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1.
Am J Transplant ; 2024 Apr 19.
Artigo em Inglês | MEDLINE | ID: mdl-38642711

RESUMO

Biopsy-proven acute rejection (BPAR) occurs in approximately 10% of kidney transplant recipients in the first year, making superiority trials unfeasible. iBOX, a quantitative composite of estimated glomerular filtration rate, proteinuria, antihuman leukocyte antigen donor-specific antibody, and + full/- abbreviated kidney histopathology, is a new proposed surrogate endpoint. BPAR's prognostic ability was compared with iBOX in a pooled cohort of 1534 kidney transplant recipients from 4 data sets, including 2 prospective randomized controlled trials. Discrimination analyses showed mean c-statistic differences between both iBOX compared with BPAR of 0.25 (95% confidence interval: 0.17-0.32) for full iBOX and 0.24 (95% confidence interval: 0.16-0.32) for abbreviated iBOX, indicating statistically significantly higher c-statistic values for the iBOX prognosis of death-censored graft survival. Mean (± standard error) c-statistics were 0.81 ± 0.03 for full iBOX, 0.80 ± 0.03 for abbreviated iBOX, and 0.57 ± 0.03 for BPAR. In calibration analyses, predicted graft loss events from both iBOX models were not significantly different from those observed. However, for BPAR, the predicted events were significantly (P < .01) different (observed: 64; predicted: 70; full iBOX: 76; abbreviated iBOX: 173 BPAR). IBOX at 1-year posttransplant is superior to BPAR in the first year posttransplant in graft loss prognostic performance, providing valuable additional information and facilitating the demonstration of superiority of novel immunosuppressive regimens.

3.
Ther Innov Regul Sci ; 58(1): 175-183, 2024 01.
Artigo em Inglês | MEDLINE | ID: mdl-37872439

RESUMO

BACKGROUND: Health care inequity includes the lack of adequate representation of various populations in clinical trials. Government, academic and industry organizations have highlighted these issues and committed to actions to improve. In order to assess the current status and future success of these initiatives a quantitative objective measure to assess the state of clinical trial diversity is needed. METHODS: FDA review documents for all novel drug approvals from January 2022 through March 2023 were assessed using a scorecard that considers diversity across different demographic subgroups including age (≥ 65 years old), sex (female), race (Black and Asian) and ethnicity (Hispanic/Latino). The scorecard assigns each drug a letter grade, between A and F, for each subgroup (and overall) based on (1) the percent of each sub-population included in the trials and grades relative to the percent of the US population per the 2020 Census, (2) the number of participants from each subpopulation that received the novel new drug in the trials, (3) the incidence or prevalence of the disease/condition in each of the sub-populations. RESULTS: The FDA approved 49 novel new drugs for 50 indications (one drug was simultaneously approved for two indications). There was good representation of elderly and females with only two drugs receiving a D grade in either of these sub-populations. In contrast, Black (5 F grades) and Hispanic (4 F grades) representation was often inadequate. There were 10 drugs (20.0%) where there were no Black participants receiving the novel new drug and 16 (32.0%) approvals where there were 1-9 Black participants receiving the novel drug. In the Hispanic/Latino population there were 4 (8.0%) approvals with no Hispanic participants receiving the novel drug and 15 (30.0%) approvals where there were 1-9 Hispanic participants receiving the drug. CONCLUSIONS: This scorecard provides an objective quantitative approach to assess the current state of diversity in clinical trials supporting new drug approvals. Substantial improvement in racial and ethnic representation is needed. Meaningful change will require actions and cooperation among all stakeholders to address this multifaceted issue and will take commitment, perseverance, and appropriate incentives.


Assuntos
Aprovação de Drogas , Etnicidade , Humanos , Feminino , Idoso , Estados Unidos , Projetos de Pesquisa , United States Food and Drug Administration , Indústrias
4.
Am J Transplant ; 24(2): 250-259, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-37832826

RESUMO

To address the challenges of assessing the impact of a reasonably likely surrogate endpoint on long-term graft survival in prospective kidney transplant clinical trials, the Transplant Therapeutics Consortium established a real-world evidence workgroup evaluating the scientific value of using transplant registry data as an external control to supplement the internal control group. The United Network for Organ Sharing retrospectively simulated the use of several distinct contemporaneous external control groups, applied multiple cause inference methods, and compared treatment effects to those observed in the BENEFIT study. Applying BENEFIT study enrollment criteria produced a smaller historical cyclosporine control arm (n = 153) and a larger, alternative (tacrolimus) historical control arm (n = 1069). Following covariate-balanced propensity scoring, Kaplan-Meier 5-year all-cause graft survivals were 81.3% and 81.7% in the Organ Procurement and Transplantation Network (OPTN) tacrolimus and cyclosporine external control arms, similar to 80.3% observed in the BENEFIT cyclosporine treatment arm. Five-year graft survival in the belatacept-less intensive arm was significantly higher than the OPTN controls using propensity scoring for comparing cyclosporine and tacrolimus. Propensity weighting using OPTN controls closely mirrored the BENEFIT study's long-term control (cyclosporine) arm's survival rate and the less intensive arm's treatment effect (significantly higher survival vs control). This study supports the feasibility and validity of using supplemental external registry controls for long-term survival in kidney transplant clinical trials.


Assuntos
Imunossupressores , Tacrolimo , Humanos , Estados Unidos , Imunossupressores/uso terapêutico , Tacrolimo/uso terapêutico , Estudos Retrospectivos , Rejeição de Enxerto/etiologia , Rejeição de Enxerto/prevenção & controle , Ciclosporina/uso terapêutico , Sistema de Registros , Sobrevivência de Enxerto
5.
Transpl Int ; 36: 11951, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37822449

RESUMO

New immunosuppressive therapies that improve long-term graft survival are needed in kidney transplant. Critical Path Institute's Transplant Therapeutics Consortium received a qualification opinion for the iBOX Scoring System as a novel secondary efficacy endpoint for kidney transplant clinical trials through European Medicines Agency's qualification of novel methodologies for drug development. This is the first qualified endpoint for any transplant indication and is now available for use in kidney transplant clinical trials. Although the current efficacy failure endpoint has typically shown the noninferiority of therapeutic regimens, the iBOX Scoring System can be used to demonstrate the superiority of a new immunosuppressive therapy compared to the standard of care from 6 months to 24 months posttransplant in pivotal or exploratory drug therapeutic studies.


Assuntos
Transplante de Rim , Humanos , Imunossupressores/uso terapêutico , Terapia de Imunossupressão , Rejeição de Enxerto/prevenção & controle
6.
Am J Transplant ; 23(10): 1496-1506, 2023 10.
Artigo em Inglês | MEDLINE | ID: mdl-37735044

RESUMO

New immunosuppressive therapies that improve long-term graft survival are needed in kidney transplant. Critical Path Institute's Transplant Therapeutics Consortium received a qualification opinion for the iBOX Scoring System as a novel secondary efficacy endpoint for kidney transplant clinical trials through European Medicines Agency's qualification of novel methodologies for drug development. This is the first qualified endpoint for any transplant indication and is now available for use in kidney transplant clinical trials. Although the current efficacy failure endpoint has typically shown the noninferiority of therapeutic regimens, the iBOX Scoring System can be used to demonstrate the superiority of a new immunosuppressive therapy compared to the standard of care from 6 months to 24 months posttransplant in pivotal or exploratory drug therapeutic studies.


Assuntos
Transplante de Rim , Rejeição de Enxerto/etiologia , Rejeição de Enxerto/prevenção & controle , Terapia de Imunossupressão , Imunossupressores/uso terapêutico , Transplante de Rim/efeitos adversos , Ensaios Clínicos como Assunto
7.
Transplant Proc ; 55(7): 1692-1705, 2023 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-37438193

RESUMO

BACKGROUND: This retrospective analysis of the US Scientific Registry of Transplant Recipients was undertaken to obtain real-world evidence concerning the efficacy and safety of tacrolimus-based immunosuppression in pediatric lung transplant recipients to support a supplemental New Drug Application. METHODS: Overall, 725 pediatric recipients of a primary deceased-donor lung transplant between January 1, 1999, and December 31, 2017, were followed for up to 3 years post-transplant based on an immunosuppressive regimen at hospital discharge: immediate-release tacrolimus (TAC)+mycophenolate mofetil (MMF), TAC+azathioprine (AZA), cyclosporine (CsA)+MMF, or CsA+AZA. The primary outcome was the composite endpoint of graft failure or death (all-cause) at 1 year post-transplant, calculated by Kaplan-Meier analysis. RESULTS: The use of TAC+MMF increased over time. During 2010 to 2017, 91.7% of pediatric lung transplant recipients were receiving TAC+MMF at the time of discharge. The proportion of recipients continuing their discharge regimen at 1 year post-transplant was 83.7% with TAC+MMF and 40.4% to 59.7% with the other regimens. Cumulative incidence of the composite endpoint of graft failure or death at 1 year post-transplant was 7.7% with TAC+MMF, 13.9% with TAC+AZA, 8.9% with CsA+MMF, and 9.1% with CsA+AZA. There was no significant difference in the risk of graft failure or death at 1 year post-transplant between groups from 1999 to 2005 (the only era when adequate numbers on each regimen allowed statistical comparison). No increase in hospitalization for infection or malignancy was seen with TAC+MMF. CONCLUSION: The real-world evidence from the US database of transplant recipients supported the Food and Drug Administration's approval of tacrolimus-based maintenance immunosuppression in pediatric lung transplant recipients.


Assuntos
Transplante de Rim , Transplante de Pulmão , Humanos , Criança , Tacrolimo/efeitos adversos , Estudos Retrospectivos , Transplantados , Alta do Paciente , Imunossupressores/efeitos adversos , Ciclosporina , Azatioprina , Ácido Micofenólico , Transplante de Pulmão/efeitos adversos , Rejeição de Enxerto/prevenção & controle , Rejeição de Enxerto/epidemiologia
8.
Clin Transl Sci ; 16(9): 1680-1690, 2023 09.
Artigo em Inglês | MEDLINE | ID: mdl-37350196

RESUMO

Kidney transplantation is the preferred treatment for individuals with end-stage kidney disease. From a modeling perspective, our understanding of kidney function trajectories after transplantation remains limited. Current modeling of kidney function post-transplantation is focused on linear slopes or percent decline and often excludes the highly variable early timepoints post-transplantation, where kidney function recovers and then stabilizes. Using estimated glomerular filtration rate (eGFR), a well-known biomarker of kidney function, from an aggregated dataset of 4904 kidney transplant patients including both observational studies and clinical trials, we developed a longitudinal model of kidney function trajectories from time of transplant to 6 years post-transplant. Our model is a nonlinear, mixed-effects model built in NONMEM that captured both the recovery phase after kidney transplantation, where the graft recovers function, and the long-term phase of stabilization and slow decline. Model fit was assessed using diagnostic plots and individual fits. Model performance, assessed via visual predictive checks, suggests accurate model predictions of eGFR at the median and lower 95% quantiles of eGFR, ranges which are of critical clinical importance for assessing loss of kidney function. Various clinically relevant covariates were also explored and found to improve the model. For example, transplant recipients of deceased donors recover function more slowly after transplantation and calcineurin inhibitor use promotes faster long-term decay. Our work provides a generalizable, nonlinear model of kidney allograft function that will be useful for estimating eGFR up to 6 years post-transplant in various clinically relevant populations.


Assuntos
Falência Renal Crônica , Transplante de Rim , Humanos , Transplante de Rim/efeitos adversos , Taxa de Filtração Glomerular , Ensaios Clínicos como Assunto , Rim/fisiologia , Falência Renal Crônica/cirurgia
9.
Influenza Other Respir Viruses ; 17(4): e13141, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37127782

RESUMO

BACKGROUND: Serological responses from influenza vaccination or infection are typically measured by hemagglutinin inhibition (HAI) or microneutralization (MN). Both methods are limited in feasibility, standardization, and generalizability to recent strains. We developed a luciferase MN (LMN) assay that combines the advantages of the conventional MN assay with the ease of the HAI assay. METHODS: Sera were obtained from the HIVE study, a Michigan household cohort. Reverse genetics was used to generate recombinant influenza viruses expressing the hemagglutinin and neuraminidase of test strains, all other viral proteins from an A/WSN/1933 backbone, and a NanoLuc reporter. Serum neutralization of luciferase-expressing targets was quantified as a reduction in light emission from infected cells. Neutralization titers were measured for cell- and egg-adapted versions of A/Hong Kong/4801/2014 and A/Singapore/INFIMH-16-0019/2016 and compared to HAI titers against egg-grown antigens. RESULTS: Three hundred thirty-three sera were collected from 259 participants between May 2016 and July 2018. Sampled participants were 7-68 years of age, and >80% were vaccinated against influenza. HAI and LMN titers were correlated for A/Hong Kong/4801/2014 (ρ = 0.52, p ≤ 0.01) and A/Singapore/INFIMH-16-0019/2016 (ρ = 0.79, p ≤ 0.01). LMN titers were lower for cell strains compared to egg strains (A/Hong Kong/4801/2014 mean log2 fold change = -2.66, p ≤ 0.01 and A/Singapore/INFIMH-16-0019/2016 mean log2 fold change = -3.15, p ≤ 0.01). CONCLUSIONS: The LMN assay was feasible using limited sample volumes and able to differentiate small antigenic differences between egg-adapted and cell-derived strains. The correspondence of these results with the commonly used HAI confirms the utility of this assay for high-throughput studies of correlates of protection and vaccine response.


Assuntos
Vacinas contra Influenza , Influenza Humana , Orthomyxoviridae , Humanos , Influenza Humana/prevenção & controle , Hemaglutininas , Anticorpos Antivirais , Testes de Inibição da Hemaglutinação
10.
Open Forum Infect Dis ; 10(2): ofad061, 2023 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-36861093

RESUMO

Background: Hospital-acquired influenza virus infection (HAII) can cause severe morbidity and mortality. Identifying potential transmission routes can inform prevention strategies. Methods: We identified all hospitalized patients testing positive for influenza A virus at a large, tertiary care hospital during the 2017-2018 and 2019-2020 influenza seasons. Hospital admission dates, locations of inpatient service, and clinical influenza testing information were retrieved from the electronic medical record. Time-location groups of epidemiologically linked influenza patients were defined and contained ≥1 presumed HAII case (first positive ≥48 hours after admission). Genetic relatedness within time-location groups was assessed by whole genome sequencing. Results: During the 2017-2018 season, 230 patients tested positive for influenza A(H3N2) or unsubtyped influenza A including 26 HAIIs. There were 159 influenza A(H1N1)pdm09 or unsubtyped influenza A-positive patients identified during the 2019-2020 season including 33 HAIIs. Consensus sequences were obtained for 177 (77%) and 57 (36%) of influenza A cases in 2017-2018 and 2019-2020, respectively. Among all influenza A cases, there were 10 time-location groups identified in 2017-2018 and 13 in 2019-2020; 19 of 23 groups included ≤4 patients. In 2017-2018, 6 of 10 groups had ≥2 patients with sequence data, including ≥1 HAII case. Two of 13 groups met this criteria in 2019-2020. Two time-location groups from 2017-2018 each contained 3 genetically linked cases. Conclusions: Our results suggest that HAIIs arise from outbreak transmission from nosocomial sources as well as single infections from unique community introductions.

11.
Clin Transplant ; 37(3): e14876, 2023 03.
Artigo em Inglês | MEDLINE | ID: mdl-36465024

RESUMO

This viewpoint aims to "set the stage" and provide the rationale for the proposed development of a large-scale, comprehensive survey assessing transplant patients' perceived unmet immunosuppressive therapy needs. Research in organ transplantation has historically focused on reducing the incidence and impact of rejection on allograft survival and minimizing or eliminating the need for chronic immunosuppressive therapies. There has been less emphasis and investment in therapies to improve patient-reported outcomes including health-related quality of life and side-effects. Patient-focused drug development (PFDD) is a new and important emphasis of the Food and Drug Administration (FDA) that provides a guiding philosophy for incorporating the patient experience into drug development and evaluation. The American Society of Transplantation (AST) Board of Directors commissioned this working group to prepare for the conduct of a comprehensive patient survey assessing unmet immunosuppressive therapy needs. This paper aims to describe the basis for why it is important to conduct this survey and briefly outline the plan for broad stakeholder engagement to ensure the information gained is diverse, inclusive, and relevant for advancing PFDD in organ transplant recipients.


Assuntos
Imunossupressores , Transplante de Órgãos , Humanos , Estados Unidos , Imunossupressores/uso terapêutico , Qualidade de Vida , Terapia de Imunossupressão , Inquéritos e Questionários , Rejeição de Enxerto/epidemiologia
12.
Hum Vaccin Immunother ; 18(5): 2068338, 2022 11 30.
Artigo em Inglês | MEDLINE | ID: mdl-35511579

RESUMO

Individuals who experience severe COVID-19-vaccine-related adverse reactions such as transverse myelitis may be precluded from receiving further vaccination to protect from SARS-CoV-2 infection. Although the mechanism of autoimmune spinal cord inflammation resulting in transverse myelitis is unclear, it may be safe to administer antibody therapy for preventing COVID-19. Recently, Evusheld, tixagevimab with cilgavimab, two spike-protein directed monoclonal antibodies were authorized by the U.S. FDA and U.K. MHRA for administration to individuals when vaccination is not recommended. We report the safe administration of Evusheld to a patient who experienced transverse myelitis 11 months previously as a result of receiving the Moderna mRNA vaccine. This patient has experienced no adverse events to Evusheld. Additional experience and data collection are warranted to determine the safety of this prophylactic therapy.


Assuntos
Vacinas contra COVID-19 , COVID-19 , Mielite Transversa , Anticorpos Monoclonais , COVID-19/prevenção & controle , Vacinas contra COVID-19/efeitos adversos , Humanos , Mielite Transversa/etiologia , Mielite Transversa/terapia , SARS-CoV-2 , Vacinação/efeitos adversos , Vacinas Sintéticas , Vacinas de mRNA
13.
bioRxiv ; 2022 Feb 07.
Artigo em Inglês | MEDLINE | ID: mdl-35169800

RESUMO

FKBP, a naturally occurring ubiquitous intracellular protein, has been proposed as a potential target for coronavirus replication. A non-immunosuppressive FKBP ligand, FK1706, was studied in vitro in a Vero cell model to assess potential activity alone and in combination with antivirals against SARS-CoV-2 replication. When combined with remdesivir, synergistic activity was seen (summary synergy score 24.7±9.56). FK1706 warrants in vivo testing as a potential new combination therapeutic for the treatment of COVID-19 infections.

14.
Transplantation ; 106(6): 1233-1242, 2022 06 01.
Artigo em Inglês | MEDLINE | ID: mdl-34974456

RESUMO

BACKGROUND: The Scientific Registry of Transplant Recipients was retrospectively analyzed to provide real-world evidence of the efficacy and safety of tacrolimus-based immunosuppressive regimens in adult lung transplant recipients in the United States. METHODS: Adult recipients (N = 25 355; ≥18 y) of a primary deceased-donor lung transplant between January 1, 1999, and December 31, 2017, were followed for 3 y posttransplant based on immunosuppressive regimen at discharge: immediate-release tacrolimus (TAC) + mycophenolate mofetil (MMF), TAC + azathioprine (AZA), cyclosporine (CsA) + MMF, or CsA + AZA. The primary outcome was the composite endpoint of graft failure or death (all-cause) at 1 y posttransplant (calculated via a modified Kaplan-Meier method). RESULTS: Discharge immunosuppressive regimens in lung transplant recipients changed over time, with a substantial increase in the use of TAC + MMF. TAC + MMF was the most common immunosuppressive regimen (received by 61.0% of individuals at discharge). The cumulative incidence of graft failure or death at 1 y posttransplant in adult lung transplant patients receiving TAC + MMF was 8.6% (95% confidence interval 8.1-9.1). Risk of graft failure or death was significantly higher in adults receiving CsA + MMF or CsA + AZA compared with TAC + MMF, with no significant difference seen between TAC + MMF and TAC + AZA. TAC + MMF had the highest continued use at 1 y posttransplant (72.0% versus 35.4%-51.5% for the other regimens). There was no increase in the rate of infection or malignancy in the TAC + MMF group. CONCLUSIONS: Real-world evidence from the most comprehensive database of transplant recipients in the United States supports the use of TAC in combination with MMF or AZA as maintenance immunosuppression in adult lung transplant recipients.


Assuntos
Transplante de Rim , Transplante de Pulmão , Adulto , Azatioprina/efeitos adversos , Ciclosporina/efeitos adversos , Rejeição de Enxerto/epidemiologia , Rejeição de Enxerto/prevenção & controle , Humanos , Imunossupressores/efeitos adversos , Transplante de Rim/métodos , Transplante de Pulmão/efeitos adversos , Ácido Micofenólico/efeitos adversos , Estudos Retrospectivos , Tacrolimo , Estados Unidos/epidemiologia
15.
Open Forum Infect Dis ; 8(11): ofab518, 2021 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-34805437

RESUMO

BACKGROUND: Coronavirus disease 2019 (COVID-19) has had high incidence rates at institutions of higher education (IHE) in the United States, but the transmission dynamics in these settings are poorly understood. It remains unclear to what extent IHE-associated outbreaks have contributed to transmission in nearby communities. METHODS: We implemented high-density prospective genomic surveillance to investigate these dynamics at the University of Michigan and the surrounding community during the Fall 2020 semester (August 16-November 24). We sequenced complete severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from 1659 individuals, including 468 students, representing 20% of cases in students and 25% of total cases in Washtenaw County over the study interval. RESULTS: Phylogenetic analysis identified >200 introductions into the student population, most of which were not related to other student cases. There were 2 prolonged student transmission clusters, of 115 and 73 individuals, that spanned multiple on-campus residences. Remarkably, <5% of nonstudent genomes were descended from student clusters, and viral descendants of student cases were rare during a subsequent wave of infections in the community. CONCLUSIONS: The largest outbreaks among students at the University of Michigan did not significantly contribute to the rise in community cases in Fall 2020. These results provide valuable insights into SARS-CoV-2 transmission dynamics at the regional level.

16.
J Infect Dis ; 224(8): 1287-1293, 2021 10 28.
Artigo em Inglês | MEDLINE | ID: mdl-33870434

RESUMO

BACKGROUND: Previous studies demonstrated that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA can be detected for weeks after infection. The significance of this finding is unclear and, in most patients, does not represent active infection. Detection of subgenomic RNA has been proposed to represent productive infection and may be a useful marker for monitoring infectivity. METHODS: We used quantitative reverse-transcription polymerase chain reaction (RT-qPCR) to quantify total and subgenomic nucleocapsid (sgN) and envelope (sgE) transcripts in 185 SARS-CoV-2-positive nasopharyngeal swab samples collected on hospital admission and to relate to symptom duration. RESULTS: We find that all transcripts decline at the same rate; however, sgE becomes undetectable before other transcripts. The median duration of symptoms to a negative test is 14 days for sgE and 25 days for sgN. There is a linear decline in subgenomic compared to total RNA, suggesting that subgenomic transcript copy number is dependent on copy number of total transcripts. The mean difference between total and sgN is 16-fold and the mean difference between total and sgE is 137-fold. This relationship is constant over duration of symptoms, allowing prediction of subgenomic copy number from total copy number. CONCLUSIONS: Subgenomic RNA may be no more useful in determining infectivity than a copy number threshold determined for total RNA.


Assuntos
Teste de Ácido Nucleico para COVID-19/métodos , COVID-19/diagnóstico , RNA Viral/isolamento & purificação , SARS-CoV-2/isolamento & purificação , Carga Viral , Idoso , COVID-19/transmissão , COVID-19/virologia , Teste de Ácido Nucleico para COVID-19/normas , Teste de Ácido Nucleico para COVID-19/estatística & dados numéricos , Proteínas do Envelope de Coronavírus/genética , Proteínas do Nucleocapsídeo de Coronavírus/genética , Estudos de Viabilidade , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Nasofaringe/patologia , Nasofaringe/virologia , Fosfoproteínas/genética , Reação em Cadeia da Polimerase em Tempo Real/estatística & dados numéricos , Valores de Referência , Estudos Retrospectivos , SARS-CoV-2/genética , SARS-CoV-2/patogenicidade
17.
Cell ; 184(10): 2595-2604.e13, 2021 05 13.
Artigo em Inglês | MEDLINE | ID: mdl-33891875

RESUMO

The emergence and spread of SARS-CoV-2 lineage B.1.1.7, first detected in the United Kingdom, has become a global public health concern because of its increased transmissibility. Over 2,500 COVID-19 cases associated with this variant have been detected in the United States (US) since December 2020, but the extent of establishment is relatively unknown. Using travel, genomic, and diagnostic data, we highlight that the primary ports of entry for B.1.1.7 in the US were in New York, California, and Florida. Furthermore, we found evidence for many independent B.1.1.7 establishments starting in early December 2020, followed by interstate spread by the end of the month. Finally, we project that B.1.1.7 will be the dominant lineage in many states by mid- to late March. Thus, genomic surveillance for B.1.1.7 and other variants urgently needs to be enhanced to better inform the public health response.


Assuntos
Teste para COVID-19 , COVID-19 , Modelos Biológicos , SARS-CoV-2 , COVID-19/genética , COVID-19/mortalidade , COVID-19/transmissão , Feminino , Humanos , Masculino , SARS-CoV-2/genética , SARS-CoV-2/metabolismo , SARS-CoV-2/patogenicidade , Estados Unidos/epidemiologia
18.
PLoS Pathog ; 17(4): e1009499, 2021 04.
Artigo em Inglês | MEDLINE | ID: mdl-33826681

RESUMO

Analysis of SARS-CoV-2 genetic diversity within infected hosts can provide insight into the generation and spread of new viral variants and may enable high resolution inference of transmission chains. However, little is known about temporal aspects of SARS-CoV-2 intrahost diversity and the extent to which shared diversity reflects convergent evolution as opposed to transmission linkage. Here we use high depth of coverage sequencing to identify within-host genetic variants in 325 specimens from hospitalized COVID-19 patients and infected employees at a single medical center. We validated our variant calling by sequencing defined RNA mixtures and identified viral load as a critical factor in variant identification. By leveraging clinical metadata, we found that intrahost diversity is low and does not vary by time from symptom onset. This suggests that variants will only rarely rise to appreciable frequency prior to transmission. Although there was generally little shared variation across the sequenced cohort, we identified intrahost variants shared across individuals who were unlikely to be related by transmission. These variants did not precede a rise in frequency in global consensus genomes, suggesting that intrahost variants may have limited utility for predicting future lineages. These results provide important context for sequence-based inference in SARS-CoV-2 evolution and epidemiology.


Assuntos
COVID-19/virologia , Acúmulo de Mutações , SARS-CoV-2/genética , Idoso , Sequência de Bases , COVID-19/metabolismo , Feminino , Variação Genética , Genoma Viral , Interações entre Hospedeiro e Microrganismos , Humanos , Masculino , Pessoa de Meia-Idade , Mutação/genética , Filogenia , RNA Viral/genética , Análise de Sequência de RNA/métodos
19.
medRxiv ; 2021 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-33688671

RESUMO

Understanding viral load in patients infected with SARS-CoV-2 is critical to epidemiology and infection control. Previous studies have demonstrated that SARS-CoV-2 RNA can be detected for many weeks after symptom onset. The clinical significance of this finding is unclear and, in most patients, likely does not represent active infection. There are, however, patients who shed infectious virus for weeks. Detection of subgenomic RNA transcripts expressed by SARS-CoV-2 has been proposed to represent productive infection and may be a tractable marker for monitoring infectivity. Here, we use RT-PCR to quantify total and subgenomic nucleocapsid (N) and envelope (E) transcripts in 190 SARS-CoV-2 positive samples collected on hospital admission. We relate these findings to duration of symptoms. We find that all transcripts decline at the same rate; however, subgenomic E becomes undetectable before other transcripts. In Kaplan-Meier analysis the median duration of symptoms to a negative test is 14 days for sgE and 25 days for sgN. There is a linear decline in subgenomic RNA compared to total RNA suggesting subgenomic transcript copy number is highly dependent on copy number of total transcripts. The mean difference between total N and subgenomic N is 16-fold (4.0 cycles) and the mean difference between total E and sub-genomic E is 137-fold (7.1 cycles). This relationship is constant over duration of symptoms allowing prediction of subgenomic copy number from total copy number. Although Subgenomic E is undetectable at a time that may more closely reflect the duration of infectivity, its utility in determining active infection may be no more useful than a copy number threshold determined for total transcripts.

20.
PLoS Pathog ; 17(2): e1009273, 2021 02.
Artigo em Inglês | MEDLINE | ID: mdl-33600489

RESUMO

Human-to-human transmission of influenza viruses is a serious public health threat, yet the precise role of immunity from previous infections on the susceptibility to airborne infection is still unknown. Using the ferret model, we examined the roles of exposure duration and heterosubtypic immunity on influenza transmission. We demonstrate that a 48 hour exposure is sufficient for efficient transmission of H1N1 and H3N2 viruses. To test pre-existing immunity, a gap of 8-12 weeks between primary and secondary infections was imposed to reduce innate responses and ensure robust infection of donor animals with heterosubtypic viruses. We found that pre-existing H3N2 immunity did not significantly block transmission of the 2009 H1N1pandemic (H1N1pdm09) virus to immune animals. Surprisingly, airborne transmission of seasonal H3N2 influenza strains was abrogated in recipient animals with H1N1pdm09 pre-existing immunity. This protection from natural infection with H3N2 virus was independent of neutralizing antibodies. Pre-existing immunity with influenza B virus did not block H3N2 virus transmission, indicating that the protection was likely driven by the adaptive immune response. We demonstrate that pre-existing immunity can impact susceptibility to heterologous influenza virus strains, and implicate a novel correlate of protection that can limit the spread of respiratory pathogens through the air.


Assuntos
Anticorpos Neutralizantes/imunologia , Anticorpos Antivirais/imunologia , Vírus da Influenza A Subtipo H1N1/imunologia , Vírus da Influenza A Subtipo H3N2/imunologia , Infecções por Orthomyxoviridae/transmissão , Animais , Furões , Masculino , Infecções por Orthomyxoviridae/imunologia , Infecções por Orthomyxoviridae/virologia
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