ABSTRACT
Areas of dense population congregation are prone to experience respiratory virus outbreaks. We monitored wastewater and clinic patients for the presence of respiratory viruses on a large, public university campus. Campus sewer systems were monitored in 16 locations for the presence of viruses using next generation sequencing over 22 weeks in 2023. During this period, we detected a surge in human adenovirus (HAdV) levels in wastewater. Hence, we initiated clinical surveillance at an on-campus clinic from patients presenting with acute respiratory infection. From whole genome sequencing of 123 throat and/or nasal swabs collected, we identified an outbreak of HAdV, specifically of HAdV-E4 and HAdV-B7 genotypes overlapping in time. The temporal dynamics and proportions of HAdV genotypes found in wastewater were corroborated in clinical infections. We tracked specific single nucleotide polymorphisms (SNPs) found in clinical virus sequences and showed that they arose in wastewater signals concordant with the time of clinical presentation, linking community transmission of HAdV to the outbreak. This study demonstrates how wastewater-based epidemiology can be integrated with surveillance at ambulatory healthcare settings to monitor areas prone to respiratory virus outbreaks and provide public health guidance.
Subject(s)
Respiratory Tract Infections , Wastewater , Wastewater/virology , Universities , Humans , Respiratory Tract Infections/epidemiology , Respiratory Tract Infections/virology , Adenoviruses, Human/genetics , Adenoviruses, Human/isolation & purification , Disease Outbreaks , Genotype , Environmental Monitoring/methodsABSTRACT
BACKGROUND: The 2022-23 US influenza season peaked early in fall 2022. METHODS: Late-season influenza vaccine effectiveness (VE) against outpatient, laboratory-confirmed influenza was calculated among participants of the US Influenza VE Network using a test-negative design. RESULTS: Of 2561 participants enrolled from December 12, 2022 to April 30, 2023, 91 laboratory-confirmed influenza cases primarily had A(H1N1)pdm09 (6B.1A.5a.2a.1) or A(H3N2) (3C.2a1b.2a.2b). Overall, VE was 30% (95% confidence interval -9%, 54%); low late-season activity precluded estimation for most subgroups. CONCLUSIONS: 2022-23 late-season outpatient influenza VE was not statistically significant. Genomic characterization may improve the identification of influenza viruses that circulate postinfluenza peak.
Subject(s)
Influenza A Virus, H1N1 Subtype , Influenza A Virus, H3N2 Subtype , Influenza Vaccines , Influenza, Human , Outpatients , Seasons , Vaccine Efficacy , Humans , Influenza Vaccines/immunology , Influenza Vaccines/administration & dosage , Influenza, Human/prevention & control , Influenza, Human/epidemiology , Influenza, Human/immunology , Influenza, Human/virology , Adult , Male , Female , United States/epidemiology , Middle Aged , Young Adult , Adolescent , Aged , Child , Influenza A Virus, H3N2 Subtype/immunology , Influenza A Virus, H3N2 Subtype/genetics , Child, Preschool , Influenza A Virus, H1N1 Subtype/immunology , Influenza A Virus, H1N1 Subtype/genetics , Outpatients/statistics & numerical data , Infant , Vaccination/statistics & numerical data , Aged, 80 and overABSTRACT
Declining sequencing costs coupled with the increasing availability of easy-to-use kits for the isolation of DNA and RNA transcripts from single cells have driven a rapid proliferation of studies centered around genomic and transcriptomic data. Simultaneously, a wealth of new techniques have been developed that utilize single cell technologies to interrogate a broad range of cell-biological processes. One recently developed technique, transposase-accessible chromatin with sequencing (ATAC) with select antigen profiling by sequencing (ASAPseq), provides a combination of chromatin accessibility assessments with measurements of cell-surface marker expression levels. While software exists for the characterization of these datasets, there currently exists no tool explicitly designed to reformat ASAP surface marker FASTQ data into a count matrix which can then be used for these downstream analyses. To address this, we created CountASAP, an easy-to-use Python package purposefully designed to transform FASTQ files from ASAP experiments into count matrices compatible with commonly-used downstream bioinformatic analysis packages. CountASAP takes advantage of the independence of the relevant data structures to perform fully parallelized matches of each sequenced read to user-supplied input ASAP oligos and unique cell-identifier sequences.
ABSTRACT
Valley Fever (VF), caused by fungi in the genus Coccidioides, is a prevalent disease in southwestern and western parts of the United States that affects both humans and animals, such as dogs. Although the immune responses to infection with Coccidioides spp. are not fully characterized, antibody-detection assays are used in conjunction with clinical presentation and radiologic findings to aid in the diagnosis of VF. These assays often use Complement Fixation (CF) and Tube Precipitin (TP) antigens as the main targets of IgG and IgM reactivity, respectively. Our group previously reported evidence of over 800 genes expressed at the protein level in C. posadasii. However, antibody reactivity to the majority of these proteins has never been explored. Using a new, high-throughput screening technology, the Nucleic Acid Programmable Protein Array (NAPPA), we screened serum specimens from dogs against 708 of these previously identified proteins for IgG reactivity. Serum from three separate groups of dogs was analyzed and revealed a small panel of proteins to be further characterized for immuno-reactivity. In addition to CF/CTS1 antigen, sera from most infected dogs showed antibody reactivity to endo-1,3-betaglucanase, peroxisomal matrix protein, and another novel reactive protein, CPSG_05795. These antigens may provide additional targets to aid in antibody-based diagnostics.
ABSTRACT
Influenza viruses are constantly evolving and are therefore monitored worldwide in the hope to reduce the burden of disease by annual updates to vaccine recommendations. We conducted genomic sequencing of 110 influenza A and 30 influenza B viruses from specimens collected between October 2023 and February 2024 in Arizona, USA. We identified mutations in the hemagglutinin (HA) antigenic sites as well as the neuraminidase (NA) gene in our samples. We also found no unique HA and NA mutations in vaccinated yet influenza-infected individuals. Real-time genomic sequencing surveillance is important to ensure influenza vaccine effectiveness.
Subject(s)
Genome, Viral , Influenza A virus , Influenza B virus , Influenza, Human , Mutation , Neuraminidase , Arizona/epidemiology , Humans , Influenza, Human/epidemiology , Influenza, Human/virology , Neuraminidase/genetics , Influenza B virus/genetics , Influenza A virus/genetics , Influenza A virus/classification , Hemagglutinin Glycoproteins, Influenza Virus/genetics , Genomics/methods , Phylogeny , Adult , Epidemiological Monitoring , Child , Adolescent , Middle Aged , Male , Female , Child, Preschool , Aged , Influenza Vaccines/immunology , Influenza Vaccines/genetics , Young Adult , Whole Genome SequencingABSTRACT
Areas of dense population congregation are prone to experience respiratory virus outbreaks. We monitored wastewater and clinic patients for the presence of respiratory viruses on a large, public university campus. Campus sewer systems were monitored in 16 locations for the presence of viruses using next generation sequencing over 22 weeks in 2023. During this period, we detected a surge in human adenovirus (HAdV) levels in wastewater. Hence, we initiated clinical surveillance at an on-campus clinic from patients presenting with acute respiratory infection. From whole genome sequencing of 123 throat and/or nasal swabs collected, we identified an outbreak of HAdV, specifically of HAdV-E4 and HAdV-B7 genotypes overlapping in time. The temporal dynamics and proportions of HAdV genotypes found in wastewater were corroborated in clinical infections. We tracked specific single nucleotide polymorphisms (SNPs) found in clinical virus sequences and showed that they arose in wastewater signals concordant with the time of clinical presentation, linking community transmission of HAdV to the outbreak. This study demonstrates how wastewater-based epidemiology can be integrated with surveillance at ambulatory healthcare settings to monitor areas prone to respiratory virus outbreaks and provide public health guidance.
ABSTRACT
In the United States, annual influenza vaccination is recommended for all persons aged ≥6 months. Using data from four vaccine effectiveness (VE) networks during the 2023-24 influenza season, interim influenza VE was estimated among patients aged ≥6 months with acute respiratory illness-associated medical encounters using a test-negative case-control study design. Among children and adolescents aged 6 months-17 years, VE against influenza-associated outpatient visits ranged from 59% to 67% and against influenza-associated hospitalization ranged from 52% to 61%. Among adults aged ≥18 years, VE against influenza-associated outpatient visits ranged from 33% to 49% and against hospitalization from 41% to 44%. VE against influenza A ranged from 46% to 59% for children and adolescents and from 27% to 46% for adults across settings. VE against influenza B ranged from 64% to 89% for pediatric patients in outpatient settings and from 60% to 78% for all adults across settings. These findings demonstrate that the 2023-24 seasonal influenza vaccine is effective at reducing the risk for medically attended influenza virus infection. CDC recommends that all persons aged ≥6 months who have not yet been vaccinated this season get vaccinated while influenza circulates locally.
Subject(s)
Influenza Vaccines , Influenza, Human , Adolescent , Adult , Humans , Child , Influenza, Human/epidemiology , Influenza, Human/prevention & control , Seasons , Case-Control Studies , Vaccine EfficacyABSTRACT
IMPORTANCE: Serology reveals exposure to pathogens, as well as the state of autoimmune and other clinical conditions. It is used to evaluate individuals and their histories and as a public health tool to track epidemics. Employing a variety of formats, studies nearly always perform serology by testing response to only one or a few antigens. However, clinical outcomes of new infections also depend on which previous infections may have occurred. We developed a high-throughput serology method that evaluates responses to hundreds of antigens simultaneously. It can be used to evaluate thousands of samples at a time and provide a quantitative readout. This tool will enable doctors to monitor which pathogens an individual has been exposed to and how that changes in the future. Moreover, public health officials could track populations and look for infectious trends among large populations. Testing many potential antigens at a time may also aid in vaccine development.
Subject(s)
Immune System , Serology , Humans , Public Health , Serology/methodsABSTRACT
We conducted surveillance of respiratory syncytial virus (RSV) genomic sequences for 100 RSV-A and 27 RSV-B specimens collected during November 2022-April 2023 in Arizona, USA. We identified mutations within prefusion F-protein antigenic sites in both subtypes. Continued genomic surveillance will be critical to ensure RSV vaccine effectiveness.
Subject(s)
Respiratory Syncytial Virus Infections , Respiratory Syncytial Virus, Human , Humans , Respiratory Syncytial Virus Infections/epidemiology , Arizona/epidemiology , Viral Fusion Proteins/genetics , Respiratory Syncytial Virus, Human/genetics , Antibodies, Neutralizing , Antibodies, Viral , MutationABSTRACT
Background: The COVID-19 pandemic has had important implications for college students' socioemotional and academic well-being. Sleep problems were common during this time, which may have further impacted well-being. Methods: Five hundred and fifty-two college students (Mage = 19.81; 58% female; 42% White) completed a survey in Fall 2021 reflecting on behaviors/emotions (sleep, depressive symptoms, loneliness, academic engagement) experienced during the first peak of COVID-19 and over the past month. Latent profile analysis was conducted to identify subgroups of sleepers during peak-COVID in relation to well-being during and after the initial peak. Results: Four sleep profiles were identified: Optimal (49%), High Latency/Medicated (23%), Average/Fair (16%), Low-Duration (12%). During peak-COVID, depression and loneliness were highest in High Latency/Medicated and Low-Duration subgroups; academic engagement was highest for Optimal sleepers. Following peak-COVID, academic engagement was highest for Average/Fair sleepers. Conclusions: Findings highlight heterogeneity in students' sleep patterns during the initial peak of COVID-19 and their relation to well-being during and post-peak-pandemic.
ABSTRACT
OBJECTIVE: This study investigated the seroprevalence of SARS-CoV-2 antibodies among adults over 18 years. DESIGN: Prospective cohort study. SETTINGS: A large public university. PARTICIPANTS: This study took volunteers over 5 days and recruited 1064 adult participants. PRIMARY OUTCOME MEASURES: Seroprevalence of SARS-CoV-2-specific antibodies due to previous exposure to SARS-CoV-2 and/or vaccination. RESULTS: The seroprevalence of the antireceptor binding domain (RBD) antibody was 90% by a lateral flow assay and 88% by a semiquantitative chemiluminescent immunoassay. The seroprevalence for antinucleocapsid was 20%. In addition, individuals with previous natural COVID-19 infection plus vaccination had higher anti-RBD antibody levels compared with those who had vaccination only or infection only. Individuals who had a breakthrough infection had the highest anti-RBD antibody levels. CONCLUSION: Accurate estimates of the cumulative incidence of SARS-CoV-2 infection can inform the development of university risk mitigation protocols such as encouraging booster shots, extending mask mandates or reverting to online classes. It could help us to have clear guidance to act at the first sign of the next surge as well, especially since there is a surge of COVID-19 subvariant infections.
Subject(s)
COVID-19 , Adult , Humans , Cross-Sectional Studies , Prospective Studies , Seroepidemiologic Studies , Universities , COVID-19/epidemiology , SARS-CoV-2 , Antibodies, ViralABSTRACT
OBJECTIVES: Access to readily available, reliable, and easy-to-use coronavirus disease 2019 (COVID-19) tests remains critical, despite great vaccination progress. Universal back-to-school testing offered at early care and education ([ECE]; ie, preschool) sites to screen for positive cases may help preschoolers safely return to, and stay in, ECE. We examined the acceptability and feasibility of using a quantitative polymerase chain reaction COVID-19 saliva test for young children (n = 227, 54.0% girls: mean age = 52.3 ± 8.1 months) and their caregivers (n = 70 teachers: mean = 36.6 ± 14.7 years; n = 227 parents: mean = 35.5 ± 9.1 years) to mitigate the spread of COVID-19 and reduce days of school and work missed for households with children who test positive. METHODS: Participants were recruited at ECE sites serving low-income communities as part of the Rapid Acceleration of Diagnostic Testing-Underserved Populations Back to Early Care and Education Safely with Sustainability via Active Garden Education project (NCT05178290). RESULTS: Surveys in English or Spanish administered at testing events to children and caregivers at ECE sites showed child and adult acceptability and feasibility ratings were generally high. More favorable child and parent ratings were positively associated with child age and whether the child was able to produce a saliva sample. Language preference was not associated with any outcomes. CONCLUSIONS: Saliva sampling for COVID-19 at ECE sites is an acceptable strategy as an additional layer of protection for 4- and 5-year-olds; however, alternate testing strategies may be needed for younger children.
Subject(s)
COVID-19 , Female , Adult , Child, Preschool , Child , Humans , Male , COVID-19/diagnosis , Feasibility Studies , Saliva , Polymerase Chain Reaction , Surveys and Questionnaires , COVID-19 TestingABSTRACT
OBJECTIVE: In April 2021, the US government made substantial investments in students' safe return to school by providing resources for school-based coronavirus disease 2019 (COVID-19) mitigation strategies, including COVID-19 diagnostic testing. However, testing uptake and access among vulnerable children and children with medical complexities remained unclear. METHODS: The Rapid Acceleration of Diagnostics Underserved Populations program was established by the National Institutes of Health to implement and evaluate COVID-19 testing programs in underserved populations. Researchers partnered with schools to implement COVID-19 testing programs. The authors of this study evaluated COVID-19 testing program implementation and enrollment and sought to determine key implementation strategies. A modified Nominal Group Technique was used to survey program leads to identify and rank testing strategies to provide a consensus of high-priority strategies for infectious disease testing in schools for vulnerable children and children with medical complexities. RESULTS: Among the 11 programs responding to the survey, 4 (36%) included prekindergarten and early care education, 8 (73%) worked with socioeconomically disadvantaged populations, and 4 focused on children with developmental disabilities. A total of 81 916 COVID-19 tests were performed. "Adapting testing strategies to meet the needs, preferences, and changing guidelines," "holding regular meetings with school leadership and staff," and "assessing and responding to community needs" were identified as key implementation strategies by program leads. CONCLUSIONS: School-academic partnerships helped provide COVID-19 testing in vulnerable children and children with medical complexities using approaches that met the needs of these populations. Additional work is needed to develop best practices for in-school infectious disease testing in all children.
Subject(s)
COVID-19 , Vulnerable Populations , Child , Humans , COVID-19 Testing , COVID-19/diagnosis , Schools , StudentsABSTRACT
Patients with 2019 coronavirus disease (COVID-19) exhibit a broad spectrum of clinical presentations. A person's antimicrobial antibody profile, as partially shaped by past infection or vaccination, can reflect the immune system health that is critical to control and resolve the infection. We performed an explorative immunoproteomics study using microbial protein arrays displaying 318 full-length antigens from 77 viruses and 3 bacteria. We compared antimicrobial antibody profiles between 135 patients with mild COVID-19 disease and 215 patients with severe disease in 3 independent cohorts from Mexico and Italy. Severe disease patients were older with higher prevalence of comorbidities. We confirmed that severe disease patients elicited a stronger anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) response. We showed that antibodies against HCoV-229E and HcoV-NL63 but not against HcoV-HKU1 and HcoV-OC43 were also higher in those who had severe disease. We revealed that for a set of IgG and IgA antibodies targeting coronaviruses, herpesviruses, and other respiratory viruses, a subgroup of patients with the highest reactivity levels had a greater incidence of severe disease compared to those with mild disease across all three cohorts. On the contrary, fewer antibodies showed consistent greater prevalence in mild disease in all 3 cohorts. IMPORTANCE The clinical presentations of COVID-19 range from asymptomatic to critical illness that may lead to intensive care or even death. The health of the immune system, as partially shaped by past infections or vaccinations, is critical to control and resolve the infection. Using an innovative protein array platform, we surveyed antibodies against hundreds of full-length microbial antigens from 80 different viruses and bacteria in COVID-19 patients from different geographic regions with mild or severe disease. We not only confirmed the association of severe COVID-19 disease with higher reactivity of antibody responses to SARS-CoV-2 but also uncovered known and novel associations with antibody responses against herpesviruses and other respiratory viruses. Our study represents a significant step forward in understanding the factors contributing to COVID-19 disease severity. We also demonstrate the power of comprehensive antimicrobial antibody profiling in deciphering risk factors for severe COVID-19. We anticipate that our approach will have broad applications in infectious diseases.
Subject(s)
COVID-19 , Coronavirus 229E, Human , Coronavirus OC43, Human , Humans , COVID-19/epidemiology , SARS-CoV-2 , Antibodies, ViralABSTRACT
The adaptive evolution of SARS-CoV-2 variants is driven by selection for increased viral fitness in transmissibility and immune evasion. Understanding the dynamics of how an emergent variant sweeps across populations can better inform public health response preparedness for future variants. Here, we investigated the state-level genomic epidemiology of SARS-CoV-2 through baseline genomic sequencing surveillance of 27,071 public testing specimens and 1,125 hospital inpatient specimens diagnosed between November 1, 2021, and January 31, 2022, in Arizona. We found that the Omicron variant rapidly displaced Delta variant in December 2021, leading to an "Omicron surge" of COVID-19 cases in early 2022. Wastewater sequencing surveillance of 370 samples supported the synchronous sweep of Omicron in the community. Hospital inpatient COVID-19 cases of Omicron variant presented to three major hospitals 10.51 days after its detection from public clinical testing. Nonsynonymous mutations in nsp3, nsp12, and nsp13 genes were significantly associated with Omicron hospital cases compared to community cases. To model SARS-CoV-2 transmissions across the state population, we developed a scalable sequence network methodology and showed that the Omicron variant spread through intracounty and intercounty transmissions. Finally, we demonstrated that the temporal emergence of Omicron BA.1 to become the dominant variant (17.02 days) was 2.3 times faster than the prior Delta variant (40.70 days) or subsequent Omicron sublineages BA.2 (39.65 days) and BA.5 (35.38 days). Our results demonstrate the uniquely rapid sweep of Omicron BA.1. These findings highlight how integrated public health surveillance can be used to enhance preparedness and response to future variants. IMPORTANCE SARS-CoV-2 continues to evolve new variants throughout the pandemic. However, the temporal dynamics of how SARS-CoV-2 variants emerge to become the dominant circulating variant is not precisely known. Genomic sequencing surveillance offers unique insights into how SARS-CoV-2 spreads in communities and the lead-up to hospital cases during a surge. Specifically, baseline sequencing surveillance through random selection of positive diagnostic specimens provides a representative outlook of the virus lineages circulating in a geographic region. Here, we investigated the emergence of the Omicron variant of concern in Arizona by leveraging baseline genomic sequence surveillance of public clinical testing, hospitals, and community wastewater. We tracked the spread and evolution of the Omicron variant as it first emerged in the general public, and its rapid shift in hospital admissions in the state health system. This study demonstrates the timescale of public health preparedness needed to respond to an antigenic shift in SARS-CoV-2.
Subject(s)
COVID-19 , SARS-CoV-2 , Humans , Arizona/epidemiology , SARS-CoV-2/genetics , COVID-19/epidemiology , Wastewater , Hospitals , COVID-19 TestingABSTRACT
BACKGROUND: The role of microbes in chronic rhinosinusitis (CRS) is poorly understood. We hypothesize that analyzing prior microbial exposures via assessing microbial protein serological reactivity in CRS versus controls may offer insights for CRS etiopathogenesis. METHODS: We profiled IgG and IgA antibodies to individual microbial proteins in serum samples of CRS patients and controls using a novel high-throughput microarray protein technology, Nucleic Acid Programmable Protein Array (NAPPA). The study was conducted on 118 subjects (39 CRS, 79 controls). A CRS-focused NAPPA array, with 1557 potentially sero-reactive microbial proteins elected from a pre-screening of 6500 genes of interest was constructed. It included membrane-associated proteins from 47 bacterial species and all proteins from 43 viral strains. Differences between CRS and controls were compared across individual antimicrobial antibodies and the species. RESULTS: Chronic rhinosinusitis patients had significantly elevated antimicrobial antibodies compared with controls. One bacterium (Staphylococcus aureus) and three viral strains (human metapneumovirus, human herpesvirus 5, and human herpesvirus 4) were identified as sources of the proteins that showed significantly elevated sero-reactivity in CRS patients. Within CRS, patients with polyps had elevated antibodies against S. aureus, influenza A virus (H1N1, H3N2), and rhinovirus B14. CRS patients without polyps showed more antibodies against human herpesvirus 1 and vaccinia virus WR. CONCLUSIONS: Compared with healthy controls, CRS patients' serum samples showed significantly increased sero-reactivity to both bacterial and viral proteins, reflecting recent or current infection or active colonization. Significantly higher antibodies against S. aureus, human metapneumovirus, human herpesvirus 5, and human herpesvirus 4 in CRS need further study.
Subject(s)
Anti-Infective Agents , Influenza A Virus, H1N1 Subtype , Microbiota , Rhinitis , Sinusitis , Humans , Staphylococcus aureus , Antibody Formation , Influenza A Virus, H3N2 Subtype , Chronic DiseaseABSTRACT
BACKGROUND: CT screening can detect lung cancer early but suffers a high false-positive rate. There is a need for molecular biomarkers that can distinguish malignant and benign indeterminate pulmonary nodules (IPN) detected by CT scan. METHODS: We profiled antibodies against 901 individual microbial antigens from 27 bacteria and 29 viruses in sera from 127 lung adenocarcinoma (ADC), 123 smoker controls (SMC), 170 benign nodule controls (BNC) individuals using protein microarrays to identify ADC and BNC specific antimicrobial antibodies. RESULTS: Analyzing fourth quartile ORs, we found more antibodies with higher prevalence in the three BNC subgroups than in ADC or SMC. We demonstrated that significantly more anti-Helicobacter pylori antibodies showed higher prevalence in ADC relative to SMC. We performed subgroup analysis and found that more antibodies with higher prevalence in light smokers (≤20 pack-years) compared with heavy smokers (>20 pack-years), in BNC with nodule size >1 cm than in those with ≤1 cm nodules, and in stage I ADC than in stage II and III ADC. We performed multivariate analysis and constructed antibody panels that can distinguish ADC versus SMC and ADC versus BNC with area under the ROC curve (AUC) of 0.88 and 0.80, respectively. CONCLUSIONS: Antimicrobial antibodies have the potential to reduce the false positive rate of CT screening and provide interesting insight in lung cancer development. IMPACT: Microbial infection plays an important role in lung cancer development and the formation of benign pulmonary nodules.
Subject(s)
Adenocarcinoma of Lung , Anti-Infective Agents , Lung Neoplasms , Multiple Pulmonary Nodules , Humans , Antibody Formation , Lung Neoplasms/diagnosis , Lung Neoplasms/pathologyABSTRACT
BACKGROUND: The healthcare burden of inflammatory bowel disease (IBD) is rising globally and there are limited non-invasive biomarkers for accurate and early diagnosis. AIM: To understand the important role that intestinal microbiota play in IBD pathogenesis and identify anti-microbial antibody signatures that benefit clinical management of IBD patients. METHODS: We performed serological profiling of 100 Crohn's disease (CD) patients, 100 ulcerative colitis (UC) patients and 100 healthy controls against 1173 bacterial and 397 viral proteins from 50 bacteria and 33 viruses on protein microarrays. The study subjects were randomly divided into discovery (n = 150) and validation (n = 150) sets. Statistical analysis was performed using R packages. RESULTS: Anti-bacterial antibody responses showed greater differential prevalence among the three subject groups than anti-viral antibody responses. We identified novel antibodies against the antigens of Bacteroidetes vulgatus (BVU_0562) and Streptococcus pneumoniae (SP_1992) showing higher prevalence in CD patients relative to healthy controls. We also identified antibodies against the antigen of Streptococcus pyogenes (SPy_2009) showing higher prevalence in healthy controls relative to UC patients. Using these novel antibodies, we built biomarker panels with area under the curve (AUC) of 0.81, 0.87, and 0.82 distinguishing CD vs control, UC vs control, and CD vs UC, respectively. Subgroup analysis revealed that penetrating CD behavior, colonic CD location, CD patients with a history of surgery, and extensive UC exhibited highest antibody prevalence among all patients. We demonstrated that autoantibodies and anti-microbial antibodies in CD patients had minimal correlation. CONCLUSION: We have identified antibody signatures for CD and UC using a comprehensive analysis of anti-microbial antibody response in IBD. These antibodies and the source microorganisms of their target antigens improve our understanding of the role of specific microorganisms in IBD pathogenesis and, after future validation, should aid early and accurate diagnosis of IBD.
Subject(s)
Colitis, Ulcerative , Crohn Disease , Inflammatory Bowel Diseases , Autoantibodies , Biomarkers , Humans , Viral ProteinsABSTRACT
In October 2020, the National Cancer Institute (NCI) Serological Sciences Network (SeroNet) was established to study the immune response to COVID-19, and "to develop, validate, improve, and implement serological testing and associated technologies" (https://www.cancer.gov/research/key-initiatives/covid-19/coronavirus-research-initiatives/serological-sciences-network). SeroNet is comprised of 25 participating research institutions partnering with the Frederick National Laboratory for Cancer Research (FNLCR) and the SeroNet Coordinating Center. Since its inception, SeroNet has supported collaborative development and sharing of COVID-19 serological assay procedures and has set forth plans for assay harmonization. To facilitate collaboration and procedure sharing, a detailed survey was sent to collate comprehensive assay details and performance metrics on COVID-19 serological assays within SeroNet. In addition, FNLCR established a protocol to calibrate SeroNet serological assays to reference standards, such as the U.S. severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) serology standard reference material and first WHO international standard (IS) for anti-SARS-CoV-2 immunoglobulin (20/136), to facilitate harmonization of assay reporting units and cross-comparison of study data. SeroNet institutions reported development of a total of 27 enzyme-linked immunosorbent assay (ELISA) methods, 13 multiplex assays, and 9 neutralization assays and use of 12 different commercial serological methods. FNLCR developed a standardized protocol for SeroNet institutions to calibrate these diverse serological assays to reference standards. In conclusion, SeroNet institutions have established a diverse array of COVID-19 serological assays to study the immune response to SARS-CoV-2 and vaccines. Calibration of SeroNet serological assays to harmonize results reporting will facilitate future pooled data analyses and study cross-comparisons. IMPORTANCE SeroNet institutions have developed or implemented 61 diverse COVID-19 serological assays and are collaboratively working to harmonize these assays using reference materials to establish standardized reporting units. This will facilitate clinical interpretation of serology results and cross-comparison of research data.
Subject(s)
COVID-19 , Antibodies, Viral , COVID-19/diagnosis , COVID-19 Testing , Humans , SARS-CoV-2 , Serologic Tests/methodsABSTRACT
As the SARS-CoV-2 virus evolves, mutations may result in diminished sensitivity to qRT-PCR diagnostic assays. We investigated four polymorphisms circulating in the SARS-CoV-2 Delta lineage that result in N gene target failure (NGTF) on the TaqPath COVID-19 Combo Kit. These mutations were detected from the SARS-CoV-2 genome sequences that matched with the diagnostic assay results of saliva specimens. Full length N genes from the samples displaying NGTF were cloned into plasmids and assayed using three SARS-CoV-2 qRT-PCR assays. These constructs resulted in reduced sensitivity to the TaqPath COVID-19 Combo Kit compared to the controls (mean Ct differences of 3.06, 7.70, 12.46, and 14.12), but were detected equivalently on the TaqPath COVID-19 Fast PCR Combo 2.0 or CDC 2019_nCoV_N2 assays. This work highlights the importance of genomic sequencing to monitor circulating mutations and provide guidance in improving diagnostic assays.