Immunodeficiency Virus Type 1 and Human Endogenous Retrovirus HERV-K ( HML 2 ) Sequences † (2008) (26)
- Using nearly full-genome HIV sequence data improves phylogeny reconstruction in a simulated epidemic (2016) (26)
- Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function (2022) (25)
- Effectiveness of the Ad26.COV2.S vaccine in health-care workers in South Africa (the Sisonke study): results from a single-arm, open-label, phase 3B, implementation study (2022) (25)
- Molecular characteristics of HIV-1 Subtype C viruses from KwaZulu-Natal, South Africa: implications for vaccine and antiretroviral control strategies (2003) (25)
- The political theatre of the UK's travel ban on South Africa (2021) (25)
- Origin, imports and exports of HIV-1 subtype C in South Africa: A historical perspective. (2016) (24)
- BioAfrica's HIV-1 Proteomics Resource: Combining protein data with bioinformatics tools (2005) (24)
- HIV drug resistance levels in adults failing first‐line antiretroviral therapy in an urban and a rural setting in South Africa (2017) (24)
- Genomic surveillance activities unveil the introduction of the SARS‐CoV‐2 B.1.525 variant of interest in Brazil: Case report (2021) (24)
- Novel evolutionary analyses of full-length HIV type 1 subtype C molecular clones from Cape Town, South Africa. (2002) (24)
- Transmission dynamics of SARS-CoV-2 within-host diversity in two major hospital outbreaks in South Africa (2021) (23)
- Next Generation Sequencing and Bioinformatics Analysis of Family Genetic Inheritance (2020) (23)
- Trends in HIV Prevention, Treatment, and Incidence in a Hyperendemic Area of KwaZulu-Natal, South Africa (2019) (23)
- HIV-1 Subtypes B and C Unique Recombinant Forms (URFs) and Transmitted Drug Resistance Identified in the Western Cape Province, South Africa (2014) (23)
- Africa: tackle HIV and COVID-19 together (2021) (23)
- Understanding Specific Contexts of Antiretroviral Therapy Adherence in Rural South Africa: A Thematic Analysis of Digital Stories from a Community with High HIV Prevalence (2016) (22)
- Zika virus complete genome from Salvador, Bahia, Brazil. (2016) (22)
- Major new lineages of SARS-CoV-2 emerge and spread in South Africa during lockdown. (2020) (22)
- The 2012 southern African ARV drug resistance testing guidelines (2012) (22)
- Rates of virological suppression and drug resistance in adult HIV-1-positive patients attending primary healthcare facilities in KwaZulu-Natal, South Africa (2017) (21)
- Social Disequilibrium and the Risk of HIV Acquisition: A Multilevel Study in Rural KwaZulu-Natal Province, South Africa (2017) (21)
- Persistent SARS-CoV-2 infection with accumulation of mutations in a patient with poorly controlled HIV infection (2022) (20)
- Replacement of the Gamma by the Delta variant in Brazil: Impact of lineage displacement on the ongoing pandemic (2021) (20)
- HIV status alters disease severity and immune cell responses in beta variant SARS-CoV-2 infection wave. (2021) (20)
- Genetic Characteristics, Coreceptor Usage Potential and Evolution of Nigerian HIV-1 Subtype G and CRF02_AG Isolates (2011) (20)
- HIV-1 Full-Genome Phylogenetics of Generalized Epidemics in Sub-Saharan Africa: Impact of Missing Nucleotide Characters in Next-Generation Sequences (2017) (20)
- Multiple Early Introductions of SARS-CoV-2 to Cape Town, South Africa (2021) (19)
- Unlocking the efficiency of genomics laboratories with robotic liquid-handling (2020) (19)
- Two doses of SARS-CoV-2 vaccination induce more robust immune responses to emerging SARS-CoV-2 variants of concern than does natural infection. (2021) (19)
- An early warning system for emerging SARS-CoV-2 variants (2022) (19)
- The RNA Virus Database (2008) (19)
- Accelerating genomics-based surveillance for COVID-19 response in Africa (2020) (18)
- Tracking external introductions of HIV using phylodynamics reveals a major source of infections in rural KwaZulu-Natal, South Africa (2018) (18)
- SARS-CoV-2 shifting transmission dynamics and hidden reservoirs potentially limit efficacy of public health interventions in Italy (2021) (18)
- Detection of SARS-CoV-2 variants by Abbott molecular, antigen, and serological tests (2021) (17)
- A novel variant of interest of SARS-CoV-2 with multiple spike mutations is identified from travel surveillance in Africa (2021) (17)
- Protocol: Leveraging a demographic and health surveillance system for Covid-19 Surveillance in rural KwaZulu-Natal. (2020) (17)
- Implementing antiretroviral resistance testing in a primary health care HIV treatment programme in rural KwaZulu-Natal, South Africa: early experiences, achievements and challenges (2014) (16)
- Genome-Wide Association Study of HIV Whole Genome Sequences Validated using Drug Resistance (2016) (16)
- The Development of Computational Biology in South Africa: Successes Achieved and Lessons Learnt (2016) (16)
- Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage (2022) (16)
- Temporal Changes in Vaginal Microbiota and Genital Tract Cytokines Among South African Women Treated for Bacterial Vaginosis (2021) (16)
- Appropriate names for COVID-19 variants (2021) (16)
- HIV-1 Adaptation to Antigen Processing Results in Population-Level Immune Evasion and Affects Subtype Diversification (2014) (15)
- Immunogenicity of SARS-CoV-2 infection and Ad26.CoV2.S vaccination in people living with HIV. (2021) (15)
- A Novel and Expanding SARS-CoV-2 Variant, B.1.1.318, dominates infections in Mauritius (2021) (15)
- Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil (2022) (15)
- Longitudinal Trends in the Prevalence of Detectable HIV Viremia: Population-Based Evidence From Rural KwaZulu-Natal, South Africa (2018) (14)
- Comparative performance of the REGA subtyping tool version 2 versus version 1. (2010) (14)
- High Resolution analysis of Transmission Dynamics of Sars-Cov-2 in Two Major Hospital Outbreaks in South Africa Leveraging Intrahost Diversity (2020) (14)
- Short Report: Early genomic detection of SARS-CoV-2 P.1 variant in Northeast Brazil (2021) (14)
- Identification of SARS‐CoV‐2 Omicron variant using spike gene target failure and genotyping assays, Gauteng, South Africa, 2021 (2022) (14)
- Surveillance of resistance in KZN South Africa, including mother-infant pairs 6 weeks after single-dose NVP (2004) (14)
- Development and Evaluation of an Affordable Real-Time Qualitative Assay for Determining HIV-1 Virological Failure in Plasma and Dried Blood Spots (2013) (14)
- The Art of HIV Elimination: Past and Present Science. (2015) (14)
- SARS-CoV-2 cell-to-cell spread occurs rapidly and is insensitive to antibody neutralization (2021) (13)
- Genetic and biologic characterization of HIV type 1 subtype C isolates from south Brazil. (2007) (13)
- Space-time clustering of recently-diagnosed tuberculosis and impact of ART scale-up: Evidence from an HIV hyper-endemic rural South African population (2019) (13)
- The tainted milk of human kindness (2012) (12)
- Collaborative annotation of genes and proteins between UniProtKB/Swiss-Prot and dictyBase (2009) (12)
- Ethical issues associated with HIV phylogenetics in HIV transmission dynamics research: A review of the literature using the Emanuel Framework. (2019) (12)
- Re-mapping the molecular features of the human immunodeficiency virus type 1 and human T-cell lymphotropic virus type 1 Brazilian sequences using a bioinformatics unit established in Salvador, Bahia, Brazil, to give support to the viral epidemiology studies. (2007) (12)
- CD4+ T-cell Count may not be a Useful Strategy to Monitor Antiretroviral Therapy Response in HTLV-1/HIV Co-infected Patients. (2017) (12)
- Field and classroom initiatives for portable sequence-based monitoring of dengue virus in Brazil (2021) (11)
- Moderate-to-High Levels of Pretreatment HIV Drug Resistance in KwaZulu-Natal Province, South Africa. (2019) (11)
- An integrated genetic data environment (GDE)-based LINUX interface for analysis of HIV-1 and other microbial sequences (2003) (11)
- Genomic evidence of SARS-CoV-2 reinfection case with the emerging B.1.2 variant in Brazil (2021) (11)
- Community engagement with HIV drug adherence in rural South Africa: a transdisciplinary approach (2018) (11)
- Immunogenicity of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection and Ad26.CoV2.S Vaccination in People Living With Human Immunodeficiency Virus (HIV) (2021) (11)
- 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) (11)
- Unravelling the complicated evolutionary and dissemination history of HIV-1M subtype A lineages (2018) (11)
- High level of HIV‐2 false positivity in KwaZulu‐Natal province: A region of South Africa with a very high HIV‐1 subtype C prevalence (2013) (10)
- Early Detection of Emergent Extensively Drug-Resistant Tuberculosis by Flow Cytometry-Based Phenotyping and Whole-Genome Sequencing (2019) (10)
- Detection of Transmission Clusters of HIV-1 Subtype C over a 21-Year Period in Cape Town, South Africa (2014) (10)
- Whole genome sequencing for drug-resistant tuberculosis management in South Africa: What gaps would this address and what are the challenges to implementation? (2019) (10)
- Primary HIV-1 Drug Resistant Minority Variants. (2017) (10)
- Complex Subtype Diversity of HIV-1 Among Drug Users in Major Kenyan Cities. (2017) (9)
- Short report: Introduction of chikungunya virus ECSA genotype into the Brazilian Midwest and its dispersion through the Americas (2021) (9)
- Analysis of Viral Diversity in Relation to the Recency of HIV-1C Infection in Botswana (2016) (9)
- Southern African Treatment Resistance Network (SATuRN) RegaDB HIV drug resistance and clinical management database: supporting patient management, surveillance and research in southern Africa (2014) (9)
- Experts’ Perspectives on Key Ethical Issues Associated With HIV Phylogenetics as Applied in HIV Transmission Dynamics Research (2018) (9)
- HIV Drug Resistance Patterns at the Epicentre of the HIV-1 Epidemic in Kwazulu-Natal, South Africa 2003-2013 (2014) (9)
- Evidence of Long-Lived Founder Virus in Mother-to-Child HIV Transmission (2015) (8)
- Return of the founder Chikungunya virus to its place of introduction into Brazil is revealed by genomic characterization of exanthematic disease cases (2019) (8)
- Pervasive and non-random recombination in near full-length HIV genomes from Uganda (2020) (8)
- High Rates of Transmission of Drug-resistant HIV in Aruba Resulting in Reduced Susceptibility to the WHO Recommended First-line Regimen in Nearly Half of Newly Diagnosed HIV-infected Patients (2017) (8)
- Divergence of delta and beta variants and SARS-CoV-2 evolved in prolonged infection into distinct serological phenotypes (2021) (8)
- Reduced amplification efficiency of the RNA-dependent-RNA-polymerase target enables tracking of the Delta SARS-CoV-2 variant using routine diagnostic tests (2021) (8)
- The effect of interventions on the transmission and spread of HIV in South Africa: a phylodynamic analysis (2019) (8)
- 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 (2015) (8)
- Effectiveness of the Ad26.Cov2.S Vaccine in Health Care Workers in South Africa (2021) (8)
- Chikungunya virus ECSA lineage reintroduction in the northeasternmost region of Brazil. (2021) (8)
- Loss of recognition of SARS-CoV-2 B.1.351 variant spike epitopes but overall preservation of T cell immunity (2021) (7)
- Sociobehavioral and community predictors of unsuppressed HIV viral load: multilevel results from a hyperendemic rural South African population (2019) (7)
- Improving HIV proteome annotation: new features of BioAfrica HIV Proteomics Resource (2016) (7)
- HTLV-1aA introduction into Brazil and its association with the trans-Atlantic slave trade. (2017) (7)
- Ethical issues associated with HIV molecular epidemiology: a qualitative exploratory study using inductive analytic approaches (2019) (7)
- Protocol: Leveraging a demographic and health surveillance system for Covid-19 Surveillance in rural KwaZulu-Natal (2020) (7)
- Genomic epidemiology of SARS-CoV-2 in Mauritius reveals a new wave of infections dominated by the B.1.1.318, a variant under investigation (2021) (7)
- Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes (2020) (7)
- Human Retrovirus Codon Usage from tRNA Point of View: Therapeutic Insights (2013) (6)
- Implementation of an efficient SARS-CoV-2 specimen pooling strategy for high throughput diagnostic testing (2021) (6)
- Naturally-acquired immunity in Syrian Golden Hamsters provides protection from re-exposure to emerging heterosubtypic SARS-CoV-2 variants B.1.1.7 and B.1.351 (2021) (6)
- Brief Report: Virologic Monitoring Can Be a Cost-Effective Strategy to Diagnose Treatment Failure on First-Line ART (2016) (6)
- Peer-mediated HIV assisted partner services to identify and link to care HIV-positive and HCV-positive people who inject drugs: a cohort study protocol (2021) (6)
- West Nile Virus in Brazil (2021) (6)
- Rates of virological suppression and drug resistance in adult HIV-1-positive patients attending primary healthcare facilities in KwaZulu-Natal, South Africa. (2017) (6)
- Combining Phylogenetic and Network Approaches to Identify HIV-1 Transmission Links in San Mateo County, California (2018) (6)
- Author Correction: T cell responses to SARS-CoV-2 spike cross-recognize Omicron (2022) (5)
- Rapid Replacement of SARS-CoV-2 Variants by Delta and Subsequent Arrival of Omicron, Uganda, 2021 (2022) (5)
- 2018 update to the HIV-TRePS system: the development of new computational models to predict HIV treatment outcomes, with or without a genotype, with enhanced usability for low-income settings (2018) (5)
- Impact of pretreatment low-abundance HIV-1 drug-resistant variants on virological failure among HIV-1/TB-co-infected individuals (2020) (5)
- Targeted Sanger sequencing to recover key mutations in SARS-CoV-2 variant genome assemblies produced by next-generation sequencing (2022) (5)
- Genomic epidemiology reveals how restriction measures shaped the SARS-CoV-2 epidemic in Brazil (2021) (5)
- External introductions helped drive and sustain the high incidence of HIV-1 in rural KwaZulu-Natal, South Africa (2017) (5)
- Comparison of SARS-CoV-2 sequencing using the ONT GridION and the Illumina MiSeq (2022) (5)
- Illumina Nextera DNA Flex library construction and sequencing for SARS-CoV-2: Adapting COVID-19 ARTIC protocol v1 (2020) (5)
- SARS-CoV-2 shifting transmission dynamics and hidden reservoirs limited the efficacy of public health interventions in Italy (2020) (4)
- Oral abstracts of the 21st International AIDS Conference 18–22 July 2016, Durban, South Africa (2016) (4)
- Oral abstracts of the 21st International AIDS Conference 18–22 July 2016, Durban, South Africa (2016) (4)
- Sequence of the env gene of some KwaZulu-Natal, South African strains of HTLV type I. (1999) (4)
- High levels of drug resistance after failure of first-line antiretroviral therapy in rural South Africa: impact on standardised second-line regimens (2012) (4)
- Socio-behavioural and community predictors of unsuppressed viral load: multi-level results from a hyper-endemic rural South African population. (2019) (4)
- Factors influencing HIV-1 phylogenetic clustering (2019) (4)
- Molecular Characterization of the Human Immunodeficiency Virus Type 1 in Women and Their Vertically Infected Children. (2015) (4)
- Analysis of Dominant HIV Quasispecies Suggests Independent Viral Evolution Within Spinal Granulomas Coinfected with Mycobacterium tuberculosis and HIV-1 Subtype C. (2016) (4)
- New nomenclature for mpox (monkeypox) and monkeypox virus clades (2023) (3)
- The CNS in the face of ART contains T cell origin HIV which can lead to drug resistance (2019) (3)
- Genomic surveillance of Rift Valley fever virus: from sequencing to lineage assignment (2022) (3)
- HIV viral load and pregnancy loss: Results from a population-based cohort study in rural KwaZulu-Natal, South Africa. (2020) (3)
- Pairwise diversity and tMRCA as potential markers for HIV infection recency (2017) (3)
- Voices of biotech research (2021) (3)
- Patterns of genomic site inheritance in HIV-1M inter-subtype recombinants delineate the most likely genomic sites of subtype-specific adaptation (2018) (3)
- Epidemiologic History and Genetic Diversity Origins of Chikungunya and Dengue Viruses, Paraguay (2021) (3)
- Correction for Giovanetti et al., “Yellow Fever Virus Reemergence and Spread in Southeast Brazil, 2016–2019” (2020) (3)
- New Genomes from the Congo Basin Expand History of CRF01_AE Origin and Dissemination (2020) (3)
- An Investigation of Classification Algorithms for Predicting HIV Drug Resistance without Genotype Resistance Testing (2013) (3)
- HIV & TB Drug Resistance and Clinical Management Case Book (2013) (3)
- Mosquito-Borne Viral Diseases: Control and Prevention in the Genomics Era (2019) (3)
- Author Correction: T cell responses to SARS-CoV-2 spike cross-recognize Omicron (2022) (3)
- Identification and characterization of previously described epitopes in HIV-1 subtypes B, C, F and BF in Brazil. (2007) (2)
- Comparison of SARS-CoV-2 sequencing using the ONT GridION and the Illumina MiSeq (2022) (2)
- Chikungunya virus ECSA lineage reintroduction in the northeasternmost region of Brazil (2021) (2)
- Infectious diseases science in Africa takes a leading place in the world (2022) (2)
- SARS-CoV-2 Genetic Diversity and Lineage Dynamics in Egypt during the First 18 Months of the Pandemic (2022) (2)
- A Retrospective Overview of Zika Virus Evolution in the Midwest of Brazil (2022) (2)
- A genome-wide polygenic approach to HIV acquisition uncovers link to inflammatory bowel disease and identifies potential novel genetic variants (2017) (2)
- HIV-1 Evolutionary Dynamics under Nonsuppressive Antiretroviral Therapy (2021) (2)
- Adding a Voice to the Unique Ethical Considerations in Molecular HIV Surveillance (2020) (1)
- C URRENT OPINION Concentrated HIV subepidemics in generalized epidemic settings (2014) (1)
- Yellow fever virus spread in Rio de Janeiro and Espírito Santo, 2016-2019: Phylodynamic assessment to improve intervention strategies (2019) (1)
- Erratum for O’Donnell et al., “Early Detection of Emergent Extensively Drug-Resistant Tuberculosis by Flow Cytometry-Based Phenotyping and Whole-Genome Sequencing” (2019) (1)
- Portable sequencing in the field and the classroom: a retrospective examination of the circulation of DENV1 and DENV2 in Brazil (2020) (1)
- Human T cell lymphotropic virus type 1 (HTLV-1) infection increases the CD4 count in human immunodeficiency virus type 1 (HIV-1) infected patients submitted to antiretroviral therapy (ARV) (2014) (1)
- The role of high-risk geographies in the perpetuation of the HIV epidemic in rural South Africa: A spatial molecular epidemiology study (2022) (1)
- Genomic epidemiology reveals the impact of national and international restrictions measures on the SARS-CoV-2 epidemic in Brazil (2022) (1)
- Undetectable proviral deoxyribonucleic acid in an adolescent perinatally infected with human immunodeficiency virus-1C and on long-term antiretroviral therapy resulted in viral rebound following antiretroviral therapy termination (2019) (1)
- Low-frequency HIV-1 drug resistance mutations in antiretroviral naïve individuals in Botswana (2022) (1)
- Using the Emanuel Framework to Explore the Ethical Issues Raised in a Participatory Visual Research Project in Rural South Africa (2021) (1)
- Acquired HIV drug resistance and virologic monitoring in a HIV hyper-endemic setting in KwaZulu-Natal Province, South Africa (2021) (1)
- Complementation can maintain a quasispecies of drug sensitive and resistant HIV (2020) (1)
- Primary health care implementation of an antiretroviral treatment failure clinic model in rural KwaZulu-Natal (2012) (1)
- HIV-1 drug resistance in adults and adolescents on protease inhibitor-based antiretroviral treatment in KwaZulu-Natal Province, South Africa (2021) (1)
- Libya should stop denying scientific evidence on HIV (2007) (1)
- Universal Test and Treat and the HIV epidemic in rural South Africa ; a community cluster randomized trial (2017) (1)
- Principles of HIV drug resistance for clinical management in South Africa (2012) (1)
- CD 4 + T-cell count may not be a useful strategy to monitor antiretroviral therapy response in HTLV-1 / HIV co-infected patients (2018) (1)
- Title Evolution and spatial dissemination of the highly pathogenicAsian H 5 avian influenza viruses (2017) (0)
- SARS-CoV-2 evolves increased infection elicited cell death and fusion in an immunosuppressed individual (2022) (0)
- A34 Automated profiling of the human virome from raw metagenomic data (2017) (0)
- Explorer The RNA Virus Database (2018) (0)
- Early genomic detection of the Cosmopolitan Genotype of Dengue Virus 2 in Angola, 2018 (2018) (0)
- SARS-CoV-2 shifting transmission dynamics and hidden reservoirs potentially limit efficacy of public health interventions in Italy (2021) (0)
- Performance of Rapid Antigen Tests in Identifying Omicron Ba.4 and Ba.5 Infections in South Africa (2023) (0)
- The effect of interventions on the transmission and spread of HIV in South Africa: a phylodynamic analysis (2019) (0)
- Genomics and public health (2021) (0)
- The origin of HTLV-1 in southern Bahia by b , go b , phylogenetic , mtDNA and β-globin analysis (2015) (0)
- Human T cell lymphotropic virus type 1 (HTLV-1) infection increases the CD4 count in human immunodeficiency virus type 1 (HIV-1) infected patients submitted to antiretroviral therapy (ARV) (2014) (0)
- Deep sequencing analysis of Human T cell lymphotropic virus type 1 (HTLV-1) long terminal repeat (LTR) region of tropical spastic paraparesis (TSP)/HTLV-1 associated myelopathy (HAM) and asymptomatic carriers (2014) (0)
- Molecular Epidemiology of Human Immunodeficiency Virus type 2 Infection in KwaZulu Natal Province, South Africa (2010) (0)
- Combination HIV prevention and the battle of the sexes (2015) (0)
- Differential Distribution and Evolution of HIV-1 RNA Variants in the Gastrointestinal Tract of Antiretroviral Naïve African AIDS Patients with Diarrhea and (or) Weight Loss (2019) (0)
- mining HIV-1 virological failure in plasma and dried blood spots (2013) (0)
- Ethics and governance challenges related to genomic data sharing in southern Africa: the case of SARS-CoV-2 (2022) (0)
- PhyloType schematic of the various clusters found in the analyses of the Bayesian pol tree topology. (2014) (0)
- Molecular characterization of the brazilian HTLV-1 sequences to vaccine design (2006) (0)
- Infectious diseases science in Africa takes a leading place in the world (2022) (0)
- A19 Genetic markers for protease inhibitor drug resistance in regions outside of the protease gene (2017) (0)
- 22nd International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology (2018) (0)
- Reply to Molldrem. (2023) (0)
- Unlocking the efficiency of genomics laboratories with robotic liquid-handling (2020) (0)
- Human Immunodeficiency Virus Type 1 Subtype C Drug Resistance Analyses and Protein Bioinformatics Resource Development. (2012) (0)
- Human immunodeficiency virus (HIV) proteomics resource at BioAfrica (2015) (0)
- Genome-wide association study of HIV whole genome sequences validated using drug 1 resistance 2 (2016) (0)
- Author response: HIV status alters disease severity and immune cell responses in Beta variant SARS-CoV-2 infection wave (2021) (0)
- Investigating the origin and nature of epidemics in the history of HIV-1 (2007) (0)
- HIV-1 Molecular Characterization and Transmitted Drug Resistance Prevalence among Treatment-Naïve Individuals (2017) (0)
- HIV & Hepatitis in the Americas 28–30 April 2016, Mexico City, Mexico (2016) (0)
- SARS-CoV-2 variants from COVID-19 positive cases in the Free State province, South Africa from July 2020 to December 2021 (2022) (0)
- Pan-genomics of virus and its applications (2020) (0)
- industrial and developing countries with the shared goal of ending the HIV/AIDS pandemic. (2015) (0)
- Early Genomic Detection of an Outbreak of Dengue Virus 2 Cosmopolitan Genotype in Angola, 2018 (2018) (0)
- Antiretroviral therapy adherence patterns, virological suppression, and emergence of drug resistance: A nested case–control study from Uganda and South Africa (2022) (0)
- The potential utility of Xpert® MTB/RIF for real-time surveillance of drug resistance in rural KwaZulu-Natal, South Africa (2012) (0)
- A40 Persistent circulation of highly divergent HIV-1M lineages in the Congo Basin Region (2017) (0)
- An automated method for the identification of Dengue, Zika, Yellow Fever and Chikungunya virus species and genotypes (2017) (0)
- HIV-specific CD8+ T-cells in tonsils express exhaustive TRM-like signatures (2021) (0)
- Investigating the origin of the HTLV-1 in Brazil using host and virus genetic data (2005) (0)
- Evaluation of miniaturized Illumina DNA preparation protocols for SARS-CoV-2 whole genome sequencing (2023) (0)
- Erratum: Correction for Giovanetti et al., "Yellow Fever Virus Reemergence and Spread in Southeast Brazil, 2016-2019" (Journal of virology (2019) 94 1 PII: e02008-19) (2020) (0)
- Global disparities in SARS-CoV-2 genomic surveillance (2022) (0)
- SARS-CoV-2 Africa dashboard for real-time COVID-19 information (2022) (0)
- Space-time clustering of recently-diagnosed tuberculosis and impact of ART scale-up: Evidence from an HIV hyper-endemic rural South African population (2019) (0)
- Correction: Short Report: Early genomic detection of SARS-CoV-2 P.1 variant in Northeast Brazil (2022) (0)
- Deep sequencing analysis of Human T cell lymphotropic virus type 1 (HTLV-1) long terminal repeat (LTR) region of tropical spastic paraparesis (TSP)/HTLV-1 associated myelopathy (HAM) and asymptomatic carriers (2014) (0)
- 2021 update to HIV-TRePS: a highly flexible and accurate system for the prediction of treatment response from incomplete baseline information in different healthcare settings. (2021) (0)
- Consequences of rpoB mutations missed by the GenoType MTBDRplus assay in a programmatic setting in South Africa (2023) (0)
- Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis (2019) (0)
- Deep Sequencing Analysis of Human T Cell Lymphotropic Virus Type 1 Long Terminal Repeat 5' Region from Patients with Tropical Spastic Paraparesis/Human T Cell Lymphotropic Virus Type 1-Associated Myelopathy and Asymptomatic Carriers. (2016) (0)
- Diversity and molecular epidemiology of HIV-1 in Cape Town; 1984 to 2010 (2011) (0)
- Molecular Epidemiology and Trends in HIV-1 Transmitted Drug Resistance in Mozambique 1999–2018 (2022) (0)
- A1 Pairwise diversity and tMRCA as potential markers of HIV infection recency (2018) (0)
- Ethical issues associated with HIV molecular epidemiology: a qualitative exploratory study using inductive analytic approaches (2019) (0)
- HIV specific CD8+ TRM-like cells in tonsils express exhaustive signatures in the absence of natural HIV control (2022) (0)
- Track B Clinical Science (2012) (0)
- West Nile virus detection in horses in three Brazilian states (2021) (0)
- Omicron infection enhances Delta antibody immunity in vaccinated persons (2022) (0)
- Sequence analysis Genome Detective : an automated system for virus identification from high-throughput sequencing data (2018) (0)
- Track B Clinical Science (2012) (0)
- A67 Use of next-generation whole-genome sequencing to understand drug-resistant Mycobacterium tuberculosis in Botswana (2018) (0)
- Genomic surveillance of Rift Valley fever virus: from sequencing to lineage assignment (2022) (0)
- Molecular Epidemiology and Diversity of SARS-CoV-2 in Ethiopia, 2020–2022 (2023) (0)
- Genomic epidemiology of SARS-CoV-2 during the first four waves in Mozambique (2023) (0)
- SeqPanther: Sequence manipulation and mutation statistics toolset (2023) (0)
- Short Communication Evidence for recombination in natural populations of porcine circovirus type 2 in Hong Kong and mainland China (2007) (0)
- HIV cell-to-cell spread slows evolution of drug resistance (2020) (0)
- The geography and inter-community configuration of new sexual partnership formation in a rural South African population over fourteen years (2003–2016) (2022) (0)
- Development and evaluation of an affordable real-time qualitative assay for deter-1 mining HIV-1 virological failure in plasma and dried blood spots 2 3 (2013) (0)
- Advancing detection and response capacities for emerging and re-emerging pathogens in Africa (2022) (0)
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