Clinical and epidemiological aspects of viral infections: a molecular approach

Molecular tests have gained a solid position in clinical virology. Developments in molecular diagnostics go rapidly; within a few hours several viruses can be detected in one single, sensitive laboratory test. These developments do raise questions regarding the clinical value of these tests. What does the outcome of a diagnostic test means for the patient, for treatment and additional diagnostic procedures, and preventive measures to reduce further spread of viruses. In this thesis the advantages of molecular diagnostic tests are described by studies into enterovirus 68 , rhinovirus and influenza virus. By combining clinical and epidemiological data with the outcome of viral diagnostic tests, the role of these viruses in causing respiratory tract infections are described. Despite the presence of a potential viral cause of a respiratory tract infection, antibiotic therapy is often still continued. The studies presented in this thesis also show that characterizing viruses using sequence analysis methods is important to understand the transmission of viruses in the hospital. Sequence based information serves as input for the implementation of appropriate infection control measures, focused on the most likely route of transmission. This enables the efficient use of human and material resources. Cost effectiveness studies are needed to address the impact of a timely and accurate diagnosis on all aspects of patient care. Besides, education of health care providers on the proper use and interpretation of molecular tests is crucial for the optimal integration of these tests in patient management

European multicenter evaluation of Xpert® Xpress SARS-CoV-2/Flu/RSV test

Rapid diagnostics for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are paramount for reducing the spread of the current pandemic. During additional seasonal epidemics with influenza A/B and respiratory syncytial virus (RSV), the clinical signs and symptoms cannot be distinguished easily from SARS-CoV-2. Therefore, a new assay combining four targets in the form of the new Xpert Xpress SARS-CoV-2/Flu/RSV assay was evaluated. The assay was compared to the Xpert Xpress SARS-CoV-2, Xpert Xpress Flu/RSV, Seegene Flu/RSV, influenza A/B r-gene® and RSV/hMPV r-gene®. A total of 295 nasopharyngeal and throat swabs were tested at four institutes throughout Europe including 72 samples positive for SARS-CoV-2, 65 for influenza A, 47 for influenza B, and 77 for RSV. The sensitivity of the new assay was above 95% for all targets, with the highest for SARS-CoV-2 (97.2%). The overall correlation of SARS-CoV-2 Ct values between Xpert Xpress SARS-CoV-2 assay and Xpert Xpress SARS-CoV-2/Flu/RSV assay was high. The agreement between Ct values above 30 showed the multiplex giving higher Ct values for SARS-CoV-2 on average than the singleplex assay. In conclusion, the new assay is a rapid and reliable alternative with less hands-on time for the detection of not one, but four upper respiratory tract pathogens that may circulate at the same time

Strong associations and moderate predictive value of early symptoms for SARS-CoV-2 test positivity among healthcare workers, the Netherlands, March 2020.

Healthcare workers (n = 803) with mild symptoms were tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (n = 90 positive) and asked to complete a symptom questionnaire. Anosmia, muscle ache, ocular pain, general malaise, headache, extreme tiredness and fever were associated with positivity. A predictive model based on these symptoms showed moderate discriminative value (sensitivity: 91.2%; specificity: 55.6%). While our models would not justify presumptive SARS-CoV-2 diagnosis without molecular confirmation, it can contribute to targeted screening strategies

Development of endotoxin tolerance does not influence the response to a challenge with the mucosal live-attenuated influenza vaccine in humans in vivo

Introduction: The effects of bacterial infections on the response to subsequent viral infections are largely unknown. This is important to elucidate to increase insight into the pathophysiology of bacterial and viral co-infections, and to assess whether bacterial infections may influence the course of viral infections. Methods: Healthy male subjects received either bacterial endotoxin [Escherichia coli-derived lipopolysaccharide (LPS), 2 ng/kg, n = 15] or placebo (n = 15) intravenously, followed by intranasal Fluenz (live-attenuated influenza vaccine) 1 week later. Results: LPS administration resulted in increased plasma cytokine levels and development of endotoxin tolerance in vivo and ex vivo, illustrated by attenuated cytokine production upon rechallenge with LPS. Following Fluenz administration, infectivity for the Fluenz A/B strains was similar between the LPS-Fluenz and placebo-Fluenz groups (13/15 subjects in both groups). Also, the Fluenz-induced increase in temperature and IL-6, G-CSF and IP-10 concentrations in nasal wash were similar between both groups. Conclusion: While endotoxemia profoundly attenuates the immune response upon a second LPS challenge, it does not influence the Fluenz-induced immune response. These results suggest immune suppression after bacterial infection does not alter the response to a subsequent viral infection

Laboratory-based surveillance in the molecular era: The typened model, a joint data-sharing platform for clinical and public health laboratories

Laboratory-based surveillance, one of the pillars of monitoring infectious disease trends, relies on data produced in clinical and/or public health laboratories. Currently, diagnostic laboratories worldwide submit strains or samples to a relatively small number of reference laboratories for characterisation and typing. However, with the introduction of molecular diagnostic methods and sequencing in most of the larger diagnostic and university hospital centres in high-income countries, the distinction between diagnostic and reference/public health laboratory functions has become less clear-cut. Given these developments, new ways of networking and data sharing are needed. Assuming that clinical and public health laboratories may be able to use the same data for their own purposes when sequence-based testing and typing are used, we explored ways to develop a collaborative approach and a jointly owned database (TYPENED) in the Netherlands. The rationale was that sequence data - whether produced to support clinical care or for surveillance -can be aggregated to meet both needs. Here we describe the development of the TYPENED approach and supporting infrastructure, and the implementation of a pilot laboratory network sharing enterovirus sequences and metadata

An evaluation of COVID-19 serological assays informs future diagnostics and exposure assessment

The world is entering a new era of the COVID-19 pandemic in which there is an increasing call for reliable antibody testing. To support decision making on the deployment of serology for either population screening or diagnostics, we present a detailed comparison of serological COVID-19 assays. We show that among the selected assays there is a wide diversity in assay performance in different scenarios and when correlated to virus neutralizing antibodies. The Wantai ELISA detecting total immunoglobulins against the receptor binding domain of SARS CoV-2, has the best overall characteristics to detect functional antibodies in different stages and severity of disease, including the potential to set a cut-off indicating the presence of protective antibodies. The large variety of available serological assays requires proper assay validation before deciding on deployment of assays for specific applications

Enterovirus 68 and Human Respiratory Infections

This chapter deals with Enterovirus 68 (EV68). It provides an overview of the current knowledge of EV68, from virology to clinical disease patterns and prevention and control. EV68 was first isolated in 1962 in respiratory samples received from four children with pneumonia and bronchiolitis, using primary monkey-kidney cell cultures. Patients with a respiratory disease are generally not systematically tested for the presence of enterovirus. From 2009 onward, a growing number of reports have been published describing outbreaks or clusters of EV68 infection, indicating that EV68 is an emerging respiratory pathogen. Transmission of EV68 from one person to the other most likely occurs via the respiratory route. Similar to other viruses causing respiratory tract infections, hand contact with respiratory secretions and autoinoculation to the mouth, nose, or eyes are probably the most important routes. Nosocomial transmission has been well documented for respiratory viruses and for enteroviruses.</p