Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 20 de 85
Filter
Add more filters

Publication year range
1.
Cell ; 184(10): 2595-2604.e13, 2021 05 13.
Article in English | MEDLINE | ID: mdl-33891875

ABSTRACT

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.


Subject(s)
COVID-19 Testing , COVID-19 , Models, Biological , SARS-CoV-2 , COVID-19/genetics , COVID-19/mortality , COVID-19/transmission , Female , Humans , Male , SARS-CoV-2/genetics , SARS-CoV-2/metabolism , SARS-CoV-2/pathogenicity , United States/epidemiology
2.
Cell ; 181(5): 990-996.e5, 2020 05 28.
Article in English | MEDLINE | ID: mdl-32386545

ABSTRACT

The novel coronavirus SARS-CoV-2 was first detected in the Pacific Northwest region of the United States in January 2020, with subsequent COVID-19 outbreaks detected in all 50 states by early March. To uncover the sources of SARS-CoV-2 introductions and patterns of spread within the United States, we sequenced nine viral genomes from early reported COVID-19 patients in Connecticut. Our phylogenetic analysis places the majority of these genomes with viruses sequenced from Washington state. By coupling our genomic data with domestic and international travel patterns, we show that early SARS-CoV-2 transmission in Connecticut was likely driven by domestic introductions. Moreover, the risk of domestic importation to Connecticut exceeded that of international importation by mid-March regardless of our estimated effects of federal travel restrictions. This study provides evidence of widespread sustained transmission of SARS-CoV-2 within the United States and highlights the critical need for local surveillance.


Subject(s)
Betacoronavirus/genetics , Coronavirus Infections/transmission , Pneumonia, Viral/transmission , Travel , Betacoronavirus/isolation & purification , COVID-19 , Connecticut/epidemiology , Coronavirus Infections/epidemiology , Coronavirus Infections/virology , Epidemiological Monitoring , Humans , Likelihood Functions , Pandemics , Phylogeny , Pneumonia, Viral/epidemiology , Pneumonia, Viral/virology , SARS-CoV-2 , Travel/legislation & jurisprudence , United States/epidemiology , Washington/epidemiology
3.
J Clin Microbiol ; 62(5): e0013924, 2024 May 08.
Article in English | MEDLINE | ID: mdl-38597655

ABSTRACT

We compared the performance of a new modified two-tier testing (MTTT) platform, the Diasorin Liaison chemiluminescent immunoassay (CLIA), to the Zeus enzyme-linked immunoassay (ELISA) MTTT and to Zeus ELISA/Viramed immunoblot standard two-tier testing (STTT) algorithm. Of 537 samples included in this study, 91 (16.9%) were positive or equivocal by one or more screening tests. Among these 91 samples, only 57 samples were concordant positive by first-tier screening tests, and only 19 of 57 were concordant by the three second-tier methods. For IgM results, positive percent agreement (PPA) was 68.1% for Diasorin versus 89.4% for Zeus compared to immunoblot. By contrast, the PPA for IgG for both Diasorin and Zeus was 100%. Using a 2-out-of-3 consensus reference standard, the PPAs for IgM were 75.6%, 97.8%, and 95.6% for Diasorin, Zeus, and immunoblot, respectively. The difference between Zeus MTTT and Diasorin MTTT for IgM detection was significant (P = 0.0094). PPA for both Diasorin and Zeus MTTT IgG assays was 100% but only 65.9% for immunoblot STTT (P = 0.0005). In total, second-tier positive IgM and/or IgG results were reported for 57 samples by Diasorin MTTT, 63 by Zeus MTTT, and 54 by Viramed STTT. While Diasorin CLIA MTTT had a much more rapid, automated, and efficient workflow, Diasorin MTTT was less sensitive for the detection of IgM than Zeus MTTT and STTT including in 5 early Lyme cases that were IgM negative but IgG positive. IMPORTANCE: The laboratory diagnosis of Lyme disease relies upon the detection of antibodies to Borrelia species. Standard two tier testing (STTT) methods rely upon immunoblots which have clinical and technical limitations. Modified two-tier testing (MTTT) methods have recently become available and are being widely adopted. There are limited independent data available assessing the performance of MTTT and STTT methods.


Subject(s)
Algorithms , Antibodies, Bacterial , Immunoglobulin G , Immunoglobulin M , Lyme Disease , Sensitivity and Specificity , Serologic Tests , Humans , Lyme Disease/diagnosis , Lyme Disease/immunology , Lyme Disease/blood , Immunoglobulin M/blood , Immunoglobulin G/blood , Serologic Tests/methods , Serologic Tests/standards , Antibodies, Bacterial/blood , Luminescent Measurements/methods , Immunoblotting/methods
4.
PLoS Biol ; 19(5): e3001236, 2021 05.
Article in English | MEDLINE | ID: mdl-33961632

ABSTRACT

With the emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants that may increase transmissibility and/or cause escape from immune responses, there is an urgent need for the targeted surveillance of circulating lineages. It was found that the B.1.1.7 (also 501Y.V1) variant, first detected in the United Kingdom, could be serendipitously detected by the Thermo Fisher TaqPath COVID-19 PCR assay because a key deletion in these viruses, spike Δ69-70, would cause a "spike gene target failure" (SGTF) result. However, a SGTF result is not definitive for B.1.1.7, and this assay cannot detect other variants of concern (VOC) that lack spike Δ69-70, such as B.1.351 (also 501Y.V2), detected in South Africa, and P.1 (also 501Y.V3), recently detected in Brazil. We identified a deletion in the ORF1a gene (ORF1a Δ3675-3677) in all 3 variants, which has not yet been widely detected in other SARS-CoV-2 lineages. Using ORF1a Δ3675-3677 as the primary target and spike Δ69-70 to differentiate, we designed and validated an open-source PCR assay to detect SARS-CoV-2 VOC. Our assay can be rapidly deployed in laboratories around the world to enhance surveillance for the local emergence and spread of B.1.1.7, B.1.351, and P.1.


Subject(s)
COVID-19/virology , SARS-CoV-2/genetics , COVID-19/diagnosis , COVID-19/genetics , DNA Primers , Humans , Multiplex Polymerase Chain Reaction/methods , Mutation , Polyproteins/genetics , Viral Proteins/genetics
5.
J Infect Dis ; 225(1): 55-64, 2022 01 05.
Article in English | MEDLINE | ID: mdl-34139752

ABSTRACT

BACKGROUND: Although a human adenovirus (HAdV) vaccine is available for military use, officers-in-training are not routinely vaccinated. We describe an HAdV-associated respiratory outbreak among unvaccinated cadets at the US Coast Guard Academy and its impact on cadet training. METHODS: We defined a case as a cadet with new onset cough or sore throat during August 1-October 4, 2019. We reviewed medical records and distributed a questionnaire to identify cases and to estimate impact on cadet training. We performed real-time polymerase chain reaction testing on patient and environmental samples and whole genome sequencing on a subset of positive patient samples. RESULTS: Among the 1072 cadets, 378 (35%) cases were identified by medical records (n = 230) or additionally by the questionnaire (n = 148). Of the 230 cases identified from medical records, 138 (60%) were male and 226 (98%) had no underlying conditions. From questionnaire responses, 113 of 228 (50%) cases reported duty restrictions. Of cases with respiratory specimens, 36 of 50 (72%) were HAdV positive; all 14 sequenced specimens were HAdV-4a1. Sixteen (89%) of 18 environmental specimens from the cadet dormitory were HAdV-positive. CONCLUSIONS: The HAdV-4-associated outbreak infected a substantial number of cadets and significantly impacted cadet training. Routine vaccination could prevent HAdV respiratory outbreaks in this population.


Subject(s)
Adenovirus Infections, Human/epidemiology , Adenovirus Vaccines , Adenoviruses, Human/isolation & purification , Military Personnel/statistics & numerical data , Polymerase Chain Reaction/methods , Respiratory Tract Infections/epidemiology , Adenoviruses, Human/genetics , Adolescent , Disease Outbreaks , Female , Humans , Male , Respiratory Tract Infections/virology , United States/epidemiology , Young Adult
6.
Ann Emerg Med ; 79(2): 182-186, 2022 02.
Article in English | MEDLINE | ID: mdl-34756452

ABSTRACT

STUDY OBJECTIVE: Our institution experienced a change in SARS-CoV-2 testing policy as well as substantial changes in local COVID-19 prevalence, allowing for a unique examination of the relationship between SARS-CoV-2 testing and emergency department (ED) length of stay. METHODS: This was an observational interrupted time series of all patients admitted to an academic health system between March 15, 2020, and September 30, 2020. Given testing limitations from March 15 to April 24, all patients receiving SARS-CoV-2 tests were symptomatic. On April 24, testing was expanded to all ED admissions. The primary and secondary outcomes were ED length of stay and number needed to test to obtain a positive, respectively. RESULTS: A total of 70,856 patients were cared for in the EDs during the 7-month period. The testing change increased admission length of stay by 1.89 hours (95% confidence interval 1.39 to 2.38). The number needed to test was 2.5 patients and was highest yield on April 1, 2020, when the state positivity rate was 39.7%; however, the number needed to test exceeded 170 patients by Sept 1, 2020, at which point the state positivity rate was 0.5%. CONCLUSION: Although universal SARS-CoV-2 testing of ED admissions may meaningfully support mitigation and containment efforts, the clinical cost of testing all admissions amid low community positivity is notable. In our system, universal ED SARS-CoV-2 testing was associated with a 24% increase in admission length of stay alongside the detection of only 1 positive case every other day. Given the known harms and risks of ED boarding and crowding, solutions must be developed to support regular operational flow while balancing infection prevention needs.


Subject(s)
COVID-19 Testing/methods , COVID-19/diagnosis , Emergency Service, Hospital/statistics & numerical data , Length of Stay/statistics & numerical data , COVID-19/epidemiology , Humans , Pandemics , SARS-CoV-2 , United States/epidemiology
7.
J Clin Microbiol ; 58(2)2020 01 28.
Article in English | MEDLINE | ID: mdl-31776192

ABSTRACT

The Singulex Clarity C. diff toxins A/B (Clarity) assay is an automated, ultrasensitive immunoassay for the detection of Clostridioides difficile toxins in stool. In this study, the performance of the Clarity assay was compared to that of a multistep algorithm using an enzyme immunoassay (EIA) for detection of glutamate dehydrogenase (GDH) and toxins A and B arbitrated by a semiquantitative cell cytotoxicity neutralization assay (CCNA). The performance of the assay was evaluated using 211 residual deidentified stool samples tested with a GDH-and-toxin EIA (C. Diff Quik Chek Complete; Techlab), with GDH-and-toxin discordant samples tested with CCNA. The stool samples were stored at -80°C before being tested with the Clarity assay. For samples discordant between Clarity and the standard-of-care algorithm, the samples were tested with PCR (Xpert C. difficile; Cepheid), and chart review was performed. The testing algorithm resulted in 34 GDH+/toxin+, 53 GDH-/toxin-, and 124 GDH+/toxin- samples, of which 39 were CCNA+ and 85 were CCNA- Clarity had 96.2% negative agreement with GDH-/toxin- samples, 100% positive agreement with GDH+/toxin+ samples, and 95.3% agreement with GDH+/toxin-/CCNA- samples. The Clarity result was invalid for one sample. Clarity agreed with 61.5% of GDH+/toxin-/CCNA+ samples, 90.0% of GDH+/toxin-/CCNA+ (high-positive) samples, and 31.6% of GDH+/toxin-/CCNA+ (low-positive) samples. The Singulex Clarity C. diff toxins A/B assay demonstrated high agreement with a testing algorithm utilizing a GDH-and-toxin EIA and CCNA. This novel automated assay may offer an accurate, stand-alone solution for C. difficile infection (CDI) diagnostics, and further prospective clinical studies are merited.


Subject(s)
Bacterial Proteins/analysis , Bacterial Toxins/analysis , Clostridioides difficile/chemistry , Clostridioides difficile/enzymology , Enterotoxins/analysis , Glutamate Dehydrogenase/analysis , Immunoenzyme Techniques/standards , Adult , Algorithms , Automation, Laboratory , Clostridium Infections/diagnosis , Feces/chemistry , Female , Humans , Male , Sensitivity and Specificity
8.
J Infect Dis ; 217(6): 897-905, 2018 03 05.
Article in English | MEDLINE | ID: mdl-29281100

ABSTRACT

Background: Despite the high burden of respiratory infection and the importance of early and accurate diagnosis, there is no simple diagnostic test to rule in viral infection as a cause of respiratory symptoms. Methods: We performed RNA sequencing on human nasal epithelial cells following stimulation of the intracellular viral recognition receptor RIG-I. Next, we evaluated whether measuring identified host mRNAs and proteins from patient nasopharyngeal swabs could predict the presence of a respiratory virus in the sample. Results: Our first study showed that a signature of 3 mRNAs, CXCL10, IFIT2, and OASL, predicted respiratory virus detection with an accuracy of 97% (95% confidence interval [CI], 0.9-1.0), and identified proteins correlating with virus detection. In a second study, elevated CXCL11 or CXCL10 protein levels identified samples containing respiratory viruses, including viruses not on the initial test panel. Overall area under the curve (AUC) values were: CXCL11 AUC = 0.901 (95% CI, 0.86-0.94); CXCL10 AUC = 0.85 (95% CI, 0.80-0.91). Conclusions: Host antiviral mRNAs and single host proteins detectable using nasopharyngeal swabs accurately predict the presence of viral infection. This approach holds promise for developing rapid, cost-effective tests to improve management of patients with respiratory illnesses.


Subject(s)
Antiviral Agents/therapeutic use , Nasopharynx/virology , Respiratory Tract Infections/drug therapy , Virus Diseases/drug therapy , Biomarkers , Chemokine CXCL10/metabolism , Chemokine CXCL11/metabolism , Female , Gene Expression Regulation/immunology , Humans , Male , RNA, Messenger/genetics , RNA, Viral , Respiratory Tract Infections/virology , Virus Diseases/diagnosis
9.
Emerg Infect Dis ; 24(2): 201-209, 2018 02.
Article in English | MEDLINE | ID: mdl-29350143

ABSTRACT

Human adenovirus type 4 (HAdV-4) is most commonly isolated in military settings. We conducted detailed molecular characterization on 36 HAdV-4 isolates recovered from civilian adults with acute respiratory disease (ARD) in the northeastern United States during 2011-2015. Specimens came from college students, residents of long-term care facilities or nursing homes, a cancer patient, and young adults without co-morbidities. HAdV-4 genome types 4a1 and 4a2, the variants most frequently detected among US military recruits in basic training before the restoration of vaccination protocols, were isolated in most cases. Two novel a-like variants were recovered from students enrolled at a college in Tompkins County, New York, USA, and a prototype-like variant distinguishable from the vaccine strain was isolated from an 18-year-old woman visiting a physician's office in Ulster County, New York, USA, with symptoms of influenza-like illness. Our data suggest that HAdV-4 might be an underestimated causative agent of ARD among civilian adults.


Subject(s)
Adenovirus Infections, Human/epidemiology , Adenovirus Infections, Human/virology , Adenoviruses, Human/classification , Respiratory Tract Infections/epidemiology , Respiratory Tract Infections/virology , Adenovirus Infections, Human/diagnosis , Adenoviruses, Human/genetics , Adult , Disease Outbreaks , Genome, Viral , Humans , Molecular Epidemiology , New England/epidemiology , Retrospective Studies
11.
J Clin Microbiol ; 56(7)2018 07.
Article in English | MEDLINE | ID: mdl-29695519

ABSTRACT

An accurate laboratory diagnosis of influenza, respiratory syncytial virus (RSV), and other respiratory viruses can help to guide patient management, antiviral therapy, infection prevention strategies, and epidemiologic monitoring. Influenza has been the primary driver of rapid laboratory testing due to its morbidity and mortality across all ages, the availability of antiviral therapy, which must be given early to have an effect, and the constant threat of new pandemic strains. Over the past 30 years, there has been an evolution in viral diagnostic testing, from viral culture to rapid antigen detection, and more recently, to highly sensitive nucleic acid amplification tests (NAAT), as well as a trend to testing at the point of care (POC). Simple rapid antigen immunoassays have long been the mainstay for POC testing for influenza A and B viruses and respiratory syncytial virus (RSV) but have been faulted for low sensitivity. In 2015, the first POC NAAT for the detection of influenza was approved by the Food and Drug Administration (FDA), ushering in a new era. In 2017, the FDA reclassified rapid influenza diagnostic tests (RIDTs) from class I to class II devices with new minimum performance standards and a requirement for annual reactivity testing. Consequently, many previously available RIDTs can no longer be purchased in the United States. In this review, recent developments in Clinical Laboratory Improvement Amendments of 1988 (CLIA)-waived testing for respiratory virus infections will be presented, with the focus on currently available FDA-cleared rapid antigen and molecular tests primarily for influenza A and B viruses and RSV.


Subject(s)
Diagnostic Tests, Routine/standards , Molecular Diagnostic Techniques , Nasopharynx/virology , Point-of-Care Systems/standards , Respiratory Tract Infections/diagnosis , Respiratory Tract Infections/virology , Diagnostic Tests, Routine/trends , Humans , Immunoassay/standards , Influenza A virus/genetics , Influenza B virus/genetics , Molecular Diagnostic Techniques/standards , Point-of-Care Systems/trends , Respiratory Syncytial Virus, Human/genetics
12.
Emerg Infect Dis ; 21(3): 400-8, 2015 Mar.
Article in English | MEDLINE | ID: mdl-25694248

ABSTRACT

Conventional methods for detection and discrimination of influenza viruses are time consuming and labor intensive. We developed a diagnostic platform for simultaneous identification and characterization of influenza viruses that uses a combination of nanomicroarray for screening and multiplex next-generation sequencing (NGS) assays for laboratory confirmation. The nanomicroarray was developed to target hemagglutinin, neuraminidase, and matrix genes to identify influenza A and B viruses. PCR amplicons synthesized by using an adapted universal primer for all 8 gene segments of 9 influenza A subtypes were detected in the nanomicroarray and confirmed by the NGS assays. This platform can simultaneously detect and differentiate multiple influenza A subtypes in a single sample. Use of these methods as part of a new diagnostic algorithm for detection and confirmation of influenza infections may provide ongoing public health benefits by assisting with future epidemiologic studies and improving preparedness for potential influenza pandemics.


Subject(s)
High-Throughput Nucleotide Sequencing , Influenza, Human/diagnosis , Influenza, Human/virology , Nanotechnology , Neuraminidase/genetics , Oligonucleotide Array Sequence Analysis , Orthomyxoviridae/classification , Orthomyxoviridae/genetics , Genotype , Hemagglutinin Glycoproteins, Influenza Virus/genetics , High-Throughput Nucleotide Sequencing/methods , Humans , Multiplex Polymerase Chain Reaction , Oligonucleotide Array Sequence Analysis/methods , Phylogeny
15.
J Clin Microbiol ; 53(4): 1445-7, 2015 Apr.
Article in English | MEDLINE | ID: mdl-25673791

ABSTRACT

In Italy, Toscana virus is the most common cause of meningitis from May to October. Though only a few cases have been reported in U.S. travelers returning from Europe, most cases are likely unrecognized due to lack of familiarity with the disease. Here, we describe the case of an 82-year-old man presenting with fever, profound weakness, and hearing loss after returning to the United States following a 2-week summertime vacation in southern Italy who was ultimately diagnosed with Toscana virus encephalitis. This case should alert clinicians to the possibility of Toscana virus infection in returning travelers and provides information on how to obtain testing if Toscana virus is suspected.


Subject(s)
Encephalitis, Viral/virology , Sandfly fever Naples virus/isolation & purification , Aged, 80 and over , Encephalitis, Viral/epidemiology , Humans , Italy/epidemiology , Male , Travel , United States/epidemiology
16.
J Clin Microbiol ; 52(8): 3057-9, 2014 Aug.
Article in English | MEDLINE | ID: mdl-24850350

ABSTRACT

To compare Simplexa Flu A/B & RSV PCR with cytospin-immunofluorescence and laboratory-developed TaqMan PCR methods, 445 nasopharyngeal samples were tested. Of these, 199 were positive (46 for respiratory syncytial virus [RSV], 120 for influenza A, and 33 for influenza B) and 246 were negative. The direct fluorescent-antibody assay (DFA) detected 132 (66.3%) positive samples, Simplexa direct detected 162 (81.4%), Simplexa using extracts detected 177 (88.9%), and lab-developed TaqMan PCR reference methods detected 199 (100%). The specificities were 99.6%, 100%, 100%, and 100%, respectively. The two Simplexa methods were more sensitive than the DFA (P = 0.0001) but less sensitive than the TaqMan reverse transcriptase PCR (P = 0.0001).


Subject(s)
Diagnostic Tests, Routine/methods , Influenza, Human/diagnosis , Polymerase Chain Reaction/methods , Adult , Aged , Aged, 80 and over , Fluorescent Antibody Technique/methods , Hospitals , Humans , Influenza, Human/virology , Middle Aged , Nasopharynx/virology , Sensitivity and Specificity
17.
J Clin Microbiol ; 52(1): 275-80, 2014 Jan.
Article in English | MEDLINE | ID: mdl-24226924

ABSTRACT

Simplexa Clostridium difficile universal direct PCR, a real-time PCR assay for the detection of the C. difficile toxin B (tcdB) gene using the 3M integrated cycler, was compared with a two-step algorithm which includes the C. Diff Chek-60 glutamate dehydrogenase (GDH) antigen assay followed by cytotoxin neutralization. Three hundred forty-two liquid or semisolid stools submitted for diagnostic C. difficile testing, 171 GDH antigen positive and 171 GDH antigen negative, were selected for the study. All samples were tested by the C. Diff Chek-60 GDH antigen assay, cytotoxin neutralization, and Simplexa direct PCR. Of 171 GDH-positive samples, 4 were excluded (from patients on therapy or from whom duplicate samples were obtained) and 88 were determined to be true positives for toxigenic C. difficile. Of the 88, 67 (76.1%) were positive by the two-step method and 86 (97.7%) were positive by PCR. Seventy-nine were positive by the GDH antigen assay only. Of 171 GDH antigen-negative samples, none were positive by PCR. One antigen-negative sample positive by the cytotoxin assay only was deemed a false positive based on chart review. Simplexa C. difficile universal direct PCR was significantly more sensitive for detecting toxigenic C. difficile bacteria than cytotoxin neutralization (P = 0.0002). However, most PCR-positive/cytotoxin-negative patients did not have clear C. difficile disease. The estimated cost avoidance provided by a more rapid molecular diagnosis was outweighed by the cost of isolating and treating PCR-positive/cytotoxin-negative patients. The costs, clinical consequences, and impact on nosocomial transmission of treating and/or isolating patients positive for toxigenic C. difficile by PCR but negative for in vivo toxin production merit further study.


Subject(s)
Bacterial Proteins/analysis , Bacterial Proteins/genetics , Bacterial Toxins/analysis , Bacterial Toxins/genetics , Biological Assay/methods , Clostridioides difficile/isolation & purification , Clostridium Infections/diagnosis , Diarrhea/diagnosis , Real-Time Polymerase Chain Reaction/methods , Clostridioides difficile/genetics , Clostridium Infections/microbiology , Diarrhea/microbiology , Glutamate Dehydrogenase/analysis , Humans , Neutralization Tests/methods , Sensitivity and Specificity
18.
J Clin Microbiol ; 52(12): 4385-7, 2014 Dec.
Article in English | MEDLINE | ID: mdl-25297327

ABSTRACT

We report the development of a novel europium nanoparticle-based immunoassay (ENIA) for rapid detection of influenza A and influenza B viruses. The ENIA demonstrated sensitivities of 90.7% (147/162) for influenza A viruses and 81.80% (9/11) for influenza B viruses compared to those for an in-house reverse transcription (RT)-PCR assay in testing of influenza-positive clinical samples.


Subject(s)
Antigens, Viral/analysis , Diagnostic Tests, Routine/methods , Europium , Influenza A virus/isolation & purification , Influenza B virus/isolation & purification , Influenza, Human/diagnosis , Nanoparticles , Humans , Immunoassay/methods , Influenza, Human/virology , Sensitivity and Specificity
19.
J Exp Med ; 221(9)2024 09 02.
Article in English | MEDLINE | ID: mdl-38949638

ABSTRACT

Studies during the COVID-19 pandemic showed that children had heightened nasal innate immune responses compared with adults. To evaluate the role of nasal viruses and bacteria in driving these responses, we performed cytokine profiling and comprehensive, symptom-agnostic testing for respiratory viruses and bacterial pathobionts in nasopharyngeal samples from children tested for SARS-CoV-2 in 2021-22 (n = 467). Respiratory viruses and/or pathobionts were highly prevalent (82% of symptomatic and 30% asymptomatic children; 90 and 49% for children <5 years). Virus detection and load correlated with the nasal interferon response biomarker CXCL10, and the previously reported discrepancy between SARS-CoV-2 viral load and nasal interferon response was explained by viral coinfections. Bacterial pathobionts correlated with a distinct proinflammatory response with elevated IL-1ß and TNF but not CXCL10. Furthermore, paired samples from healthy 1-year-olds collected 1-2 wk apart revealed frequent respiratory virus acquisition or clearance, with mucosal immunophenotype changing in parallel. These findings reveal that frequent, dynamic host-pathogen interactions drive nasal innate immune activation in children.


Subject(s)
COVID-19 , Immunity, Innate , SARS-CoV-2 , Humans , Immunity, Innate/immunology , Child, Preschool , Infant , COVID-19/immunology , COVID-19/virology , Child , SARS-CoV-2/immunology , Female , Male , Nasopharynx/immunology , Nasopharynx/virology , Nasopharynx/microbiology , Viral Load , Nasal Mucosa/immunology , Nasal Mucosa/virology , Nasal Mucosa/microbiology , Cytokines/metabolism , Cytokines/immunology , Host-Pathogen Interactions/immunology , Adolescent , Nose/immunology , Nose/virology , Nose/microbiology , Coinfection/immunology , Coinfection/virology
20.
J Clin Microbiol ; 51(11): 3765-9, 2013 Nov.
Article in English | MEDLINE | ID: mdl-24006008

ABSTRACT

The Simplexa HSV 1 & 2 direct PCR assay was compared with conventional cell culture, cytospin-enhanced direct fluorescent antibody (DFA), and a laboratory-developed real-time TaqMan PCR (LDT HSV PCR) using extracted nucleic acid for the detection of herpes simplex virus (HSV) in dermal, genital, mouth, ocular, and other swab samples. One hundred seventy-one swabs were tested prospectively, and 58 were positive for HSV (34 HSV-1 and 24 HSV-2). Cytospin-DFA detected 50 (86.2%), conventional cell culture 51 (87.9%), Simplexa direct 55 (94.8%), and LDT HSV PCR 57 (98.3%) of 58 true positives. Simplexa direct detected more positives than DFA and culture, but the differences were not significant (P = 0.0736 and P = 0.3711, respectively, by the McNemar test). Samples that were positive by all methods (n = 48) were strong positives (LDT cycle threshold [CT] value, 14.4 to 26.1). One strongly positive sample was falsely negative by LDT HSV PCR due to a failure of TaqMan probe binding. Three samples falsely negative by Simplexa direct had high CT values by LDT HSV PCR (LDT CT, 35.8 to 38.2). Omission of the DNA extraction step by Simplexa direct led to a drop in sensitivity compared to the sensitivity of LDT HSV PCR using extracted samples (94.8% versus 98.3%, respectively), but the difference was not significant (P = 0.6171). Simplexa HSV 1 & 2 direct PCR was the most expensive but required the least training of the assays used, had the lowest hands-on time and fastest assay time (75 min, versus 3 h by LDT HSV PCR), and provided the HSV type.


Subject(s)
Clinical Laboratory Techniques/methods , Herpes Simplex/diagnosis , Simplexvirus/isolation & purification , Adolescent , Adult , Aged , Aged, 80 and over , Child , Child, Preschool , Costs and Cost Analysis , Female , Fluorescent Antibody Technique/methods , Herpes Simplex/virology , Humans , Infant , Infant, Newborn , Male , Middle Aged , Polymerase Chain Reaction/methods , Sensitivity and Specificity , Time Factors , Virus Cultivation/methods , Young Adult
SELECTION OF CITATIONS
SEARCH DETAIL