Can variants, reinfection, symptoms and test types affect COVID-19 diagnostic performance? A large-scale retrospective study of AG-RDTs during circulation of Delta and Omicron variants, Czechia, December 2021 to February 2022

BackgroundThe sensitivity and specificity of selected antigen detection rapid diagnostic tests (AG-RDTs) for SARS-CoV-2 were determined in the unvaccinated population when the Delta variant was circulating. Viral loads, dynamics, symptoms and tissue tropism differ between Omicron and Delta.AimWe aimed to compare AG-RDT sensitivity and specificity in selected subgroups during Omicron vs Delta circulation.MethodsWe retrospectively paired AG-RDT results with PCRs registered in Czechia's Information System for Infectious Diseases from 1 to 25 December 2021 (Delta, n = 20,121) and 20 January to 24 February 2022 (Omicron, n = 47,104).ResultsWhen confirmatory PCR was conducted on the same day as AG-RDT as a proxy for antigen testing close to peak viral load, the average sensitivity for Delta was 80.4% and for Omicron 81.4% (p < 0.05). Sensitivity in vaccinated individuals was lower for Omicron (OR = 0.94; 95% confidence interval (CI): 0.87-1.03), particularly in reinfections (OR = 0.83; 95% CI: 0.75-0.92). Saliva AG-RDT sensitivity was below average for both Delta (74.4%) and Omicron (78.4%). Tests on the European Union Category A list had higher sensitivity than tests in Category B. The highest sensitivity for Omicron (88.5%) was recorded for patients with loss of smell or taste, however, these symptoms were almost 10-fold less common than for Delta. The sensitivity of AG-RDTs performed on initially asymptomatic individuals done 1, 2 or 3 days before a positive PCR test was consistently lower for Omicron compared with Delta.ConclusionSensitivity for Omicron was lower in subgroups that may become more common if SARS-CoV-2 becomes an endemic virus.

New perspectives on respiratory syncytial virus surveillance at the national level: lessons from the COVID-19 pandemic

The emergence of SARS-CoV-2 and the resulting coronavirus disease 2019 (COVID-19) pandemic has led to the reconsideration of surveillance strategies for respiratory syncytial virus (RSV) and other respiratory viruses. The COVID-19 pandemic and the non-pharmaceutical interventions for COVID-19 had a substantial impact on RSV transmission in many countries, with close to no transmission detected during parts of the usual season of 2020–2021. Subsequent relaxation of social restrictions has resulted in unusual out-of-season resurgences of RSV in several countries, causing a higher healthcare burden and often a higher proportion of hospitalisations than usual among children older than 1 year in age [1]. In case of an emerging infectious disease with pandemic potential, preparedness to scale up surveillance for the emerging disease while continuing the maintenance of surveillance activities of pre-existing seasonal diseases is necessary.

Learning from the COVID-19 pandemic and considering the effects of this pandemic, we provide recommendations that can guide towards sustainable RSV surveillance with the potential to be integrated into the broader perspective of respiratory surveillance. https://bit.ly/40TsO0G

Retrospective Analysis Revealed an April Occurrence of Monkeypox in the Czech Republic

Herein, we present our findings of an early appearance of the Monkeypox virus in Prague, Czech Republic. A retrospective analysis of biological samples, carried out on the 28th of April, revealed a previously unrecognized case of Monkeypox virus (MPxV) infection. Subsequent data analysis confirmed that the virus strain belongs to the ongoing outbreak. Combined with clinical and epidemiological investigations, we extended the roots of the current outbreak at least back to 16th of April, 2022.

Role of population and test characteristics in antigen-based SARS-CoV-2 diagnosis, Czechia, August to November 2021

Background

Analyses of diagnostic performance of SARS-CoV-2 antigen rapid diagnostic tests (AG-RDTs) based on long-term data, population subgroups and many AG-RDT types are scarce.

Aim

We aimed to analyse sensitivity and specificity of AG-RDTs for subgroups based on age, incidence, sample type, reason for test, symptoms, vaccination status and the AG-RDT’s presence on approved lists.

Methods

We included AG-RDT results registered in Czechia’s Information System for Infectious Diseases between August and November 2021. Subpopulations were analysed based on 346,000 test results for which a confirmatory PCR test was recorded ≤ 3 days after the AG-RDT; 38 AG-RDTs with more than 100 PCR-positive and 300 PCR-negative samples were individually evaluated.

Results

Average sensitivity and specificity were 72.4% and 96.7%, respectively. We recorded lower sensitivity for age groups 0–12 (65.5%) and 13–18 years (65.3%). The sensitivity level rose with increasing SARS-CoV-2 incidence from 66.0% to 76.7%. Nasopharyngeal samples had the highest sensitivity and saliva the lowest. Sensitivity for preventive reasons was 63.6% vs 86.1% when testing for suspected infection. Sensitivity was 84.8% when one or more symptoms were reported compared with 57.1% for no symptoms. Vaccination was associated with a 4.2% higher sensitivity. Significantly higher sensitivity levels pertained to AG-RDTs on the World Health Organization Emergency Use List (WHO EUL), European Union Common List and the list of the United Kingdom’s Department of Health and Social Care.

Conclusion

AG-RDTs from approved lists should be considered, especially in situations associated with lower viral load. Results are limited to SARS-CoV-2 delta variant.

Multi-branch cooperation on SARS-CoV-2 omicron capture: a case report

Shortly after the WHOs first notice a suspected case of omicron SARS-CoV-2 was reported in Liberec, Czech Republic. The primary goal of the following actions was to test the presence of the variant and stop the spread of the virus variant. On November 25 a sixty-year-old lady, who had recently returned from Namibia, visited a GP with flu-like symptoms and a rash on her chest. The antigen test was positive for SARS-CoV-2, a PCR test was planned. At that time, it was not known that a new variant of concern was spreading from Africa. On November 26 in the morning the GP announced a suspected omicron case to the Regional public health authority, who organized the following steps. A mobile sampling team was sent to the patient&#39;s home immediately, sample transported into the regional hospital and analyzed with the help of the national reference laboratory. The captured virus SARS-CoV-2 fitted the description of the omicron variant, was shared in the GISAID database and named hCoV-19/Czech Republic/KNL_2021-110119140/2021. Contact tracing was started immediately, eleven persons were tested and quarantined. One of them positive with no further spread. It is the first documented omicron case in the Czech Republic and one of the first cases in Europe, with an excellent systemic response to the alert. The laboratory was able to detect the omicron variant instantly after the request. This case also demonstrates how easily the virus spreads on long distances and how important it might be to increase the uptake of the booster vaccine.

COVID-19 reinfections

Reports of SARS-CoV-2 reinfections are on the rise. This study focused on reinfections in patients with confirmed COVID-19 in the Czech Republic. Between 1 March 2020 and 9 November 2020, 362 084 cases with the onset of symptoms before 31 October 2020 were reported. Overall, 28 cases of symptomatic SARS-CoV-2 reinfections were identified, 11 in males and 17 in females, age range 25-80 years, median age 46 years. The interval between the first and second episodes of the disease ranged from 101 to 231 days, and the median interval was 201.5 days. During both symptomatic episodes, all patients have been tested by RT-PCR. Altogether 26 patients (92.9%) have been tested negative after recovery from the first episode of COVID-19. Symptomatic reinfections occurred in nearly 0.2% of all patients at risk. Most patients with reinfection had mild symptoms in both episodes, and only three episodes were moderate to severe. Thus, reinfections may have been underdiagnosed. In summary, COVID-19 reinfections are possible and not exceptional.

Correction: MeltMan: Optimization, Evaluation, and Universal Application of a qPCR System Integrating the TaqMan qPCR and Melting Analysis into a Single Assay

[This corrects the article DOI: 10.1371/journal.pone.0151204.].

Evaluation of TaqMan qPCR System Integrating Two Identically Labelled Hydrolysis Probes in Single Assay

Ongoing evolution of viral pathogens is a significant issue in diagnostic virology employing TaqMan qPCR/RT-qPCR. Specific concerns are related to false negativity due to probe binding failure. One option for compensating for such deficiency is to integrate a second identically labelled probe in the assay. However, how this alteration influences the reaction parameters has not been comprehensively demonstrated. In the present study, we evaluate a TaqMan protocol using two identically labelled hydrolysis probes (simple, LNA (locked-nucleic-acid)) and MGB (minor-groove-binder) modified probes and combinations thereof in a single assay. Our results based on a synthetic amplicon suggest that the second probe does not compromise the TaqMan qPCR/RT-qPCR parameters, which repeatedly and reproducibly remained comparable to those of the corresponding single-probe assays, irrespective of the relative probe orientation, whether opposite or tandem, and probe modifications or combinations thereof. On the other hand, the second probe additively contributed to the overall fluorescence signal. The utility of the dual-probe approach was demonstrated on practical examples by using field specimens. We hope that the present study might serve as a theoretical basis for the development or improvement of TaqMan qPCR/RT-qPCR assays for the detection of highly variable nucleic acid templates.

Mumps in the Czech Republic in 2013: Clinical Characteristics, Mumps Virus Genotyping, and Epidemiological Links

AIM

The aim of the study was to map the incidence of mumps in the Czech Republic in terms of clinical symptoms, epidemiological links, and characteristics of circulating genotypes.

METHODS

Patients with suspected mumps examined in the Infectious Diseases Clinic of the Na Bulovce Hospital in 2013 were enrolled in the study. Buccal swab specimens were tested by means of nucleic acid detection (RT-qPCR) and when positive, they were cultured in tissue culture. Sequencing was carried out using the BigDye Terminator v3.1 Cycle Sequencing Kit and Genetic Analyzer 3500. The SeqScape software was used for the analysis of sequencing data and filtering out low quality reads. The phylogenetic analysis and genotyping were performed using the Mega 6 software. To generate the phylogenetic tree, all sequences were aligned by the MAFFT tool and the alignment obtained was edited using the BioEdit software. In all patients, selected biochemical markers (C-reactive protein, white blood cell count and serum amylase) were measured. The EPIDAT system used for reporting infectious diseases, record keeping, and data analysis in the Czech Republic was the source of statistical data.

RESULTS

Eighty-nine patients with suspected mumps were examined in the Na Bulovce Hospital and 65 of them were laboratory confirmed with mumps: 40 males (61.5%) and 25 females (38.5%). The mean age of the study cohort was 25.9 years (median age of 23 years, age range from 10 to 73 years) and 14 patients were under 18 years of age. Thirty-four (52.3%) patients were vaccinated in childhood, 28 (43.1%) were unvaccinated, and for three persons, vaccination data were not available. A severe course of the disease was reported in 15 (23.1%) patients. Fourteen of them needed hospitalization because of orchitis (9 males) and meningitis (5 patients). One patient with orchitis was treated on an outpatient basis. The need for hospitalization tended to be lower in the unvaccinated patients (14.7% vs. 35.7%, p=0.076). In 2013, 1,553 cases of mumps were reported to the EPIDAT system. Of these, 640 were laboratory confirmed. The most often reported complications were orchitis (90 cases, i.e. 10.3%) and meningitis (21 cases, i.e. 1.4%). Orchitis was diagnosed in 30.3% of the unvaccinated and in 6.4% of the vaccinated males. Meningitis occurred in 3.1% of the unvaccinated and in 1.0% of the vaccinated patients.

CONCLUSION

Despite the emergence of mumps among the vaccinated population, the present study has confirmed a positive effect of the vaccine, particularly on the incidence of complications and inflammatory markers. All 30 sequenced mumps virus strains were assigned to group G. A secondary vaccine failure due to waning immunity seems to be a plausible explanation for the rise in mumps cases.

MeltMan: Optimization, Evaluation, and Universal Application of a qPCR System Integrating the TaqMan qPCR and Melting Analysis into a Single Assay

In the present work, we optimised and evaluated a qPCR system integrating 6-FAM (6-carboxyfluorescein)-labelled TaqMan probes and melting analysis using the SYTO 82 (S82) DNA binding dye in a single reaction. We investigated the influence of the S82 on various TaqMan and melting analysis parameters and defined its optimal concentration. In the next step, the method was evaluated in 36 different TaqMan assays with a total of 729 paired reactions using various DNA and RNA templates, including field specimens. In addition, the melting profiles of interest were correlated with the electrophoretic patterns. We proved that the S82 is fully compatible with the FAM-TaqMan system. Further, the advantages of this approach in routine diagnostic TaqMan qPCR were illustrated with practical examples. These included solving problems with flat or other atypical amplification curves or even false negativity as a result of probe binding failure. Our data clearly show that the integration of the TaqMan qPCR and melting analysis into a single assay provides an additional control option as well as the opportunity to perform more complex analyses, get more data from the reactions, and obtain analysis results with higher confidence.

[Differential diagnosis of the viral etiology of suspected mumps in a population with high vaccine coverage]

AIM

In this study, buccal swabs from patients with the clinical picture of parotitis epidemica in whom mumps virus (MV) infection was not confirmed by direct detection or serologically were tested. The aim was to detect by molecular methods nucleic acids (NAs) of other respiratory viruses possibly involved in salivary gland swelling. At the same time, paired sera, if available, were tested.

MATERIAL AND METHODS

The study group consisted of 72 buccal swabs from patients of the Clinic of infectious, tropical, and parasitic diseases, Na Bulovce Hospital. Paired sera were available from ten patients. Samples were collected in 2013 to 2015. Buccal swabs were tested by PCR for the presence of NAs of adenoviruses (AdV), bocaviruses (hBoV), parainfluenza viruses of types 1-4 (HPIV), human metapneumovirus (hMPV), coronaviruses (HCoV: NL63, OC43, HKU1, and 229E), respiratory syncytial virus (RSV), influenza A virus, influenza B virus, and Epstein-Barr virus (EBV). Paired sera were screened by the complement fixation test (AdV and influenza A and B viruses), hemagglutination inhibition test (HPIV types 2 and 3), ELISA (AdV, EBV), and immunofluorescence (EBV).

RESULTS

NAs from viruses other than the mumps virus were detected in 27 of 72 patients with clinical symptoms of parotitis epidemica, and serological tests revealed etiological links with parainfluenza viruses in three more cases. Overall, 30 (41.7%) of 72 patients with suspected mumps tested positive for one or more viruses from the study panel. The most commonly detected viruses were AdV 11/72 (15.3%), EBV 9/72 (12.5%), and HPIV 3/72 (4.2%), but influenza A virus (H3N2) 1/72 (1.4%) was also found. Some patients tested positive for more than one virus: 2/72 (3%) for AdV plus hBoV and 1/72 (1.4%) for HPIV plus HCoV. In addition, examination of paired sera revealed HPIV positivity in three more patients. PCR and serology detected etiological link with HPIV in six (8.3%) of 72 patients tested.

CONCLUSION

In our study group, nearly 42% of patients with the clinical picture of parotitis epidemica in whom mumps virus (MV) infection was not confirmed by direct detection or serologically tested positive for viruses other than the mumps virus. Thorough laboratory diagnosis of suspected mumps in vaccinated persons is important not only for the treatment of patients and adoption of isolation and other measures, but also for a better understanding of the epidemiology of the disease and outcomes of the immunisation programmes.

Molecular and antigenic characterization of the H3 hemagglutinin of H3N2 influenza A virus strains collected in the Czech Republic during the 2014/2015 epidemic season

The 2014/2015 influenza epidemic season was characterized by the predominance of the H3N2 subtype. The presented study investigated the genetic and antigenic heterogeneity of the H3N2 strains collected in the Czech Republic from November 2014 to March 2015. Phylogenetic analysis of the representative H3 hemagglutinin sequences was performed and the glycosylation status and crucial antigenic mutations were compared relative to the 2014 and 2015 vaccine strains (A/Texas/50/2012 and A/Switzerland/9715293/2013) and visualized in the H3 crystal structure. The molecular data were further supplemented by hemagglutination-inhibition test (HIT) results on fifteen H3N2 2014/2015 strains by using the A/Texas/50/2012 (H3N2) and A/Switzerland/9715293/13 (H3N2) antisera. Our data on the Czech H3N2 viruses from the 2014/2015 epidemic season could supplement the reports of official authorities with data from a particular geographi-cal area.

[Enterovirus sequencing as a new approach to the laboratory diagnosis for clinical and epidemiological purposes]

OBJECTIVE

Introducing enterovirus sequencing as an advanced approach to classify the viruses isolated according to the novel nomenclature and to characterize isolates in detail.

MATERIAL AND METHODS

Seventy-five specimens collected from 64 patients in two hospitals, Liberec Regional Hospital, and Plzeň University Hospital, were analyzed. The study patients' age ranged from four to 54 years, with a median of 15 years in males and 16 years in females. In most patients, the reasons for admission were intense headache, fever, vomiting, tiredness, meningeal symptoms, intestinal symptoms (in two patients), and skin symptoms (in one patient). The specimens collected were rectal and throat swabs, cerebrospinal fluid (CSF) and stool specimens. Molecular detection and typing were performed using the RT-PCR method. A segment of the 5´non-coding RNA was selected for typing. Specimens were amplified using single-step PCR with external primers and with the same primers extended to include M13 sequences (Generi-Biotech). The LASERGENE software (DIASTAR) was used in sequence editing, alignment, and quality check. The sequences obtained were checked against the central GenBank sequence database using the BLAST algorithm.

RESULTS

The identification of the study isolates resulted in 61 ECHO viruses 30, three coxsackie viruses B1, one coxsackie virus B3, one coxsackie virus A9, one enterovirus 86, one enterovirus 71, Two ECHO viruses 13/coxsackie virus B5, one ECHO virus 7/30/coxsackie virus B4, one coxsackie virus B4/enterovirus B, one enterovirus 87/ECHO virus 30/enterovirus B, and one ECHO virus 3. All viruses isolated, except enterovirus 71 classified into group A, were of group B.

CONCLUSION

The enteroviruses were identified unambigously, although the sequencing only targeted a short, conserved segment that showed considerable variability. The sequencing was an effective alternative to enterovirus identification by the neutralisation test and allowed for detailed characterization of the isolates. The predominance of ECHO 30 as the cause of aseptic meningitis is in accordance with the literature data.

Local-scale diversity and between-year "frozen evolution" of avian influenza A viruses in nature

Influenza A virus (IAV) in wild bird reservoir hosts is characterized by the perpetuation in a plethora of subtype and genotype constellations. Multiyear monitoring studies carried out during the last two decades worldwide have provided a large body of knowledge regarding the ecology of IAV in wild birds. Nevertheless, other issues of avian IAV evolution have not been fully elucidated, such as the complexity and dynamics of genetic interactions between the co-circulating IAV genomes taking place at a local-scale level or the phenomenon of frozen evolution. We investigated the IAV diversity in a mallard population residing in a single pond in the Czech Republic. Despite the relative small number of samples collected, remarkable heterogeneity was revealed with four different IAV subtype combinations, H6N2, H6N9, H11N2, and H11N9, and six genomic constellations in co-circulation. Moreover, the H6, H11, and N2 segments belonged to two distinguishable sub-lineages. A reconstruction of the pattern of genetic reassortment revealed direct parent-progeny relationships between the H6N2, H11N9 and H6N9 viruses. Interestingly the IAV, with the H6N9 subtype, was re-detected a year later in a genetically unchanged form in the close proximity of the original sampling locality. The almost absolute nucleotide sequence identity of all the respective genomic segments between the two H6N9 viruses indicates frozen evolution as a result of prolonged conservation in the environment. The persistence of the H6N9 IAV in various abiotic and biotic environmental components was also discussed.

[Phylogenetic and molecular analysis of A/H1N1pdm influenza viruses isolated in the epidemic season 2012/2013 from hospitalised patients with -symptoms of influenza-like illness]

AIM

To perform phylogenetic and molecular analysis of A/H1N1pdm influenza viruses isolated in the epidemic season 2012/2013 from hospitalised patients with symptoms of influenza-like illness (ILI).

MATERIAL AND METHODS

The study set included 34 strains of the A/H1N1pdm influenza virus isolated in the Czech Republic in the epidemic season 2012/2013. The strains were analysed by partial or whole-genome sequencing. The genome segments were compared at the nucleotide and amino acid levels, absolute and percentage sequence identity were determined, and phylogenetic relations were identified. The last steps were the comparison of the H1 molecule with that of the most recent vaccine strain and identification of the genotypic structure and molecular markers linked to the pathogenicity and antiviral resistance.

RESULTS

Phylogenetic analysis of the H1 molecule suggested that all 34 A/H1N1pdm isolates from the 2012/2013 season in the Czech Republic should be assigned to H1 group 6 divided into sublineages 6A and 6B. The comparison of the known antigenic regions of the H1 molecule with those in the most recent vaccine strain revealed two stable changes in antigenic regions Sb and Ca1. Furthermore, sporadic mutations were identified in antigenic regions Ca2, Cb, and Sb. Genotyping revealed co-circulation of two related but clearly distiguishable genotypes of A/H1N1pdm. All isolates showed sensitivity to oseltamivir. One strain consisted of two N1 sub-populations, one oseltamivir sensitive and the other oseltamivir resistant, in nearly equimolar proportions.

CONCLUSION

All A/H1N1pdm isolates from the epidemic season 2012/2013 in the Czech Republic formed a phenotypically uniform group. At the nucleotide level, the divergence was relatively more pronounced and H1 sublineages and discrete genotypes were possible to identify. H1 molecules were highly identical to those of the vaccine strain A/California/7/2009 (H1N1) which showed that the current vaccine was protective enough. All strains were sensitive to oseltamivir; however, the selection of oseltamivir resistant N1 subpopulations was observed.

[Clinical and epidemiological characteristics of patients hospitalized with severe influenza in the season 2012-2013]

AIM OF THE STUDY

To characterize the clinical and epidemiological features of patients hospitalized with moderate to severe influenza infection at the infec-tious diseases department of a tertiary care hospital in the epidemic season 2012-2013.

MATERIAL AND METHODS

A prospective observational study of patients hospitalized with influenza infection in the season 2012-2013 was carried out at the Infectious Diseases Department, Na Bulovce Hospital in Prague. Influenza infection was diagnosed by real-time quantitative polymerase chain reaction (RT-qPCR) in nasopharyngeal swab or tracheal aspirate specimens. Demographic, clinical, and laboratory data were recorded along with the disease course and outcome.

RESULTS

One hundred and ninety-nine patients, 85 females and 114 males (age median 47, range 1-87 years), were hospitalized with confirmed influenza in the epidemic season 2012-2013. Only seven of them got the influenza vaccine. Altogether 136 patients were diagnosed with influenza type A (91 with H1N1pdm, 33 with H3N2, and 12 with an unknown subtype), 66 patients with type B, and three patients with both types A and B. One hundred and eight patients (54%) had an underlying chronic disease, most often cardiovascular or pulmonary. The main symptoms of influenza were fever, cough, headache, myalgia, and arthralgia. Pneumonia was the most common complication: twenty-one patients suffered from primary viral pneumonia and 35 from bacterial pneumonia. Twenty-three patients (12%) needed intensive care. Six patients died and the leading cause of death was heart failure.

CONCLUSION

During the epidemic influenza season 2012-2013, more patients were hospitalized than in the pandemic season 2009-2010. Also the proportions of complicated cases and case fatality ratios were fully comparable in both seasons. The fact that most patients were not vaccinated clearly supports the recommendation to vaccinate every year both the individuals at high risk of complications due to comorbidities and the healthy population.

[Phylogenetic analysis and genotyping of A/H3N2 Influenza viruses isolated from patients hospitalised with influenza-like illness symptoms in the na bulovce hospital in the season 2011/2012]

Influenza A virus is an important cause of acute respiratory infections (ARI). Clinical manifestations of ARI vary from mild or moderate to life-threatening conditions requiring intensive care. Given the segmented genome, a large natural reservoir of other influenza virus subtypes, and antibody selection pressure in the population, the virus is variable and genetically unstable. The phylogenetic analysis and genotyping of A/H3N2 influenza viruses isolated from patients hospitalised with influenza-like illness symptoms in the Na Bulovce Hospital in the season 2011/2012 support the assumption that the pathogenicity is a polygenic trait modifiable by the host health status and seems not to be unambiguously associated with any specific mutations.