ABSTRACT
Background SARS-CoV-2 quick testing and reporting are now considered relevant for the containment of new pandemic waves. Antigen testing in self-collected saliva might be useful. We compared the diagnostic performance of salivary and naso-pharyngeal swab (NPS) SARS-CoV-2 antigen detection by a rapid chemiluminescent assay (CLEIA) and two different point-of-care (POC) immunochromatographic assays, with that of molecular testing. Methods 234 patients were prospectively enrolled. Paired self-collected saliva (Salivette) and NPS were obtained to perform rRT-PCR, chemiluminescent (Lumipulse G) and POC (NPS: Fujirebio and Abbott; saliva: Fujirebio) for SARS-CoV-2 antigen detection. Results The overall agreement between NPS and saliva rRT-PCR was 78.7%, reaching 91.7% at the first week from symptoms onset. SARS-CoV-2 CLEIA antigen was highly accurate in distinguishing between positive and negative NPS (ROC-AUC=0.939, 95%CI:0.903-0.977), with 81.6% sensitivity and 93.8% specificity. This assay on saliva had an overall good accuracy (ROC-AUC=0.805, 95%CI:0.740-0.870), reaching the optimal value within 7 days from symptom onset (Sensitivity: 72%; Specificity: 97%). POC antigen in saliva had a very limited sensitivity (13%), performing better in NPS (Sensitivity: 48% and 66%; Specificity: 100% and 99% for Espline and Abbott respectively), depending on viral loads. Conclusions Self-collected saliva is a valid alternative to NPS for SARS-CoV-2 detection not only by molecular, but also by CLEIA antigen testing, for which the highest diagnostic accuracy was achieved in the first week from symptom onset. Saliva is not suitable for POC, although the accuracy of these tests appears satisfactory for NPS with high viral load.
Subject(s)
PharyngitisABSTRACT
Gut microbiota plays a critical role in the induction of adaptive immune responses to influenza virus infection. However, the role of nasal bacteria in the induction of the virus-specific adaptive immunity is less clear. Here we demonstrate that while intranasal administration of influenza virus hemagglutinin vaccine alone was insufficient to induce the vaccine-specific antibody responses, disruption of nasal bacteria by lysozyme or addition of culturable oral bacteria from a healthy human volunteer rescued inability of the nasal bacteria to generate antibody responses to intranasally administered the split-virus vaccine. Myd88-depdnent signaling in the hematopoietic compartment was required for adjuvant activity of intranasally administered oral bacteria. In addition, we found that the oral bacteria-combined intranasal vaccine induced protective antibody response to influenza virus and SARS-CoV-2 infection. Our findings here have identified a previously unappreciated role for nasal bacteria in the induction of the virus-specific adaptive immune responses.
Subject(s)
COVID-19 , Influenza, HumanABSTRACT
Background: Identifying risk factors for severe novel-coronavirus disease (COVID-19) is useful to ascertain which patients may benefit from advanced supportive care. The study offers a description of COVID-19 patients, admitted to a general ward for a non-critical clinical picture, with the aim to analyse the differences between those transferred to the intensive (ICU) and/or sub-intensive care (SICU) units and those who were not. Methods: This observational retrospective study includes all COVID-19 patients admitted to the Infectious Diseases Unit. Clinical, laboratory, radiological and treatment data were collected. The primary outcome was a composite of need of transfer to the ICU and/or SICU during the hospitalization. Patients who did not require to be transferred are defined as Group 1; patients who were transferred to the ICU and/or SICU are defined as Group 2. Demographic, clinical characteristics and laboratory findings at the 1 st , 3 rd and last measurements were compared between the two groups. Results: 303 patients were included. The median age was 62 years. 69 patients (22.8%) met the primary outcome and were defined as Group 2. The overall fatality rate was 6.8%. Group 2 patients were predominantly male (76.8% vs. 55.1%, p<0.01), had a higher fatality rate (14.5% vs. 3.8%, p<0,01), had more hypertension (72.4% vs. 44%, p<0,01) and diabetes (31.9% vs. 21%, p=0.04) and were more likely to present dry cough (49.3% vs. 25.2%, p<0.01). Overall, chest X-ray at admission showed findings suggestive of pneumonia in 63.2%, and Group 2 were more likely to develop pathological findings during the hospitalization (72.7% vs. 17.2%, p=0.01). At admission, Group 2 presented significantly higher neutrophil count, aspartate-transaminase and C-reactive-protein. At the 3 rd measurement, Group 2 presented persistently higher neutrophil count, hepatic inflammation markers and C-reactive-protein. Group 1 presented a shorter duration from admission to negativization of follow-up swabs (20 vs. 35 days, p<0.01). Conclusions: The presence of comorbidities and the persistent observation of abnormal laboratory findings should be regarded as predisposing factors for clinical worsening.
Subject(s)
Pneumonia , Diabetes Mellitus , Hypertension , COVID-19 , InflammationABSTRACT
Rapid and accurate diagnostic tests are essential for controlling the ongoing COVID-19 pandemic. Although the current gold standard involves testing of nasopharyngeal swabs specimens by nucleic acid amplification test, such as real-time reverse-transcription polymerase chain reaction (rRT-PCR) to detect the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), it presents several limitations that ultimately may translate into a bottleneck in the surveillance regimen. New strategies based on frequent testing using less invasive specimens are urgently needed for containment of the infection. Rapid antigen assay using saliva as a reliable alternative to nasopharyngeal swabs should be proposed as a valuable part of the overall testing strategy.
Subject(s)
COVID-19ABSTRACT
The aim of this study is the characterization and genomic tracing by phylogenetic analyses of 59 new SARS-CoV-2 Italian isolates obtained from patients attending clinical centres in North and Central Italy until the end of April 2020. All but one of the newly characterized genomes belonged to the lineage B.1, the most frequently identified in European countries, including Italy. Only a single sequence was found to belong to lineage B. A mean of 6 nucleotide substitutions per viral genome was observed, without significant differences between synonymous and non-synonymous mutations, indicating genetic drift as a major source for virus evolution. tMRCA estimation confirmed the probable origin of the epidemic between the end of January and the beginning of February with a rapid increase in the number of infections between the end of February and mid-March. Since early February, an effective reproduction number (Re) greater than 1 was estimated, which then increased reaching the peak of 2.3 in early March, confirming the circulation of the virus before the first COVID-19 cases were documented. Continuous use of state-of-the-art methods for molecular surveillance is warranted to trace virus circulation and evolution and inform effective prevention and containment of future SARS-CoV-2 outbreaks.
Subject(s)
COVID-19ABSTRACT
The aim of this study is the characterization and genomic tracing by phylogenetic analyses of 59 new SARS-CoV-2 Italian isolates obtained from patients attending clinical centres in North and Central Italy until the end of April 2020. All but one of the newly characterized genomes belonged to the lineage B.1, the most frequently identified in European countries, including Italy. Only a single sequence was found to belong to lineage B. A mean of 6 nucleotide substitutions per viral genome was observed, without significant differences between synonymous and non-synonymous mutations, indicating genetic drift as a major source for virus evolution. tMRCA estimation confirmed the probable origin of the epidemic between the end of January and the beginning of February with a rapid increase in the number of infections between the end of February and mid-March. Since early February, an effective reproduction number (Re) greater than 1 was estimated, which then increased reaching the peak of 2.3 in early March, confirming the circulation of the virus before the first COVID-19 cases were documented. Continuous use of state-of-the-art methods for molecular surveillance is warranted to trace virus circulation and evolution and inform effective prevention and containment of future SARS-CoV-2 outbreaks.