Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 25
Filtrar
1.
Nature ; 626(7997): 145-150, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-38122820

RESUMO

How likely is it to become infected by SARS-CoV-2 after being exposed? Almost everyone wondered about this question during the COVID-19 pandemic. Contact-tracing apps1,2 recorded measurements of proximity3 and duration between nearby smartphones. Contacts-individuals exposed to confirmed cases-were notified according to public health policies such as the 2 m, 15 min guideline4,5, despite limited evidence supporting this threshold. Here we analysed 7 million contacts notified by the National Health Service COVID-19 app6,7 in England and Wales to infer how app measurements translated to actual transmissions. Empirical metrics and statistical modelling showed a strong relation between app-computed risk scores and actual transmission probability. Longer exposures at greater distances had risk similar to that of shorter exposures at closer distances. The probability of transmission confirmed by a reported positive test increased initially linearly with duration of exposure (1.1% per hour) and continued increasing over several days. Whereas most exposures were short (median 0.7 h, interquartile range 0.4-1.6), transmissions typically resulted from exposures lasting between 1 h and several days (median 6 h, interquartile range 1.4-28). Households accounted for about 6% of contacts but 40% of transmissions. With sufficient preparation, privacy-preserving yet precise analyses of risk that would inform public health measures, based on digital contact tracing, could be performed within weeks of the emergence of a new pathogen.


Assuntos
COVID-19 , Busca de Comunicante , Aplicativos Móveis , Saúde Pública , Medição de Risco , Humanos , Busca de Comunicante/métodos , Busca de Comunicante/estatística & dados numéricos , COVID-19/epidemiologia , COVID-19/transmissão , Pandemias , SARS-CoV-2 , Medicina Estatal , Fatores de Tempo , Inglaterra/epidemiologia , País de Gales/epidemiologia , Modelos Estatísticos , Características da Família , Saúde Pública/métodos , Saúde Pública/tendências
2.
J Antimicrob Chemother ; 78(3): 656-664, 2023 03 02.
Artigo em Inglês | MEDLINE | ID: mdl-36738248

RESUMO

BACKGROUND: Next-generation sequencing (NGS) is gradually replacing Sanger sequencing (SS) as the primary method for HIV genotypic resistance testing. However, there are limited systematic data on comparability of these methods in a clinical setting for the presence of low-abundance drug resistance mutations (DRMs) and their dependency on the variant-calling thresholds. METHODS: To compare the HIV-DRMs detected by SS and NGS, we included participants enrolled in the Swiss HIV Cohort Study (SHCS) with SS and NGS sequences available with sample collection dates ≤7 days apart. We tested for the presence of HIV-DRMs and compared the agreement between SS and NGS at different variant-calling thresholds. RESULTS: We included 594 pairs of SS and NGS from 527 SHCS participants. Males accounted for 80.5% of the participants, 76.3% were ART naive at sample collection and 78.1% of the sequences were subtype B. Overall, we observed a good agreement (Cohen's kappa >0.80) for HIV-DRMs for variant-calling thresholds ≥5%. We observed an increase in low-abundance HIV-DRMs detected at lower thresholds [28/417 (6.7%) at 10%-25% to 293/812 (36.1%) at 1%-2% threshold]. However, such low-abundance HIV-DRMs were overrepresented in ART-naive participants and were in most cases not detected in previously sampled sequences suggesting high sequencing error for thresholds <3%. CONCLUSIONS: We found high concordance between SS and NGS but also a substantial number of low-abundance HIV-DRMs detected only by NGS at lower variant-calling thresholds. Our findings suggest that a substantial fraction of the low-abundance HIV-DRMs detected at thresholds <3% may represent sequencing errors and hence should not be overinterpreted in clinical practice.


Assuntos
Fármacos Anti-HIV , Infecções por HIV , Soropositividade para HIV , HIV-1 , Masculino , Humanos , Infecções por HIV/tratamento farmacológico , Estudos de Coortes , Farmacorresistência Viral/genética , Carga Viral , Soropositividade para HIV/tratamento farmacológico , Mutação , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Genótipo , Fármacos Anti-HIV/uso terapêutico
3.
Nat Commun ; 14(1): 858, 2023 02 22.
Artigo em Inglês | MEDLINE | ID: mdl-36813770

RESUMO

The NHS COVID-19 app was launched in England and Wales in September 2020, with a Bluetooth-based contact tracing functionality designed to reduce transmission of SARS-CoV-2. We show that user engagement and the app's epidemiological impacts varied according to changing social and epidemic characteristics throughout the app's first year. We describe the interaction and complementarity of manual and digital contact tracing approaches. Results of our statistical analyses of anonymised, aggregated app data include that app users who were recently notified were more likely to test positive than app users who were not recently notified, by a factor that varied considerably over time. We estimate that the app's contact tracing function alone averted about 1 million cases (sensitivity analysis 450,000-1,400,000) during its first year, corresponding to 44,000 hospital cases (SA 20,000-60,000) and 9,600 deaths (SA 4600-13,000).


Assuntos
COVID-19 , Aplicativos Móveis , Humanos , SARS-CoV-2 , Medicina Estatal , País de Gales , Busca de Comunicante/métodos , Inglaterra
4.
Philos Trans A Math Phys Eng Sci ; 380(2233): 20210304, 2022 Oct 03.
Artigo em Inglês | MEDLINE | ID: mdl-35965459

RESUMO

The SARS-CoV-2 epidemic has been extended by the evolution of more transmissible viral variants. In autumn 2020, the B.1.177 lineage became the dominant variant in England, before being replaced by the B.1.1.7 (Alpha) lineage in late 2020, with the sweep occurring at different times in each region. This period coincided with a large number of non-pharmaceutical interventions (e.g. lockdowns) to control the epidemic, making it difficult to estimate the relative transmissibility of variants. In this paper, we model the spatial spread of these variants in England using a meta-population agent-based model which correctly characterizes the regional variation in cases and distribution of variants. As a test of robustness, we additionally estimated the relative transmissibility of multiple variants using a statistical model based on the renewal equation, which simultaneously estimates the effective reproduction number R. Relative to earlier variants, the transmissibility of B.1.177 is estimated to have increased by 1.14 (1.12-1.16) and that of Alpha by 1.71 (1.65-1.77). The vaccination programme starting in December 2020 is also modelled. Counterfactual simulations demonstrate that the vaccination programme was essential for reopening in March 2021, and that if the January lockdown had started one month earlier, up to 30 k (24 k-38 k) deaths could have been prevented. This article is part of the theme issue 'Technical challenges of modelling real-life epidemics and examples of overcoming these'.


Assuntos
COVID-19 , SARS-CoV-2 , COVID-19/epidemiologia , Controle de Doenças Transmissíveis , Humanos , SARS-CoV-2/genética , Estações do Ano
5.
Virus Evol ; 8(1): veac022, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35402002

RESUMO

Set-point viral load (SPVL), a common measure of human immunodeficiency virus (HIV)-1 virulence, is partially determined by viral genotype. Epidemiological evidence suggests that this viral property has been under stabilising selection, with a typical optimum for the virus between 104 and 105 copies of viral RNA per ml. Here we aimed to detect transmission fitness differences between viruses from individuals with different SPVLs directly from phylogenetic trees inferred from whole-genome sequences. We used the local branching index (LBI) as a proxy for transmission fitness. We found that LBI is more sensitive to differences in infectiousness than to differences in the duration of the infectious state. By analysing subtype-B samples from the Bridging the Evolution and Epidemiology of HIV in Europe project, we inferred a significant positive relationship between SPVL and LBI up to approximately 105 copies/ml, with some evidence for a peak around this value of SPVL. This is evidence of selection against low values of SPVL in HIV-1 subtype-B strains, likely related to lower infectiousness, and perhaps a peak in the transmission fitness in the expected range of SPVL. The less prominent signatures of selection against higher SPVL could be explained by an inherent limit of the method or the deployment of antiretroviral therapy.

6.
Science ; 375(6580): 540-545, 2022 02 04.
Artigo em Inglês | MEDLINE | ID: mdl-35113714

RESUMO

We discovered a highly virulent variant of subtype-B HIV-1 in the Netherlands. One hundred nine individuals with this variant had a 0.54 to 0.74 log10 increase (i.e., a ~3.5-fold to 5.5-fold increase) in viral load compared with, and exhibited CD4 cell decline twice as fast as, 6604 individuals with other subtype-B strains. Without treatment, advanced HIV-CD4 cell counts below 350 cells per cubic millimeter, with long-term clinical consequences-is expected to be reached, on average, 9 months after diagnosis for individuals in their thirties with this variant. Age, sex, suspected mode of transmission, and place of birth for the aforementioned 109 individuals were typical for HIV-positive people in the Netherlands, which suggests that the increased virulence is attributable to the viral strain. Genetic sequence analysis suggests that this variant arose in the 1990s from de novo mutation, not recombination, with increased transmissibility and an unfamiliar molecular mechanism of virulence.


Assuntos
Infecções por HIV/virologia , HIV-1/patogenicidade , Adulto , Fármacos Anti-HIV/uso terapêutico , Contagem de Linfócito CD4 , Evolução Molecular , Feminino , Genoma Viral , Genótipo , Infecções por HIV/tratamento farmacológico , Infecções por HIV/imunologia , Infecções por HIV/transmissão , HIV-1/genética , HIV-1/fisiologia , Humanos , Masculino , Mutação , Países Baixos , Filogenia , Carga Viral , Virulência
7.
PLoS Comput Biol ; 17(7): e1009146, 2021 07.
Artigo em Inglês | MEDLINE | ID: mdl-34252083

RESUMO

SARS-CoV-2 has spread across the world, causing high mortality and unprecedented restrictions on social and economic activity. Policymakers are assessing how best to navigate through the ongoing epidemic, with computational models being used to predict the spread of infection and assess the impact of public health measures. Here, we present OpenABM-Covid19: an agent-based simulation of the epidemic including detailed age-stratification and realistic social networks. By default the model is parameterised to UK demographics and calibrated to the UK epidemic, however, it can easily be re-parameterised for other countries. OpenABM-Covid19 can evaluate non-pharmaceutical interventions, including both manual and digital contact tracing, and vaccination programmes. It can simulate a population of 1 million people in seconds per day, allowing parameter sweeps and formal statistical model-based inference. The code is open-source and has been developed by teams both inside and outside academia, with an emphasis on formal testing, documentation, modularity and transparency. A key feature of OpenABM-Covid19 are its Python and R interfaces, which has allowed scientists and policymakers to simulate dynamic packages of interventions and help compare options to suppress the COVID-19 epidemic.


Assuntos
COVID-19/prevenção & controle , Busca de Comunicante , Análise de Sistemas , COVID-19/epidemiologia , COVID-19/transmissão , COVID-19/virologia , Teste para COVID-19 , Vacinas contra COVID-19/administração & dosagem , Surtos de Doenças , Humanos , Distanciamento Físico , Quarentena , SARS-CoV-2/isolamento & purificação
8.
Nature ; 594(7863): 408-412, 2021 06.
Artigo em Inglês | MEDLINE | ID: mdl-33979832

RESUMO

The COVID-19 pandemic has seen the emergence of digital contact tracing to help to prevent the spread of the disease. A mobile phone app records proximity events between app users, and when a user tests positive for COVID-19, their recent contacts can be notified instantly. Theoretical evidence has supported this new public health intervention1-6, but its epidemiological impact has remained uncertain7. Here we investigate the impact of the National Health Service (NHS) COVID-19 app for England and Wales, from its launch on 24 September 2020 to the end of December 2020. It was used regularly by approximately 16.5 million users (28% of the total population), and sent approximately 1.7 million exposure notifications: 4.2 per index case consenting to contact tracing. We estimated that the fraction of individuals notified by the app who subsequently showed symptoms and tested positive (the secondary attack rate (SAR)) was 6%, similar to the SAR for manually traced close contacts. We estimated the number of cases averted by the app using two complementary approaches: modelling based on the notifications and SAR gave an estimate of 284,000 (central 95% range of sensitivity analyses 108,000-450,000), and statistical comparison of matched neighbouring local authorities gave an estimate of 594,000 (95% confidence interval 317,000-914,000). Approximately one case was averted for each case consenting to notification of their contacts. We estimated that for every percentage point increase in app uptake, the number of cases could be reduced by 0.8% (using modelling) or 2.3% (using statistical analysis). These findings support the continued development and deployment of such apps in populations that are awaiting full protection from vaccines.


Assuntos
COVID-19/epidemiologia , COVID-19/prevenção & controle , Busca de Comunicante/instrumentação , Busca de Comunicante/métodos , Aplicativos Móveis/estatística & dados numéricos , Número Básico de Reprodução , COVID-19/mortalidade , COVID-19/transmissão , Inglaterra/epidemiologia , Humanos , Mortalidade , Programas Nacionais de Saúde , Quarentena , País de Gales/epidemiologia
10.
Clin Infect Dis ; 72(1): 30-37, 2021 01 23.
Artigo em Inglês | MEDLINE | ID: mdl-31922537

RESUMO

BACKGROUND: Phylogenetic analysis can be used to assess human immunodeficiency virus (HIV) transmission in populations. We inferred the direction of HIV transmission using whole-genome HIV sequences from couples with known linked infection and known transmission direction. METHODS: Complete next-generation sequencing (NGS) data were obtained for 105 unique index-partner sample pairs from 32 couples enrolled in the HIV Prevention Trials Network (HPTN) 052 study (up to 2 samples/person). Index samples were obtained up to 5.5 years before partner infection; partner samples were obtained near the time of seroconversion. The bioinformatics method, phyloscanner, was used to infer transmission direction. Analyses were performed using samples from individual sample pairs, samples from all couples (1 sample/person; group analysis), and all available samples (multisample group analysis). Analysis was also performed using NGS data from defined regions of the HIV genome (gag, pol, env). RESULTS: Using whole-genome NGS data, transmission direction was inferred correctly (index to partner) for 98 of 105 (93.3%) of the individual sample pairs, 99 of 105 (94.3%) sample pairs using group analysis, and 31 of the 32 couples (96.9%) using multisample group analysis. There were no cases where the incorrect transmission direction (partner to index) was inferred. The accuracy of the method was higher with greater time between index and partner sample collection. Pol region sequences performed better than env or gag sequences for inferring transmission direction. CONCLUSIONS: We demonstrate the potential of a phylogenetic method to infer the direction of HIV transmission between 2 individuals using whole-genome and pol NGS data.


Assuntos
Infecções por HIV , HIV-1 , Infecções por HIV/prevenção & controle , HIV-1/genética , Humanos , Filogenia
11.
Lancet Digit Health ; 2(12): e658-e666, 2020 12.
Artigo em Inglês | MEDLINE | ID: mdl-33078140

RESUMO

Background: In May 2020, the UK National Health Service (NHS) Test and Trace programme was launched in England in response to the COVID-19 pandemic. The programme was first rolled out on the Isle of Wight and included version 1 of the NHS contact tracing app. The aim of the study was to make a preliminary assessment of the epidemiological impact of the Test and Trace programme using publicly available data. Methods: We used COVID-19 daily case data from Public Health England to infer incidence of new infections and estimate the reproduction number (R) for each of the 150 Upper-Tier Local Authorities (UTLAs) in England and nationally, before and after the launch of the Test and Trace programme on the Isle of Wight. We used Bayesian and maximum-likelihood methods to estimate R and compared the Isle of Wight with other UTLAs using a synthetic control method. Findings: We observed significant decreases in incidence and R on the Isle of Wight immediately after the launch of the Test and Trace programme. The Isle of Wight had a marked reduction in R, from 1·3 before the Test and Trace programme to 0·5 after by one of our measures, and went from having the third highest R before the Test and Trace programme, to the twelfth lowest afterwards compared with other UTLAs. Interpretation: Our results show that the epidemic on the Isle of Wight was controlled quickly and effectively after the launch of Test and Trace. Our findings highlight the need for further research to determine the causes of the reduction in the spread of the disease, as these could be translated into local and national non-pharmaceutical intervention strategies in the period before a treatment or vaccination for COVID-19 becomes available. Funding: Li Ka Shing Foundation and UK Economic and Social Research Council.


Assuntos
Teste para COVID-19/métodos , COVID-19/epidemiologia , Busca de Comunicante/métodos , Ilhas/epidemiologia , Adolescente , Adulto , Fatores Etários , Idoso , COVID-19/diagnóstico , COVID-19/prevenção & controle , Teste para COVID-19/estatística & dados numéricos , Criança , Pré-Escolar , Busca de Comunicante/estatística & dados numéricos , Inglaterra/epidemiologia , Humanos , Lactente , Recém-Nascido , Funções Verossimilhança , Pessoa de Meia-Idade , Medicina Estatal , Tiocarbamatos , Reino Unido/epidemiologia , Adulto Jovem
12.
J Clin Microbiol ; 58(10)2020 09 22.
Artigo em Inglês | MEDLINE | ID: mdl-32669382

RESUMO

Viral genetic sequencing can be used to monitor the spread of HIV drug resistance, identify appropriate antiretroviral regimes, and characterize transmission dynamics. Despite decreasing costs, next-generation sequencing (NGS) is still prohibitively costly for routine use in generalized HIV epidemics in low- and middle-income countries. Here, we present veSEQ-HIV, a high-throughput, cost-effective NGS sequencing method and computational pipeline tailored specifically to HIV, which can be performed using leftover blood drawn for routine CD4 cell count testing. This method overcomes several major technical challenges that have prevented HIV sequencing from being used routinely in public health efforts; it is fast, robust, and cost-efficient, and generates full genomic sequences of diverse strains of HIV without bias. The complete veSEQ-HIV pipeline provides viral load estimates and quantitative summaries of drug resistance mutations; it also exploits information on within-host viral diversity to construct directed transmission networks. We evaluated the method's performance using 1,620 plasma samples collected from individuals attending 10 large urban clinics in Zambia as part of the HPTN 071-2 study (PopART Phylogenetics). Whole HIV genomes were recovered from 91% of samples with a viral load of >1,000 copies/ml. The cost of the assay (30 GBP per sample) compares favorably with existing VL and HIV genotyping tests, proving an affordable option for combining HIV clinical monitoring with molecular epidemiology and drug resistance surveillance in low-income settings.


Assuntos
Fármacos Anti-HIV , Infecções por HIV , HIV-1 , Fármacos Anti-HIV/uso terapêutico , Farmacorresistência Viral/genética , Genômica , Infecções por HIV/diagnóstico , Infecções por HIV/tratamento farmacológico , Infecções por HIV/epidemiologia , Humanos , Carga Viral , Zâmbia
13.
Science ; 368(6491)2020 05 08.
Artigo em Inglês | MEDLINE | ID: mdl-32234805

RESUMO

The newly emergent human virus SARS-CoV-2 (severe acute respiratory syndrome-coronavirus 2) is resulting in high fatality rates and incapacitated health systems. Preventing further transmission is a priority. We analyzed key parameters of epidemic spread to estimate the contribution of different transmission routes and determine requirements for case isolation and contact tracing needed to stop the epidemic. Although SARS-CoV-2 is spreading too fast to be contained by manual contact tracing, it could be controlled if this process were faster, more efficient, and happened at scale. A contact-tracing app that builds a memory of proximity contacts and immediately notifies contacts of positive cases can achieve epidemic control if used by enough people. By targeting recommendations to only those at risk, epidemics could be contained without resorting to mass quarantines ("lockdowns") that are harmful to society. We discuss the ethical requirements for an intervention of this kind.


Assuntos
Betacoronavirus , Telefone Celular , Busca de Comunicante/métodos , Infecções por Coronavirus/prevenção & controle , Infecções por Coronavirus/transmissão , Aplicativos Móveis , Pandemias/prevenção & controle , Pneumonia Viral/prevenção & controle , Pneumonia Viral/transmissão , Algoritmos , Doenças Assintomáticas , Número Básico de Reprodução , COVID-19 , China/epidemiologia , Busca de Comunicante/ética , Infecções por Coronavirus/epidemiologia , Epidemias/prevenção & controle , Humanos , Controle de Infecções , Aplicativos Móveis/ética , Modelos Teóricos , Pneumonia Viral/epidemiologia , Probabilidade , Quarentena , SARS-CoV-2 , Fatores de Tempo
14.
Lancet HIV ; 7(3): e173-e183, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-31953184

RESUMO

BACKGROUND: International and global organisations advocate targeting interventions to areas of high HIV prevalence (ie, hotspots). To better understand the potential benefits of geo-targeted control, we assessed the extent to which HIV hotspots along Lake Victoria sustain transmission in neighbouring populations in south-central Uganda. METHODS: We did a population-based survey in Rakai, Uganda, using data from the Rakai Community Cohort Study. The study surveyed all individuals aged 15-49 years in four high-prevalence Lake Victoria fishing communities and 36 neighbouring inland communities. Viral RNA was deep sequenced from participants infected with HIV who were antiretroviral therapy-naive during the observation period. Phylogenetic analysis was used to infer partial HIV transmission networks, including direction of transmission. Reconstructed networks were interpreted through data for current residence and migration history. HIV transmission flows within and between high-prevalence and low-prevalence areas were quantified adjusting for incomplete sampling of the population. FINDINGS: Between Aug 10, 2011, and Jan 30, 2015, data were collected for the Rakai Community Cohort Study. 25 882 individuals participated, including an estimated 75·7% of the lakeside population and 16·2% of the inland population in the Rakai region of Uganda. 5142 participants were HIV-positive (2703 [13·7%] in inland and 2439 [40·1%] in fishing communities). 3878 (75·4%) people who were HIV-positive did not report antiretroviral therapy use, of whom 2652 (68·4%) had virus deep-sequenced at sufficient quality for phylogenetic analysis. 446 transmission networks were reconstructed, including 293 linked pairs with inferred direction of transmission. Adjusting for incomplete sampling, an estimated 5·7% (95% credibility interval 4·4-7·3) of transmissions occurred within lakeside areas, 89·2% (86·0-91·8) within inland areas, 1·3% (0·6-2·6) from lakeside to inland areas, and 3·7% (2·3-5·8) from inland to lakeside areas. INTERPRETATION: Cross-community HIV transmissions between Lake Victoria hotspots and surrounding inland populations are infrequent and when they occur, virus more commonly flows into rather than out of hotspots. This result suggests that targeted interventions to these hotspots will not alone control the epidemic in inland populations, where most transmissions occur. Thus, geographical targeting of high prevalence areas might not be effective for broader epidemic control depending on underlying epidemic dynamics. FUNDING: The Bill & Melinda Gates Foundation, the National Institute of Allergy and Infectious Diseases, the National Institute of Mental Health, the National Institute of Child Health and Development, the Division of Intramural Research of the National Institute for Allergy and Infectious Diseases, the World Bank, the Doris Duke Charitable Foundation, the Johns Hopkins University Center for AIDS Research, and the President's Emergency Plan for AIDS Relief through the Centers for Disease Control and Prevention.


Assuntos
Infecções por HIV/epidemiologia , Infecções por HIV/transmissão , Adolescente , Adulto , Feminino , Infecções por HIV/virologia , HIV-1/classificação , HIV-1/genética , HIV-1/isolamento & purificação , HIV-1/fisiologia , Humanos , Masculino , Pessoa de Meia-Idade , Filogenia , Prevalência , Características de Residência/estatística & dados numéricos , Uganda/epidemiologia , Adulto Jovem
15.
Nat Commun ; 10(1): 1411, 2019 03 29.
Artigo em Inglês | MEDLINE | ID: mdl-30926780

RESUMO

To prevent new infections with human immunodeficiency virus type 1 (HIV-1) in sub-Saharan Africa, UNAIDS recommends targeting interventions to populations that are at high risk of acquiring and passing on the virus. Yet it is often unclear who and where these 'source' populations are. Here we demonstrate how viral deep-sequencing can be used to reconstruct HIV-1 transmission networks and to infer the direction of transmission in these networks. We are able to deep-sequence virus from a large population-based sample of infected individuals in Rakai District, Uganda, reconstruct partial transmission networks, and infer the direction of transmission within them at an estimated error rate of 16.3% [8.8-28.3%]. With this error rate, deep-sequence phylogenetics cannot be used against individuals in legal contexts, but is sufficiently low for population-level inferences into the sources of epidemic spread. The technique presents new opportunities for characterizing source populations and for targeting of HIV-1 prevention interventions in Africa.


Assuntos
Epidemias , Infecções por HIV/epidemiologia , Infecções por HIV/transmissão , HIV-1/fisiologia , Sequenciamento de Nucleotídeos em Larga Escala , Filogenia , Adolescente , Adulto , África/epidemiologia , Sequência de Bases , Humanos , Pessoa de Meia-Idade , Adulto Jovem
16.
Virus Evol ; 5(1): vey038, 2019 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-30723550

RESUMO

Understanding which HIV-1 variants are most likely to be transmitted is important for vaccine design and predicting virus evolution. Since most infections are founded by single variants, it has been suggested that selection at transmission has a key role in governing which variants are transmitted. We show that the composition of the viral population within the donor at the time of transmission is also important. To support this argument, we developed a probabilistic model describing HIV-1 transmission in an untreated population, and parameterised the model using both within-host next generation sequencing data and population-level epidemiological data on heterosexual transmission. The most basic HIV-1 transmission models cannot explain simultaneously the low probability of transmission and the non-negligible proportion of infections founded by multiple variants. In our model, transmission can only occur when environmental conditions are appropriate (e.g. abrasions are present in the genital tract of the potential recipient), allowing these observations to be reconciled. As well as reproducing features of transmission in real populations, our model demonstrates that, contrary to expectation, there is not a simple link between the number of viral variants and the number of viral particles founding each new infection. These quantities depend on the timing of transmission, and infections can be founded with small numbers of variants yet large numbers of particles. Including selection, or a bias towards early transmission (e.g. due to treatment), acts to enhance this conclusion. In addition, we find that infections initiated by multiple variants are most likely to have derived from donors with intermediate set-point viral loads, and not from individuals with high set-point viral loads as might be expected. We therefore emphasise the importance of considering viral diversity in donors, and the timings of transmissions, when trying to discern the complex factors governing single or multiple variant transmission.

17.
Science ; 363(6424): 240, 2019 Jan 18.
Artigo em Inglês | MEDLINE | ID: mdl-30655436
18.
Virus Evol ; 4(1): vey007, 2018 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-29876136

RESUMO

Studying the evolution of viruses and their molecular epidemiology relies on accurate viral sequence data, so that small differences between similar viruses can be meaningfully interpreted. Despite its higher throughput and more detailed minority variant data, next-generation sequencing has yet to be widely adopted for HIV. The difficulty of accurately reconstructing the consensus sequence of a quasispecies from reads (short fragments of DNA) in the presence of large between- and within-host diversity, including frequent indels, may have presented a barrier. In particular, mapping (aligning) reads to a reference sequence leads to biased loss of information; this bias can distort epidemiological and evolutionary conclusions. De novo assembly avoids this bias by aligning the reads to themselves, producing a set of sequences called contigs. However contigs provide only a partial summary of the reads, misassembly may result in their having an incorrect structure, and no information is available at parts of the genome where contigs could not be assembled. To address these problems we developed the tool shiver to pre-process reads for quality and contamination, then map them to a reference tailored to the sample using corrected contigs supplemented with the user's choice of existing reference sequences. Run with two commands per sample, it can easily be used for large heterogeneous data sets. We used shiver to reconstruct the consensus sequence and minority variant information from paired-end short-read whole-genome data produced with the Illumina platform, for sixty-five existing publicly available samples and fifty new samples. We show the systematic superiority of mapping to shiver's constructed reference compared with mapping the same reads to the closest of 3,249 real references: median values of 13 bases called differently and more accurately, 0 bases called differently and less accurately, and 205 bases of missing sequence recovered. We also successfully applied shiver to whole-genome samples of Hepatitis C Virus and Respiratory Syncytial Virus. shiver is publicly available from https://github.com/ChrisHIV/shiver.

19.
Virus Res ; 250: 51-64, 2018 05 02.
Artigo em Inglês | MEDLINE | ID: mdl-29654800

RESUMO

For the production of viral genomic RNA, HIV-1 is dependent on an early viral protein, Tat, which is required for high-level transcription. The quantity of viral RNA detectable in blood of HIV-1 infected individuals varies dramatically, and a factor involved could be the efficiency of Tat protein variants to stimulate RNA transcription. HIV-1 virulence, measured by set-point viral load, has been observed to increase over time in the Netherlands and elsewhere. Investigation of tat gene evolution in clinical isolates could discover a role of Tat in this changing virulence. A dataset of 291 Dutch HIV-1 subtype B tat genes, derived from full-length HIV-1 genome sequences from samples obtained between 1985-2012, was used to analyse the evolution of Tat. Twenty-two patient-derived tat genes, and the control TatHXB2 were analysed for their capacity to stimulate expression of an LTR-luciferase reporter gene construct in diverse cell lines, as well as for their ability to complement a tat-defective HIV-1LAI clone. Analysis of 291 historical tat sequences from the Netherlands showed ample amino acid (aa) variation between isolates, although no specific mutations were selected for over time. Of note, however, the encoded protein varied its length over the years through the loss or gain of stop codons in the second exon. In transmission clusters, a selection against the shorter Tat86 ORF was apparent in favour of the more common Tat101 version, likely due to negative selection against Tat86 itself, although random drift, transmission bottlenecks, or linkage to other variants could also explain the observation. There was no correlation between Tat length and set-point viral load; however, the number of non-intermediate variants in our study was small. In addition, variation in the length of Tat did not significantly change its capacity to stimulate transcription. From 1985 till 2012, variation in the length of the HIV-1 subtype B tat gene is increasingly found in the Dutch epidemic. However, as Tat proteins did not differ significantly in their capacity to stimulate transcription elongation in vitro, the increased HIV-1 virulence seen in recent years could not be linked to an evolving viral Tat protein.


Assuntos
Códon/genética , Evolução Molecular , HIV-1/genética , Produtos do Gene tat do Vírus da Imunodeficiência Humana/genética , Regulação Viral da Expressão Gênica , Genoma Viral , Infecções por HIV/epidemiologia , Infecções por HIV/virologia , Repetição Terminal Longa de HIV , HIV-1/classificação , Humanos , Luciferases , Países Baixos/epidemiologia , Fases de Leitura Aberta , RNA Viral , Transcrição Gênica , Ativação Transcricional , Carga Viral
20.
Methods Mol Biol ; 1746: 55-61, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29492886

RESUMO

We describe a detailed protocol for the manual workup of blood (plasma/serum) samples from individuals infected with the human immunodeficiency virus type 1 (HIV-1) for deep sequence analysis of the viral genome. The study optimizing the assay was performed in the context of the BEEHIVE (Bridging the Evolution and Epidemiology of HIV in Europe) project, which analyzes complete viral genomes from more than 3000 HIV-1-infected Europeans with high-throughput deep sequencing techniques. The goal of the BEEHIVE project is to determine the contribution of viral genetics to virulence. Recently we performed a pilot experiment with 125 patient plasma samples to identify the method that is most suitable for isolation of HIV-1 viral RNA for subsequent long-amplicon deep sequencing. We reported that manual isolation with the QIAamp Viral RNA Mini Kit (Qiagen) provides superior results over robotically extracted RNA. The latter approach used the MagNA Pure 96 System in combination with the MagNA Pure 96 Instrument (Roche Diagnostics), the QIAcube robotic system (Qiagen), or the mSample Preparation Systems RNA kit with automated extraction by the m2000sp system (Abbott Molecular). Here we present a detailed protocol for the labor-intensive manual extraction method that yielded the best results.


Assuntos
DNA Viral/genética , Genoma Viral , Infecções por HIV/sangue , HIV-1/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , DNA Viral/sangue , Infecções por HIV/diagnóstico , Infecções por HIV/virologia , HIV-1/isolamento & purificação , Humanos , Kit de Reagentes para Diagnóstico , Carga Viral
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA