Nasal Throat Swabs Research Articles

Host inflammatory response is the major marker of severe respiratory syncytial virus infection in older adults

We aim to study the viral kinetics and host inflammatory response of RSV infection in older adults, and their correlation with disease severity. We performed a prospective observational study in adults with RSV infection. We serially collected nasal-throat swabs for quantification of RSV-A and RSV-B viral load, and peripheral blood samples for measurement of cytokine/chemokine concentrations. The study endpoints were (i) requiring supplemental oxygen therapy, and (ii) non-invasive ventilation, intensive care, or died within 30 days of admission. We performed multivariable logistic regression models to identify independent variables for severe disease. We enrolled 71 hospitalized patients and 10 outpatients treated for RSV infection (median age 75 years, 51% male, and 74% with comorbidities). Among hospitalized patients, 61% required supplemental oxygen therapy, and 18% had severe disease requiring non-invasive ventilation or intensive care, or died within 30 days. Inflammatory cytokine/chemokines IL-6, CXCL8/IL-8, CXCL9/MIG and CXCL10/IP-10 increased significantly during the acute phase of illness. IL-6 concentration was independently associated with severe disease after adjusting for confounding factors. RSV viral load was not associated with disease severity throughout the course of illness. Host inflammatory response is a major marker of severe disease in older adults with RSV infection.

Low Influenza Vaccine Effectiveness Against A(H3N2)-Associated Hospitalizations in 2016-2017 and 2017-2018 of the Hospitalized Adult Influenza Vaccine Effectiveness Network (HAIVEN).

The 2016-2017 and 2017-2018 influenza seasons were notable for the high number of hospitalizations for influenza A(H3N2) despite vaccine and circulating strain match. We evaluated vaccine effectiveness (VE) against hospitalization in the test-negative HAIVEN study. Nasal-throat swabs were tested by quantitative reverse transcription polymerase chain reaction (RT-PCR) for influenza and VE was determined based on odds of vaccination by generalized estimating equations. Vaccine-specific antibody was measured in a subset of enrollees. A total of 6129 adults were enrolled from 10 hospitals. Adjusted VE against A(H3N2) was 22.8% (95% confidence interval [CI], 8.3% to 35.0%), pooled across both years and 49.4% (95% CI, 34.3% to 61.1%) against B/Yamagata. In 2017-2018, the A(H3N2) VE point estimate for the cell-based vaccine was 43.0% (95% CI, -36.3% to 76.1%; 56 vaccine recipients) compared to 24.0% (95% CI, 3.9% to 39.9%) for egg-based vaccines. Among 643 with serology data, hemagglutinin antibodies against the egg-based A(H3N2) vaccine strain were increased in influenza-negative individuals. Low VE for the A/Hong Kong/4801/2014 vaccine virus in both A(H3N2) seasons emphasizes concerns for continued changes in H3N2 antigenic epitopes, including changes that may impact glycosylation and ultimately reduce VE.

Low Seroprevalence of SARS-CoV-2 Antibodies during Systematic Antibody Screening and Serum Responses in Patients after COVID-19 in a German Transplant Center.

The coronavirus disease 2019 (COVID-19) pandemic caused by SARS-CoV-2 denotes a global health issue. Data regarding COVID-19 incidence in kidney transplant recipients (KTR) are sparse. From 19 March to 19 May 2020, we performed a systematic screening for COVID-19 in KTR. Tests included serum analysis for SARS-CoV-2 antibodies using S protein-based immunofluorescence, anti-SARS-CoV-2 S1 immunoglobulin G (IgG) and immunoglobulin A (IgA) enzyme-linked immunosorbent assays (ELISA), and/or quantitative reverse transcription polymerase chain reaction (qRT-PCR) from nasal-throat swabs. Outpatient serum samples from KTR with PCR confirmed COVID-19, and swab samples from recipients (+donors) undergoing kidney transplantation were analyzed. Out of 223 samples from outpatients, 13 patients were positive with solely anti-SARS-CoV-2-IgA and 3 with both anti-IgA and anti-IgG. In total, 53 patients were symptomatic in the past, but positive results could be found in both symptomatic and asymptomatic patients. After an in depth analysis using immunofluorescence and neutralization tests in 2 KTR, recent COVID-19 infection remained highly suspicious. Apart from outpatient visits, only 5 out of 2044 KTR were symptomatic and tested positive via PCR, of which 4 recovered and one died. All patients showed seroconversion during the course of the disease. This study demonstrated a low seroprevalence in a German KTR cohort, and seroconversion of IgA and IgG after COVID-19 could be demonstrated. Effective containment strategies enabled us to continue our transplant program.

The Virome of Acute Respiratory Diseases in Individuals at Risk of Zoonotic Infections.

The ongoing coronavirus disease 2019 (COVID-19) pandemic emphasizes the need to actively study the virome of unexplained respiratory diseases. We performed viral metagenomic next-generation sequencing (mNGS) analysis of 91 nasal-throat swabs from individuals working with animals and with acute respiratory diseases. Fifteen virus RT-PCR-positive samples were included as controls, while the other 76 samples were RT-PCR negative for a wide panel of respiratory pathogens. Eukaryotic viruses detected by mNGS were then screened by PCR (using primers based on mNGS-derived contigs) in all samples to compare viral detection by mNGS versus PCR and assess the utility of mNGS in routine diagnostics. mNGS identified expected human rhinoviruses, enteroviruses, influenza A virus, coronavirus OC43, and respiratory syncytial virus (RSV) A in 13 of 15 (86.7%) positive control samples. Additionally, rotavirus, torque teno virus, human papillomavirus, human betaherpesvirus 7, cyclovirus, vientovirus, gemycircularvirus, and statovirus were identified through mNGS. Notably, complete genomes of novel cyclovirus, gemycircularvirus, and statovirus were genetically characterized. Using PCR screening, the novel cyclovirus was additionally detected in 5 and the novel gemycircularvirus in 12 of the remaining samples included for mNGS analysis. Our studies therefore provide pioneering data of the virome of acute-respiratory diseases from individuals at risk of zoonotic infections. The mNGS protocol/pipeline applied here is sensitive for the detection of a variety of viruses, including novel ones. More frequent detections of the novel viruses by PCR than by mNGS on the same samples suggests that PCR remains the most sensitive diagnostic test for viruses whose genomes are known. The detection of novel viruses expands our understanding of the respiratory virome of animal-exposed humans and warrant further studies.

Circulação do vírus respiratório sincicial humano em cinco Estados da Região Amazônica brasileira: primeira descrição do genótipo ON1 no Pará

OBJETIVO: Realizar a deteccao e caracterizacao das cepas de virus respiratorio sincicial humano (VRSH), nos casos de infeccao respiratoria aguda (IRA), circulantes nos estados brasileiros do Acre, Amapa, Amazonas, Para e Roraima, no ano de 2015. MATERIAIS E METODOS: Foram coletadas 1.082 amostras de aspirado de nasofaringe e swab combinado narina e garganta de pacientes de diferentes generos e faixas etarias com IRA e submetidas a qRT-PCR para VRSH. As amostras positivas foram inoculadas em cultura celular HEP-2 e as que apresentaram efeito citopatico foram submetidas a tres etapas: extracao do RNA viral, amplificacao do gene G pela RT-PCR e sequenciamento genetico. RESULTADOS: Das 1.082 amostras, 57 (5,3%) foram positivas para VRSH, sendo 38 (66,7%) de pacientes de 0 a 4 anos de idade. A circulacao predominou entre marco e julho, periodo de transicao climatica na Regiao. Apenas no Acre, Amazonas e Para foram detectadas amostras positivas, 15 (26,3%), 23 (40,4%) e 19 (33,3%), respectivamente. O efeito citopatico foi avaliado em 45 (78,9%) amostras, nas quais foram identificados os subgrupos: 40 (88,9%) do VRSH-B com genotipo BA e cinco (11,1%) do VRSH-A do genotipo ON1. CONCLUSAO: Este estudo revelou uma taxa de infeccao viral relevante em criancas de 0 a 4 anos de idade. A circulacao viral ocorreu no Acre, Amazonas e Para durante o periodo de mudanca climatica. Foi notoria a ocorrencia dos genotipos BA e ON1, sendo a primeira vez que se comprova a circulacao do ON1 no Para.

A Case-Crossover Design to Examine the Role of Aeroallergens and Respiratory Viruses on Childhood Asthma Exacerbations Requiring Hospitalization: The Mapcah Study

Background: Few case-control studies of time dependent environmental exposures and respiratory outcomes have been performed. Small sample sizes pose modeling challenges for estimating interactions. In contrast, case cross-over studies are well suited where control selection and responses are low, time consuming and costly. Objective: To demonstrate feasibility in daily recruitment of children admitted to hospital with asthma and validity of the case crossover methodology for hospital based studies. Methods: The Melbourne Air Pollen Children and Adolescent Health (MAPCAH) study recruited incident asthma admissions of children and adolescents aged 2–17 years to a tertiary hospital. A case was defined by date of admission, and eligible cases served as their own controls. We used bi-directional sampling design for control selection. At time of admission, participants underwent skin prick tests and nasal/throat swabs (NTS) to test for respiratory viruses. Questionnaires collected data on asthma management, family history and environmental characteristics. Daily concentrations of ambient pollen, air pollution and weather variables were also available. Results: 644 children were recruited. More than half (63%) were male with mean age 5.2(SD 3.3) years. Non-participants were slightly younger at admission (mean age 4.4, SD 2.8, p<0.001), although the absolute differences were small. Participants and non-participants were well balanced on gender. The most common reason for refusal to participate in the study was “causing further distress to child by skin prick testing”. Gender and age distributions were similar to the overall admissions to the tertiary hospital as well as in Victoria. Our study slightly under-represented winter admissions (p<0.001), and was over-represented in spring (p<0.001). More admissions occurred during the grass pollen season in our study than in general asthma hospital admissions across Victoria (42% versus 22%, p<0.001). Conclusions: The case cross-over method is a highly feasible design for a reasonably sized hospital based study of children with asthma. MAPCAH has robust internal validity and strong generalizability. Collection of data on respiratory viruses and pollen exposure at the time of admission on children with asthma provides important information that will have clinical and public health impacts.