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1.
Nature ; 590(7844): 146-150, 2021 02.
Article in English | MEDLINE | ID: mdl-33142304

ABSTRACT

In late 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first detected in China and has since caused a pandemic of coronavirus disease 2019 (COVID-19). The first case of COVID-19 in New York City was officially confirmed on 1 March 2020 followed by a severe local epidemic1. Here, to understand seroprevalence dynamics, we conduct a retrospective, repeated cross-sectional analysis of anti-SARS-CoV-2 spike antibodies in weekly intervals from the beginning of February to July 2020 using more than 10,000 plasma samples from patients at Mount Sinai Hospital in New York City. We describe the dynamics of seroprevalence in an 'urgent care' group, which is enriched in cases of COVID-19 during the epidemic, and a 'routine care' group, which more closely represents the general population. Seroprevalence increased at different rates in both groups; seropositive samples were found as early as mid-February, and levelled out at slightly above 20% in both groups after the epidemic wave subsided by the end of May. From May to July, seroprevalence remained stable, suggesting lasting antibody levels in the population. Our data suggest that SARS-CoV-2 was introduced in New York City earlier than previously documented and describe the dynamics of seroconversion over the full course of the first wave of the pandemic in a major metropolitan area.


Subject(s)
Antibodies, Viral/blood , Antibodies, Viral/immunology , COVID-19 Serological Testing/statistics & numerical data , COVID-19/epidemiology , COVID-19/immunology , Epidemiological Monitoring , SARS-CoV-2/immunology , Adolescent , Adult , Ambulatory Care/statistics & numerical data , COVID-19/diagnosis , COVID-19/virology , Child , Child, Preschool , Cross-Sectional Studies , Female , Humans , Incidence , Infant , Infant, Newborn , Male , Middle Aged , New York City/epidemiology , Spike Glycoprotein, Coronavirus/immunology , Time Factors , Urban Population/statistics & numerical data , Young Adult
2.
J Surg Oncol ; 129(7): 1254-1264, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38505908

ABSTRACT

BACKGROUND AND METHODS: We characterized colorectal liver metastasis recurrence and survival patterns after surgical resection and intraoperative ablation ± hepatic arterial infusion pump (HAIP) placement. We estimated patterns of recurrence and survival in patients undergoing contemporary multimodal treatments. Between 2017 and 2021, patient, tumor characteristics, and recurrence data were collected. Primary outcomes included recurrence patterns and survival data based on operative intervention. RESULTS: There were 184 patients who underwent hepatectomy and intraoperative ablation. Sixty patients (32.6%) underwent HAIP placement. A total of 513 metastases were ablated, median total of 2 ablations per patient. Median time to recurrence was 31 [22-40] months. Recurrence patterns included tumor at ablative margin on first scheduled postoperative imaging (8, 4.3%), local tumor recurrence at ablative site (69, 37.5%), and non-ablated liver tumor recurrence (38, 20.6%). In patients who underwent HAIP placement, the rate of liver recurrence was reduced (45% vs 70.9%, p = 0.0001). Median overall survival was 64 [41-58] months and prolonged survival was associated with HAIP treatment (85 [66-109] vs 60 [51-70] months. CONCLUSIONS AND DISCUSSION: Hepatic recurrence is common and combination of intraoperative ablation and HAIP treatments were associated with prolonged survival. These data may reflect patient selection however, future work will clarify preoperative tumor and patient characteristics that may better predict recurrence expectations.


Subject(s)
Colorectal Neoplasms , Hepatectomy , Hepatic Artery , Infusions, Intra-Arterial , Liver Neoplasms , Neoplasm Recurrence, Local , Humans , Liver Neoplasms/secondary , Liver Neoplasms/therapy , Liver Neoplasms/surgery , Colorectal Neoplasms/pathology , Colorectal Neoplasms/therapy , Male , Female , Neoplasm Recurrence, Local/pathology , Middle Aged , Aged , Hepatectomy/methods , Combined Modality Therapy , Survival Rate , Retrospective Studies , Follow-Up Studies , Prognosis , Antineoplastic Combined Chemotherapy Protocols/therapeutic use
3.
J Virol ; 96(2): e0142121, 2022 01 26.
Article in English | MEDLINE | ID: mdl-34669506

ABSTRACT

The public health burden caused by influenza virus infections is not adequately addressed with existing vaccines and antivirals. Identifying approaches that interfere with human-to-human transmission of influenza viruses remains a pressing need. The importance of neuraminidase (NA) activity for the replication and spread of influenza viruses led us to investigate whether broadly reactive human anti-NA monoclonal antibodies (MAbs) could affect airborne transmission of the virus using the guinea pig model. In that model, infection with recent influenza virus clinical isolates resulted in 100% transmission from inoculated donors to recipients in an airborne transmission setting. Anti-NA MAbs were administered either to the inoculated animals on days 1, 2, and 4 after infection or to the naive contacts on days 2 and 4 after donor infection. Administration of NA-1G01, a broadly cross-reactive anti-NA MAb, to either the donor or recipient reduced transmission of the A/New York City/PV02669/2019 (H1N1) and A/New York City/PV01148/2018 (H3N2) viruses. Administration of 1000-3C05, an anti-N1 MAb, to either the donor or recipient reduced transmission of A/New York City/PV02669/2019 (H1N1) virus but did not reduce transmission of A/New York City/PV01148 (H3N2) virus. Conversely, 229-2C06, an anti-N2 MAb, reduced transmission of A/New York City/PV01148 (H3N2) but did not impact transmission of A/New York City/PV02669/2019 (H1N1) virus. Our work demonstrates that anti-NA MAbs could be further developed into prophylactic or therapeutic agents to prevent influenza virus transmission to control viral spread. IMPORTANCE The burden of influenza remains substantial despite unremitting efforts to reduce the magnitude of seasonal influenza epidemics and prepare for pandemics. Although vaccination remains the mainstay of these efforts, current vaccines are designed to stimulate an immune response against the viral hemagglutinin. Interest in the role immunity against neuraminidase plays in influenza virus infection and transmission has recently surged. Human antibodies that bind broadly to neuraminidases of diverse influenza viruses and protect mice against lethal viral challenge have previously been characterized. Here, we show that three such antibodies inhibit the neuraminidase activity of recent isolates and reduce their airborne transmission in a guinea pig model. In addition to contributing to the accumulating support for incorporating neuraminidase as a vaccine antigen, these findings also demonstrate the potential of direct administration of anti-neuraminidase antibodies to individuals infected with influenza virus and to individuals for postexposure prophylaxis to prevent the spread of influenza virus.


Subject(s)
Antibodies, Viral/therapeutic use , Neuraminidase/immunology , Orthomyxoviridae Infections/prevention & control , Viral Proteins/immunology , Animals , Antibodies, Monoclonal/immunology , Antibodies, Monoclonal/therapeutic use , Antibodies, Viral/immunology , Cross Reactions , Guinea Pigs , Humans , Immunization, Passive , Influenza A Virus, H1N1 Subtype/immunology , Influenza A Virus, H3N2 Subtype/immunology , Influenza, Human/immunology , Orthomyxoviridae Infections/transmission
4.
J Med Virol ; 95(6): e28878, 2023 06.
Article in English | MEDLINE | ID: mdl-37322614

ABSTRACT

Monkeypox (MPOX) is a zoonotic disease that affects humans and other primates, resulting in a smallpox-like illness. It is caused by monkeypox virus (MPXV), which belongs to the Poxviridae family. Clinically manifested by a range of cutaneous and systemic findings, as well as variable disease severity phenotypes based on the genetic makeup of the virus, the cutaneous niche and respiratory mucosa are the epicenters of MPXV pathogenicity. Herein, we describe the ultrastructural features of MPXV infection in both human cultured cells and cutaneous clinical specimens collected during the 2022-2023 MPOX outbreak in New York City that were revealed through electron microscopy. We observed typical enveloped virions with brick-shaped morphologies that contained surface protrusions, consistent with the classic ultrastructural features of MPXV. In addition, we describe morpho-functional evidence that point to roles of distinct cellular organelles in viral assembly during clinical MPXV infection. Interestingly, in skin lesions, we found abundant melanosomes near viral assembly sites, particularly in the vicinity of mature virions, which provides further insight into virus-host interactions at the subcellular level that contribute to MPXV pathogenesis. These findings not only highlight the importance of electron microscopic studies for further investigation of this emerging pathogen but also in characterizing MPXV pathogenesis during human infection.


Subject(s)
Mpox (monkeypox) , Skin Diseases , Animals , Humans , Monkeypox virus/genetics , Virulence , Primates , Genomics
5.
J Med Virol ; 95(1): e28247, 2023 01.
Article in English | MEDLINE | ID: mdl-36271493

ABSTRACT

Monkeypox virus (MPXV) is a zoonotic orthopoxvirus within the Poxviridae family. MPXV is endemic to Central and West Africa. However, the world is currently witnessing an international outbreak with no clear epidemiological links to travel or animal exposure and with ever-increasing numbers of reported cases worldwide. Here, we evaluated and validated a new, sensitive, and specific real-time PCR-assay for MPXV diagnosis in humans and compare the performance of this novel assay against a Food & Drug Administration-cleared pan-Orthopox RT-PCR assay. We determined specificity, sensitivity, and analytic performance of the PKamp™ Monkeypox Virus RT-PCR assay targeting the viral F3L-gene. In addition, we further evaluated MPXV-PCR-positive specimens by viral culture, electron microscopy, and viral inactivation assays. The limit of detection was established at 7.2 genome copies/reaction, and MPXV was successfully identified in 20 clinical specimens with 100% correlation against the reference method with 100% sensitivity and specificity. Our results demonstrated the validity of this rapid, robust, and reliable RT-PCR assay for specific and accurate diagnosis of MPXV infection in human specimens collected both as dry swabs and in viral transport media. This assay has been approved by NYS Department of Health for clinical use.


Subject(s)
Monkeypox virus , Mpox (monkeypox) , Animals , Humans , Monkeypox virus/genetics , Mpox (monkeypox)/epidemiology , Reverse Transcriptase Polymerase Chain Reaction , Nucleic Acid Amplification Techniques/methods , Real-Time Polymerase Chain Reaction
6.
Transfusion ; 63(12): 2384-2391, 2023 12.
Article in English | MEDLINE | ID: mdl-37952246

ABSTRACT

BACKGROUND: Glanzmann thrombasthenia (GT) is a rare, autosomal recessive disorder of platelet glycoprotein IIb-IIIa receptors. Pregnant patients with GT are at increased risk of maternal and fetal bleeding. There is a paucity of literature on the peripartum management of patients. CASE DESCRIPTION: We present the antepartum through the postpartum course of a patient with GT who was managed by a multidisciplinary approach that included communication across maternal-fetal medicine, hematology, transfusion medicine, and anesthesiology services. In addition to routine prepartum obstetric imaging and hematologic laboratory studies, we proactively monitored the patient for anti-platelet antibodies every 4-6 weeks to gauge the risk for neonatal alloimmune thrombocytopenia. Furthermore, we prioritized uterotonics, tranexamic acid, and transfusion of HLA-matched platelets to manage bleeding for mother and fetus intrapartum through the postpartum periods. CONCLUSION: To date, there are limited guidelines for managing bleeding or preventing alloimmunization during pregnancy in patients with GT. Here, we present a complex case with aggressive management of bleeding prophylactically for the mother while serially monitoring both mother and fetus for peripartum bleeding risks and events. Moreover, future studies warrant continued evaluation of these approaches to mitigate increased bleeding risks in subsequent pregnancies.


Subject(s)
Pregnancy Complications , Thrombasthenia , Thrombocytopenia, Neonatal Alloimmune , Pregnancy , Infant, Newborn , Female , Humans , Thrombasthenia/complications , Thrombasthenia/therapy , Hemorrhage/complications , Mothers
7.
J Surg Res ; 281: 143-154, 2023 01.
Article in English | MEDLINE | ID: mdl-36155271

ABSTRACT

INTRODUCTION: The effects of firearm sales and legislation on crime and violence are intensely debated, with multiple studies yielding differing results. We hypothesized that increased lawful firearm sales would not be associated with the rates of crime and homicide when studied using a robust statistical method. METHODS: National and state rates of crime and homicide during 1999-2015 were obtained from the United States Department of Justice and the Centers for Disease Control and Prevention. National Instant Criminal Background Check System background checks were used as a surrogate for lawful firearm sales. A general multiple linear regression model using log event rates was used to assess the effect of firearm sales on crime and homicide rates. Additional modeling was then performed on a state basis using an autoregressive correlation structure with generalized estimating equation estimates for standard errors to adjust for the interdependence of variables year to year within a particular state. RESULTS: Nationally, all crime rates except the Centers for Disease Control and Prevention-designated firearm homicides decreased as firearm sales increased over the study period. Using a naive national model, increases in firearm sales were associated with significant decreases in multiple crime categories. However, a more robust analysis using generalized estimating equation estimates on state-level data demonstrated increases in firearms sales were not associated with changes in any crime variables examined. CONCLUSIONS: Robust analysis does not identify an association between increased lawful firearm sales and rates of crime or homicide. Based on this, it is unclear if efforts to limit lawful firearm sales would have any effect on rates of crime, homicide, or injuries from violence committed with firearms.


Subject(s)
Firearms , Homicide , United States/epidemiology , Homicide/prevention & control , Violence , Commerce , Centers for Disease Control and Prevention, U.S.
8.
J Surg Oncol ; 127(8): 1271-1276, 2023 Jun.
Article in English | MEDLINE | ID: mdl-37222699

ABSTRACT

Low anterior resection syndrome represents a clinical state wherein a constellation of gastrointestinal symptoms is a direct result of anatomic changes to the rectum. Patients who undergo operations to create a neorectum often develop persistent symptoms of increased frequency, urgency, diarrhea, and these symptoms are debilitating and impact patients' quality of life. A stepwise approach to treatment can improve many patients' symptoms with the most invasive options reserved for highly refractory symptoms.


Subject(s)
Low Anterior Resection Syndrome , Rectal Neoplasms , Humans , Postoperative Complications , Quality of Life , Rectal Neoplasms/surgery , Rectum/surgery
9.
J Med Virol ; 94(7): 2911-2914, 2022 07.
Article in English | MEDLINE | ID: mdl-35243662

ABSTRACT

The coronavirus disease-2019 (COVID-19) pandemic is still challenging public health systems worldwide, particularly with the emergence of novel SARS-CoV-2 variants with mutations that increase their transmissibility and immune escape. This is the case of the variant of concern Omicron that rapidly spread globally. Here, using epidemiological and genomic data we compared the situations in South Africa as the epicenter of emergence, United Kingdom, and with particular interest New York City. This rapid global dispersal from the place of first report reemphasizes the high transmissibility of Omicron, which needed only two weeks to become dominant in the United Kingdom and New York City. Our analyses suggest that as SARS-CoV-2 continues to evolve, global authorities must prioritize equity in vaccine access and continued genomic surveillance. Future studies are still needed to fully unveil the biological properties of Omicron, but what is certain is that vaccination, large-scale testing, and infection prevention efforts are the greatest arsenal against the COVID-19 pandemic.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/epidemiology , Humans , New York City/epidemiology , Pandemics , SARS-CoV-2/genetics
10.
J Med Virol ; 94(6): 2471-2478, 2022 06.
Article in English | MEDLINE | ID: mdl-35171508

ABSTRACT

Saliva is a promising specimen for the detection of viruses that cause upper respiratory infections including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) due to its cost-effectiveness and noninvasive collection. However, together with intrinsic enzymes and oral microbiota, children's unique dietary habits may introduce substances that interfere with diagnostic testing. To determine whether children's dietary choices impact SARS-CoV-2 molecular detection in saliva, we performed a diagnostic study that simulates testing of real-life specimens provided from healthy children (n = 5) who self-collected saliva at home before and at 0, 20, and 60 min after eating 20 foods they selected. Each of 72 specimens was split into two volumes and spiked with SARS-CoV-2-negative or SARS-CoV-2-positive clinical standards before side-by-side testing by reverse-transcription polymerase chain reaction matrix-assisted laser desorption ionization time-of-flight (RT-PCR/MALDI-TOF) assay. Detection of internal extraction control and SARS-CoV-2 nucleic acids was reduced in replicates of saliva collected at 0 min after eating 11 of 20 foods. Interference resolved at 20 and 60 min after eating all foods except hot dogs in one participant. This represented a significant improvement in the detection of nucleic acids compared to saliva collected at 0 min after eating (p = 0.0005). We demonstrate successful detection of viral nucleic acids in saliva self-collected by children before and after eating a variety of foods. Fasting is not required before saliva collection for SARS-CoV-2 testing by RT-PCR/MALDI-TOF, but waiting for 20 min after eating is sufficient for accurate testing. These findings should be considered for SARS-CoV-2 testing and broader viral diagnostics in saliva specimens.


Subject(s)
COVID-19 , Nucleic Acids , COVID-19/diagnosis , COVID-19 Testing , Humans , Nasopharynx , RNA, Viral/analysis , RNA, Viral/genetics , SARS-CoV-2/genetics , Saliva , Specimen Handling
11.
J Med Virol ; 94(3): 1154-1161, 2022 03.
Article in English | MEDLINE | ID: mdl-34755347

ABSTRACT

Numerous reports of neuropsychiatric symptoms highlighted the pathologic potential of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its relationship the onset and/or exacerbation of mental disease. However, coronavirus disease 2019 (COVID-19) treatments, themselves, must be considered as potential catalysts for new-onset neuropsychiatric symptoms in COVID-19 patients. To date, immediate and long-term neuropsychiatric complications following SARS-CoV-2 infection are currently unknown. Here we report on five patients with SARS-CoV-2 infection with possible associated neuropsychiatric involvement, following them clinically until resolution of their symptoms. We will also discuss the contributory roles of chloroquine and dexamethasone in these neuropsychiatric presentations.


Subject(s)
COVID-19 Drug Treatment , COVID-19 , Mental Disorders , COVID-19/complications , Chloroquine/therapeutic use , Humans , Mental Disorders/complications , SARS-CoV-2
12.
J Med Virol ; 94(4): 1606-1616, 2022 04.
Article in English | MEDLINE | ID: mdl-34877674

ABSTRACT

The coronavirus disease 2019 (COVID-19) pandemic has sparked the rapid development of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostics. However, emerging variants pose the risk for target dropout and false-negative results secondary to primer/probe binding site (PBS) mismatches. The Agena MassARRAY® SARS-CoV-2 Panel combines reverse-transcription polymerase chain reaction and matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry to probe for five targets across N and ORF1ab genes, which provides a robust platform to accommodate PBS mismatches in divergent viruses. Herein, we utilize a deidentified data set of 1262 SARS-CoV-2-positive specimens from Mount Sinai Health System (New York City) from December 2020 to April 2021 to evaluate target results and corresponding sequencing data. Overall, the level of PBS mismatches was greater in specimens with target dropout. Of specimens with N3 target dropout, 57% harbored an A28095T substitution that is highly specific for the Alpha (B.1.1.7) variant of concern. These data highlight the benefit of redundancy in target design and the potential for target performance to illuminate the dynamics of circulating SARS-CoV-2 variants.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , Reverse Transcriptase Polymerase Chain Reaction , SARS-CoV-2/isolation & purification , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , COVID-19/epidemiology , COVID-19/virology , Coronavirus Nucleocapsid Proteins/genetics , Genetic Variation , Genome, Viral/genetics , Humans , New York City/epidemiology , Phosphoproteins/genetics , Polyproteins/genetics , RNA, Viral/genetics , SARS-CoV-2/genetics , Viral Proteins/genetics
13.
Clin Infect Dis ; 73(11): e4375-e4383, 2021 12 06.
Article in English | MEDLINE | ID: mdl-33252647

ABSTRACT

BACKGROUND: Nosocomial respiratory virus outbreaks represent serious public health challenges. Rapid and precise identification of cases and tracing of transmission chains is critical to end outbreaks and to inform prevention measures. METHODS: We combined conventional surveillance with influenza A virus (IAV) genome sequencing to identify and contain a large IAV outbreak in a metropolitan healthcare system. A total of 381 individuals, including 91 inpatients and 290 healthcare workers (HCWs), were included in the investigation. RESULTS: During a 12-day period in early 2019, infection preventionists identified 89 HCWs and 18 inpatients as cases of influenza-like illness (ILI), using an amended definition without the requirement for fever. Sequencing of IAV genomes from available nasopharyngeal specimens identified 66 individuals infected with a nearly identical strain of influenza A H1N1pdm09 (43 HCWs, 17 inpatients, and 6 with unspecified affiliation). All HCWs infected with the outbreak strain had received the seasonal influenza virus vaccination. Characterization of 5 representative outbreak viral isolates did not show antigenic drift. In conjunction with IAV genome sequencing, mining of electronic records pinpointed the origin of the outbreak as a single patient and a few interactions in the emergency department that occurred 1 day prior to the index ILI cluster. CONCLUSIONS: We used precision surveillance to delineate a large nosocomial IAV outbreak, mapping the source of the outbreak to a single patient rather than HCWs as initially assumed based on conventional epidemiology. These findings have important ramifications for more-effective prevention strategies to curb nosocomial respiratory virus outbreaks.


Subject(s)
Cross Infection , Influenza, Human , Cross Infection/prevention & control , Disease Outbreaks , Genomics , Hospitals , Humans , Influenza, Human/prevention & control
14.
J Virol ; 94(5)2020 02 14.
Article in English | MEDLINE | ID: mdl-31801862

ABSTRACT

HIV diversification facilitates immune escape and complicates antiretroviral therapy. In this study, we take advantage of a humanized-mouse model to probe the contribution of APOBEC3 mutagenesis to viral evolution. Humanized mice were infected with isogenic HIV molecular clones (HIV-WT, HIV-45G, and HIV-ΔSLQ) that differ in their abilities to counteract APOBEC3G (A3G). Infected mice remained naive or were treated with the reverse transcriptase (RT) inhibitor lamivudine (3TC). Viremia, emergence of drug-resistant variants, and quasispecies diversification in the plasma compartment were determined throughout infection. While both HIV-WT and HIV-45G achieved robust infection, over time, HIV-45G replication was significantly reduced compared to that of HIV-WT in the absence of 3TC treatment. In contrast, treatment responses differed significantly between HIV-45G- and HIV-WT-infected mice. Antiretroviral treatment failed in 91% of HIV-45G-infected mice, while only 36% of HIV-WT-infected mice displayed a similar negative outcome. Emergence of 3TC-resistant variants and nucleotide diversity were determined by analyzing 155,462 single HIV reverse transcriptase gene (RT) and 6,985 vif sequences from 33 mice. Prior to treatment, variants with genotypic 3TC resistance (RT-M184I/V) were detected at low levels in over a third of all the animals. Upon treatment, the composition of the plasma quasispecies rapidly changed, leading to a majority of circulating viral variants encoding RT-184I. Interestingly, increased viral diversity prior to treatment initiation correlated with higher plasma viremia in HIV-45G-infected animals, but not in HIV-WT-infected animals. Taken together, HIV variants with suboptimal anti-A3G activity were attenuated in the absence of selection but displayed a fitness advantage in the presence of antiretroviral treatment.IMPORTANCE Both viral (e.g., RT) and host (e.g., A3G) factors can contribute to HIV sequence diversity. This study shows that suboptimal anti-A3G activity shapes viral fitness and drives viral evolution in the plasma compartment in humanized mice.


Subject(s)
APOBEC-3G Deaminase/metabolism , Drug Resistance, Viral/physiology , HIV Infections/immunology , HIV-1/immunology , Animals , Anti-HIV Agents/pharmacology , Disease Models, Animal , Drug Resistance, Viral/drug effects , Genetic Variation , HEK293 Cells , HIV-1/drug effects , Humans , Lamivudine/pharmacology , Mice , Virus Replication/drug effects
15.
J Med Virol ; 93(9): 5481-5486, 2021 Sep.
Article in English | MEDLINE | ID: mdl-33963565

ABSTRACT

As severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infections continue, there is a substantial need for cost-effective and large-scale testing that utilizes specimens that can be readily collected from both symptomatic and asymptomatic individuals in various community settings. Although multiple diagnostic methods utilize nasopharyngeal specimens, saliva specimens represent an attractive alternative as they can rapidly and safely be collected from different populations. While saliva has been described as an acceptable clinical matrix for the detection of SARS-CoV-2, evaluations of analytic performance across platforms for this specimen type are limited. Here, we used a novel sensitive RT-PCR/MALDI-TOF mass spectrometry-based assay (Agena MassARRAY®) to detect SARS-CoV-2 in saliva specimens. The platform demonstrated high diagnostic sensitivity and specificity when compared to matched patient upper respiratory specimens. We also evaluated the analytical sensitivity of the platform and determined the limit of detection of the assay to be 1562.5 copies/ml. Furthermore, across the five individual target components of this assay, there was a range in analytic sensitivities for each target with the N2 target being the most sensitive. Overall, this system also demonstrated comparable performance when compared to the detection of SARS-CoV-2 RNA in saliva by the cobas® 6800/8800 SARS-CoV-2 real-time RT-PCR Test (Roche). Together, we demonstrate that saliva represents an appropriate matrix for SARS-CoV-2 detection on the novel Agena system as well as on a conventional real-time RT-PCR assay. We conclude that the MassARRAY® system is a sensitive and reliable platform for SARS-CoV-2 detection in saliva, offering scalable throughput in a large variety of clinical laboratory settings.


Subject(s)
COVID-19 Nucleic Acid Testing/standards , COVID-19/diagnosis , Diagnostic Tests, Routine/standards , RNA, Viral/genetics , SARS-CoV-2/genetics , Saliva/virology , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/standards , Benchmarking , COVID-19/virology , COVID-19 Nucleic Acid Testing/instrumentation , COVID-19 Nucleic Acid Testing/methods , Diagnostic Tests, Routine/instrumentation , Diagnostic Tests, Routine/methods , Humans , Limit of Detection , Nasopharynx/virology , Specimen Handling/standards , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/instrumentation , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
16.
J Med Virol ; 93(2): 1158-1163, 2021 02.
Article in English | MEDLINE | ID: mdl-32761908

ABSTRACT

We performed phylogenomic analysis of severe acute respiratory syndrome coronavirus-2 from 88 infected individuals across different regions of Colombia. Eleven different lineages were detected, suggesting multiple introduction events. Pangolin lineages B.1 and B.1.5 were the most frequent, with B.1 being associated with prior travel to high-risk areas.


Subject(s)
COVID-19/virology , Genetic Variation , Genome, Viral , Phylogeny , SARS-CoV-2/genetics , Adult , COVID-19/epidemiology , COVID-19/transmission , Colombia/epidemiology , Female , Geography , Humans , Male , Middle Aged , RNA, Viral/genetics , Travel
17.
Proc Natl Acad Sci U S A ; 115(41): E9659-E9667, 2018 10 09.
Article in English | MEDLINE | ID: mdl-30257946

ABSTRACT

HIV integrates into the host genome to create a persistent viral reservoir. Stimulation of CD4+ memory T lymphocytes with common γc-chain cytokines renders these cells more susceptible to HIV infection, making them a key component of the reservoir itself. IL-15 is up-regulated during primary HIV infection, a time when the HIV reservoir established. Therefore, we investigated the molecular and cellular impact of IL-15 on CD4+ T-cell infection. We found that IL-15 stimulation induces SAM domain and HD domain-containing protein 1 (SAMHD1) phosphorylation due to cell cycle entry, relieving an early block to infection. Perturbation of the pathways downstream of IL-15 receptor (IL-15R) indicated that SAMHD1 phosphorylation after IL-15 stimulation is JAK dependent. Treating CD4+ T cells with Ruxolitinib, an inhibitor of JAK1 and JAK2, effectively blocked IL-15-induced SAMHD1 phosphorylation and protected CD4+ T cells from HIV infection. Using high-resolution single-cell immune profiling using mass cytometry by TOF (CyTOF), we found that IL-15 stimulation altered the composition of CD4+ T-cell memory populations by increasing proliferation of memory CD4+ T cells, including CD4+ T memory stem cells (TSCM). IL-15-stimulated CD4+ TSCM, harboring phosphorylated SAMHD1, were preferentially infected. We propose that IL-15 plays a pivotal role in creating a self-renewing, persistent HIV reservoir by facilitating infection of CD4+ T cells with stem cell-like properties. Time-limited interventions with JAK1 inhibitors, such as Ruxolitinib, should prevent the inactivation of the endogenous restriction factor SAMHD1 and protect this long-lived CD4+ T-memory cell population from HIV infection.


Subject(s)
CD4-Positive T-Lymphocytes/immunology , HIV Infections/immunology , HIV-1/immunology , Interleukin-15/immunology , CD4-Positive T-Lymphocytes/pathology , CD4-Positive T-Lymphocytes/virology , Disease Susceptibility , Female , HEK293 Cells , HIV Infections/pathology , Humans , Janus Kinase 1/immunology , Janus Kinase 2/immunology , Male , Memory, Short-Term , Nitriles , Pyrazoles/pharmacology , Pyrimidines , SAM Domain and HD Domain-Containing Protein 1/immunology
18.
J Med Virol ; 92(9): 1695-1698, 2020 Sep.
Article in English | MEDLINE | ID: mdl-32383179

ABSTRACT

The urgent need to implement and rapidly expand testing for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection has led to the development of multiple assays. How these tests perform relative to one another is poorly understood. We evaluated the concordance between the Roche Diagnostics cobas 6800 SARS-CoV-2 test and a laboratory-developed test (LDT) real-time reverse transcription-polymerase chain reaction based on a modified Centers for Disease Control and Prevention protocol, for the detection of SARS-CoV-2 in samples submitted to the Clinical Laboratories of the Mount Sinai Health System. A total of 1006 nasopharyngeal swabs in universal transport medium from persons under investigation were tested for SARS-CoV-2 as part of routine clinical care using the cobas SARS-CoV-2 test with subsequent evaluation by the LDT. Cycle threshold values were analyzed and interpreted as either positive ("detected" or "presumptive positive"), negative (not detected), inconclusive, or invalid. Statistical analysis was performed using GraphPad Prism 8. The cobas SARS-CoV-2 test reported 706 positive and 300 negative results. The LDT reported 640 positive, 323 negative, 34 inconclusive, and 9 invalid results. When excluding inconclusive and invalid results, the overall percent agreement between the two platforms was 95.8%. Cohen's κ coefficient was 0.904 (95% confidence interval, 0.875-0.933), suggesting almost perfect agreement between both platforms. An overall discordance rate of 4.2% between the two systems may reflect differences in primer sequences, assay limit of detection, or other factors, highlighting the importance of comparing the performance of different testing platforms.


Subject(s)
COVID-19/diagnosis , COVID-19/virology , Nasopharynx/virology , Reverse Transcriptase Polymerase Chain Reaction , SARS-CoV-2/classification , SARS-CoV-2/genetics , Humans , RNA, Viral , Reagent Kits, Diagnostic , Reproducibility of Results , Reverse Transcriptase Polymerase Chain Reaction/instrumentation , Reverse Transcriptase Polymerase Chain Reaction/methods , SARS-CoV-2/isolation & purification , Sensitivity and Specificity
19.
World J Surg ; 44(12): 3993-3998, 2020 Dec.
Article in English | MEDLINE | ID: mdl-32737559

ABSTRACT

BACKGROUND: Comprehensive analysis of trauma care between high-, middle-, and low-income countries (HIC/MIC/LIC) is needed to improve global health. Comparison of HIC and MIC outcomes after damage control laparotomy (DCL) for patients is unknown. We evaluated DCL utilization among patients treated at high-volume trauma centers in the USA and South Africa, an MIC, hypothesizing similar mortality outcomes despite differences in resources and setting. METHODS: Post hoc analysis of prospectively collected trauma databases from participating centers was performed. Injury severity, physiologic, operative data and post-operative outcomes were abstracted. Univariate and multivariable analyses were performed to assess differences between HIC/MIC for the primary outcome of mortality. RESULTS: There were 967 HIC and 602 MIC patients who underwent laparotomy. DCL occurred in 144 MIC patients (25%) and 241 HIC (24%) patients. Most sustained (58%) penetrating trauma with higher rates in the MIC compared to the HIC (71 vs. 32%, p = 0.001). Between groups, no differences were found for admission physiology, coagulopathy, or markers of shock except for increased presence of hypotension among patients in the HIC. Crystalloid infusion volumes were greater among MIC patients, and MIC patients received fewer blood products than those in the HIC. Overall mortality was 30% with similar rates between groups (29 in HIC vs. 33% in MIC, p = 0.4). On regression, base excess and penetrating injury were independent predictors of mortality but not patient residential status. CONCLUSION: Use and survival of DCL for patients with severe abdominal trauma was similar between trauma centers in HIC and MIC settings despite increased penetrating trauma and less transfusion in the MIC center. While the results overall suggest no gap in care for patients requiring DCL in this MIC, it highlights improvements that can be made in damage control resuscitation.


Subject(s)
Abdominal Injuries/surgery , Hospitals, High-Volume/statistics & numerical data , Laparotomy/adverse effects , Laparotomy/statistics & numerical data , Abdominal Injuries/mortality , Adult , Female , Humans , Laparotomy/mortality , Male , Retrospective Studies , South Africa/epidemiology , Trauma Centers , Treatment Outcome
20.
World J Surg ; 44(5): 1485-1491, 2020 05.
Article in English | MEDLINE | ID: mdl-31933042

ABSTRACT

INTRODUCTION: We aimed to expand on the global surgical discussion around splenic trauma in order to understand locally and clinically relevant factors for operative (OP) and non-operative management (NOM) of splenic trauma in a South African setting. METHODS: A retrospective cohort study was performed using 2013-2017 data from the Pietermaritzburg Metropolitan Trauma Service. All adult patients (≥15 years) were included. Those managed with OP or NOM for splenic trauma were identified and analyzed descriptively. Multiple logistic regression analysis identified patients and clinical factors associated with management type. RESULTS: There were 127 patients with splenic injury. Median age was 29 [19-35] years with 42 (33%) women and 85 (67%) men. Blunt injuries occurred in the majority (81, 64%). Organ Injury Scale (OIS) grades included I (25, 20%), II (43, 34%), III (36, 28%), IV (15, 11%), and V (8, 6%). Nine patients expired. On univariate analysis, increasing OIS was associated with OP management, need for intensive care unit (ICU) admission, and hospital and ICU duration of stay, but not mortality. In patients with a delayed compared to early presentation, ICU utilization (62% vs. 36%, p = 0.008) and mortality (14% vs. 4%, p = 0.03) were increased. After adjusting for age, sex, presence of shock, and splenic OIS, penetrating trauma (adjusted odds ratio, 5.7; 95%CI, 1.7-9.8) and admission lactate concentration (adjusted odds ratio, 1.4; 95%CI 1.1-1.9) were significantly associated with OP compared to NOM (p = 0.002; area under the curve 0.81). CONCLUSIONS: We have identified injury mechanism and admission lactate as factors predictive of OP in South African patients with splenic trauma. Timely presentation to definitive care affects both ICU duration of stay and mortality outcomes. Future global surgical efforts may focus on expanding non-operative management protocols and improving pre-hospital care in patients with splenic trauma.


Subject(s)
Abdominal Injuries/therapy , Clinical Decision Rules , Clinical Decision-Making/methods , Conservative Treatment , Spleen/injuries , Abdominal Injuries/diagnosis , Abdominal Injuries/mortality , Adolescent , Adult , Aged , Aged, 80 and over , Female , Humans , Logistic Models , Male , Middle Aged , Retrospective Studies , South Africa , Splenectomy , Treatment Outcome , Young Adult
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