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Objective At present, false negatives/positives have been reported in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostics. Searching for the molecular basis of such tests' unreliability, this study aimed at defining how specific are the sequences used in serological and polymerase chain reaction (PCR) tests to detect SARS-CoV-2.

The paper reports the study performed to characterize the populations of Pyrenophora tritici-repentis, Parastagonospora nodorum, and Parastagonospora pseudonodorum in Tambov oblast for the presence of the Tox1, Tox3, ToxA, and ToxB effector genes using associated molecular markers. Infectious samples were collected in 2022 from the leaves of spring and winter wheats grown on a plot located in the northeastern part of the Central Black Earth Region with preceding bare fallow. P. nodorum and P. pseudonodorum were detected in spring wheat varieties at the end of the vegetation period. The P. tritici-repentis fungus infected both winter and spring wheat varieties. Molecular markers were used to identify NEs-coding genes in 68 P. tritici-repentis isolates from 19 winter wheat varieties, 100 P. nodorum isolates from ten spring wheat varieties, and 70 P. pseudonodorum isolates from seven spring wheat varieties. Among the studied P. nodorum isolates, the Tox1, Tox3, and ToxA genes both alone and in combinations by two within a single genotype were found. No ToxA gene was observed in the genotypes of P. pseudonodorum isolates. Fungal isolates carrying Tox1 and/or Tox3 genes in their genotypes were identified. The ToxB gene was not detected in the studied P. tritici-repentis population, while ToxA was found to be widely present. The frequency of ToxA, Tox1, and Tox3 genes in the P. nodorum population was 30, 20, and 30%, respectively; in the P. pseudonodorum population, Tox1 and Tox3 with the frequencies of 57.1 and 30%, respectively, were found; and ToxA was found representing 76.5% in the P. tritici-repentis population. P. tritici-repentis, P. nodorum, and P. pseudonodorum strains characterized for the presence of effector genes will be used to create artificial infectious backgrounds to identify sources and donors of resistance to leaf spot diseases. [ABSTRACT FROM AUTHOR]

Objective At present, false negatives/positives have been reported in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostics. Searching for the molecular basis of such tests' unreliability, this study aimed at defining how specific are the sequences used in serological and polymerase chain reaction (PCR) tests to detect SARS-CoV-2. Materials and Methods Analyses were performed on the leading SARS-CoV-2 biomarker spike glycoprotein (gp). Sharing of peptide sequences between the spike antigen and the human host was analyzed using the Peptide Search program from Uniprot database. Sharing of oligonucleotide sequences was investigated using the nucleotide Basic Local Alignment Search Tool (BLASTn) from National Center for Biotechnology Information (NCBI). Results Two main points stand out: (1) a massive pentapeptide sharing exists between the spike gp and the human proteome, and only a limited number of pentapeptides (namely 107) identify SARS-CoV-2 spike gp as nonself when compared with the human proteome, and (2) the small phenetic difference practically disappears at the genetic level. Indeed, almost all of the 107 pentadecameric nucleotide sequences coding for the pentapeptides unique to SARS-CoV-2 spike gp are present in human nucleic acids too. Conclusion The data are of immunological significance for defining the issue of the viral versus human specificity and likely explain the fact that false positives can occur in serological and PCR tests for SARS-CoV-2 detection. [ABSTRACT FROM AUTHOR]

Aims: With resumption of elective spine surgery services in the UK following the first wave of the COVID-19 pandemic, we conducted a multicentre British Association of Spine Surgeons (BASS) collaborative study to examine the complications and deaths due to COVID-19 at the recovery phase of the pandemic. The aim was to analyze the safety of elective spinal surgery during the pandemic. Methods: A prospective observational study was conducted from eight spinal centres for the first month of operating following restoration of elective spine surgery in each individual unit. Primary outcome measure was the 30-day postoperative COVID-19 infection rate. Secondary outcomes analyzed were the 30-day mortality rate, surgical adverse events, medical complications, and length of inpatient stay. Results: In all, 257 patients (128 males) with a median age of 54 years (2 to 88) formed the study cohort. The mean number of procedures performed from each unit was 32 (16 to 101), with 118 procedures (46%) done as category three prioritization level. The majority of patients (87%) were low-medium “risk stratification” category and the mean length of hospital stay was 5.2 days. None of the patients were diagnosed with COVID-19 infection, nor was there any mortality related to COVID-19 during the 30-day follow-up period, with 25 patients (10%) having been tested for symptoms. Overall, 32 patients (12%) developed a total of 34 complications, with the majority (19/34) being grade 1 to 2 Clavien-Dindo classification of surgical complications. No patient required postoperative care in an intensive care setting for any unexpected complication. Conclusion: This study shows that safe and effective planned spinal surgical services can be restored avoiding viral transmission, with diligent adherence to national guidelines and COVID-19-secure pathways tailored according to the resources of the individual spinal units. Cite this article: Bone Jt Open 2021;2(12):1096–1101.

Background COVID-19 vaccinations have been prioritised for high risk individuals. Aim Determine individual-level risk factors for care home residents testing positive for SARS-CoV-2. Study design Longitudinal observational cohort study using individual-level linked data from the Secure Anonymised Information Linkage (SAIL) databank. Setting Fourteen thousand seven hundred and eighty-six older care home residents (aged 65+) living in Wales between 1 September 2020 and 1 May 2021. Our dataset consisted of 2,613,341 individual-level daily observations within 697 care homes. Methods We estimated odds ratios (ORs [95% confidence interval]) using multilevel logistic regression models. Our outcome of interest was a positive SARS-CoV-2 PCR test. We included time-dependent covariates for the estimated community positive test rate of COVID-19, hospital inpatient status, vaccination status and frailty. Additional covariates were included for age, sex and specialist care home services. Results The multivariable regression model indicated an increase in age (OR 1.01 [1.00,1.01] per year), community positive test rate (OR 1.13 [1.12,1.13] per percent increase), hospital inpatients (OR 7.40 [6.54,8.36]), and residents in care homes with non-specialist dementia care (OR 1.42 [1.01,1.99]) had an increased odds of a positive test. Having a positive test prior to the observation period (OR 0.58 [0.49,0.68]) and either one or two doses of a vaccine (0.21 [0.17,0.25] and 0.05 [0.02,0.09], respectively) were associated with a decreased odds. Conclusions Care providers need to remain vigilant despite the vaccination rollout, and extra precautions should be taken when caring for the most vulnerable. Minimising potential COVID-19 infection for care home residents when admitted to hospital should be prioritised. [ABSTRACT FROM AUTHOR]

During the coronavirus disease (COVID-19) pandemic, Japanese people paid close attention to polymerase chain reaction (PCR) tests for detecting the disease. Due to the limitation of PCR test capacity during this time in Japan, all the potential patients could not be tested. The Japanese mass media often criticized the Japanese government for this poor capacity, while some critics neglected the probabilistic nature of PCR tests. In this context, this study explored how Japanese people talked about PCR tests during the pandemic. We used the microblogging service Twitter as a data resource. Through a text mining approach to over two hundred thousand Japanese tweets on PCR tests during the first two weeks of May 2020, we found the following two tendencies: 1) confusion about infection and positive results of PCR tests; and 2) lack of awareness of the probabilistic nature of PCR tests, especially when confusing infection and positive results. This is a trans-scientific problem, which can be questioned in science but solved only beyond science. Since it is not realistic that all citizens understand all of the scientific and mathematical aspects of potential social affairs in the future, we propose that ethics should be taught at all levels of mathematics education as a philosophy of governance of mathematics. These mathematics lessons should provide students with the opportunity to form shared goals, which can determine whether generalization through mathematical consideration is a suitable method of problem-solving within a given context. [ABSTRACT FROM AUTHOR]

We report a case series of 6 patients with confirmed coronavirus disease 2019 (COVID-19) in Wakayama prefecture, Japan. All 6 of the patients tested positive via pharyngeal swab polymerase chain reaction (PCR) tests, and 2 of the 6 were still positive at 3 weeks after onset. All of the patients exhibited bilateral ground glass opacities on computed tomography (CT). This article also reports narrative information on the spectrum of symptoms collected directly from the patients. It would be difficult to triage patients with COVID-19 based on the typical symptoms of fever and/or cough, although PCR and CT are definitive in diagnosis. [ABSTRACT FROM AUTHOR]

This short paper reports on the Austrian experiences with the Corona pandemic in the first quarter of 2020. In the beginning Austrian experts neglected the threat but a cluster in a skiing resort including international visitors served as a wake-up call and quickly after that strict and successful measures were applied. The paper proceeds describing the development of SARS-CoV-2 PCR testing and upgrading of testing facilities in Austria. The Austrian Agency for Health & Food Safety (AGES) played a leading role in this process. International cooperation and information exchange were fundamental to the successful implementation of specific and sensitive laboratory methods.

Objective  At present, false negatives/positives have been reported in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostics. Searching for the molecular basis of such tests' unreliability, this study aimed at defining how specific are the sequences used in serological and polymerase chain reaction (PCR) tests to detect SARS-CoV-2. Materials and Methods  Analyses were performed on the leading SARS-CoV-2 biomarker spike glycoprotein (gp). Sharing of peptide sequences between the spike antigen and the human host was analyzed using the Peptide Search program from Uniprot database. Sharing of oligonucleotide sequences was investigated using the nucleotide Basic Local Alignment Search Tool (BLASTn) from National Center for Biotechnology Information (NCBI). Results  Two main points stand out: (1) a massive pentapeptide sharing exists between the spike gp and the human proteome, and only a limited number of pentapeptides (namely 107) identify SARS-CoV-2 spike gp as nonself when compared with the human proteome, and (2) the small phenetic difference practically disappears at the genetic level. Indeed, almost all of the 107 pentadecameric nucleotide sequences coding for the pentapeptides unique to SARS-CoV-2 spike gp are present in human nucleic acids too. Conclusion  The data are of immunological significance for defining the issue of the viral versus human specificity and likely explain the fact that false positives can occur in serological and PCR tests for SARS-CoV-2 detection., Competing Interests: Conflicts of Interest None declared., (The Indian Association of Laboratory Physicians. This is an open access article published by Thieme under the terms of the Creative Commons Attribution-NonDerivative-NonCommercial License, permitting copying and reproduction so long as the original work is given appropriate credit. Contents may not be used for commercial purposes, or adapted, remixed, transformed or built upon. ( https://creativecommons.org/licenses/by-nc-nd/4.0/ ).)

Leprosy is a curable disease with well-defined etiology, but lacks better diagnostic tools, preventive and therapeutic strategies. The continued application of the Ridley–Jopling clinical classification that recognizes the natural diversity of the immune response has provided the basis for understanding leprosy, and this review proposes its implementation in all Reference Centers in order to standardize the diagnostic resources, aiming at the improvement of the disease control. Due to the broad bioepidemiological aspects of infection its eradication is difficult, and proper diagnosis of the disease and the correct clinical classification are required to ensure proper treatment. Tools and markers for diagnosis and prognosis, and the novel use of nanotechnology, as well as strategies for disease control and monitoring populations at higher risk are still continuous challenges, which will be specifically reviewed with additional insights. The use of the current diagnostic tools, such as ELISA and PCR has a very limited approach for leprosy that has been considered as a marginal disease; therefore, the current diagnostic tools must be applied extensively in the routine to accumulate clinical experience in order to improve their precise application, like what has been done in many other infectious diseases. Since a vaccine for leprosy presents an unpredictable future, the proposed chemoprophylaxis of contacts (healthy carriers and/or with subclinical infection) must also be employed in referral centers of endemic countries not only to evaluate its efficacy, but also because of the favorable cost–benefit ratio, given that there is no other available approach, besides the multi-drug therapy of patients. This strategy should readily be applied as a public health policy, and may lead to a substantial breakage of the transmission chain aiming a world without leprosy. [ABSTRACT FROM AUTHOR]

Objectives: Coronavirus disease (COVID-19) is one of the most detrimental pandemics that affected the humanity throughout the ages. The irregular historical progression of the virus over the first year of the pandemic was accompanied with far-reaching health and social damages. To prepare logistically against this worsening disaster, many public authorities around the world had set up screening and forecasting studies. This article aims to analyse the time-frequency co-evolution of the number of confirmed cases (NCC) in Tunisia and the related number of performed polymerase chain reaction (PCR) tests over the COVID-19 first year. Accurately predicting such a relationship allows Tunisian authorities to set up an effective health prevention plan., Study Design: In order to keep pace with the speed of evolution of the virus, we used uninterrupted daily time series from the Tunisian Ministry of Public Health (TMPH) recorded over the COVID-19 first year. The objective is to: (1) analyse the time-frequency progress of the NCC in relationship with the number of PCR tests, (2) identify a multi-scale two-factor stochastic model in order to develop a robust bivariate forecasting technique., Methods: We assume a bivariate stochastic process which is projected onto a set of wavelet sub-spaces to investigate the scale-by-scale co-evolvement the NCC/PCR over the COVID-19 first year. A wavelet-based multiresolutional causality test is then performed., Results: The main results recommend the rejection of the null hypothesis of no instantaneous causality in both directions, while the statistics of the Granger test suggest failing to reject the null hypothesis of non-causality. However, by proceeding scale-by-scale, the Granger causality is proven significant in both directions over varying frequency bands., Conclusions: It is important to include the NCC and PCR variables in any time series model intended to predict one of these variables. Such a bivariate and multi-scale model is supposed to better predict the needs of the public health sector in screening tests. On this basis, testing campaigns with multiple periodicities can be planned by the Tunisian authorities., (© 2022 John Wiley & Sons Ltd.)

Aims: With resumption of elective spine surgery services in the UK following the first wave of the COVID-19 pandemic, we conducted a multicentre British Association of Spine Surgeons (BASS) collaborative study to examine the complications and deaths due to COVID-19 at the recovery phase of the pandemic. The aim was to analyze the safety of elective spinal surgery during the pandemic., Methods: A prospective observational study was conducted from eight spinal centres for the first month of operating following restoration of elective spine surgery in each individual unit. Primary outcome measure was the 30-day postoperative COVID-19 infection rate. Secondary outcomes analyzed were the 30-day mortality rate, surgical adverse events, medical complications, and length of inpatient stay., Results: In all, 257 patients (128 males) with a median age of 54 years (2 to 88) formed the study cohort. The mean number of procedures performed from each unit was 32 (16 to 101), with 118 procedures (46%) done as category three prioritization level. The majority of patients (87%) were low-medium "risk stratification" category and the mean length of hospital stay was 5.2 days. None of the patients were diagnosed with COVID-19 infection, nor was there any mortality related to COVID-19 during the 30-day follow-up period, with 25 patients (10%) having been tested for symptoms. Overall, 32 patients (12%) developed a total of 34 complications, with the majority (19/34) being grade 1 to 2 Clavien-Dindo classification of surgical complications. No patient required postoperative care in an intensive care setting for any unexpected complication., Conclusion: This study shows that safe and effective planned spinal surgical services can be restored avoiding viral transmission, with diligent adherence to national guidelines and COVID-19-secure pathways tailored according to the resources of the individual spinal units. Cite this article: Bone Jt Open  2021;2(12):1096-1101.

Objective: To point out possible infection with SARS-CoV-2 in symptomatic patients despite repeated negative nasopharyngeal swab tests for SARS-CoV-2., Material and Methods: A retrospective observational study carried out at the Na Bulovce Hospital from the beginning of the pandemic until November 2020 included patients (1) who had symptoms compatible with COVID-19; (2) whose nasopharyngeal swab PCR tests in the presence of acute respiratory infection symptoms yielded two consecutive negative results; (3) in whom SARS-CoV-2 infection was subsequently confirmed by serology. Basic demographic and epidemiological data, symptoms, laboratory test results, X-ray findings and timing of virological tests were analysed for these patients., Results: Seventeen patients met the inclusion criteria, 14 men and three women, aged 19-84 years with a median of 59 years, of whom 14 were hospitalized and three were treated as outpatients. Only seven patients were aware of the previous contact with an infected person. The main symptoms were fever, cough, headache, weakness, fatigue and shortness of breath. Pneumonia was found in 12 patients, four of whom developed respiratory insufficiency requiring ventilatory support. Most patients showed a uniform combination of haematological, biochemical and radio-logical findings: absence of eosinophils and increased polymorphonuclear/lymphocyte ratio; elevation of serum lactate dehydrogenase; elevation of CRP without rise of procalcitonin; typical chest CT or X-ray findings. All patients recovered. Coronavirus antigen test was performed in six patients, with all of them testing negative. SARS-CoV-2 infection was confirmed serologically by the detection of specific IgG and IgA in all 17 patients and also IgM in six patients, not before day 8 of the onset of symptoms., Conclusions: Our study showed that some patients with acute COVID-19 may test repeatedly negative by nasopharyngeal swab PCR. These cases should be interpreted as a low viral load in the upper respiratory tract rather than false negativity of PCR. Such alternative is not envisaged in the algorithms used. Considering our results, the following recommendation can be made: If, despite negative PCR tests, COVID-19 is still suspected based on clinical symptoms and epidemiological evidence, preliminary diagnosis can be made on the basis of comprehensive assessment of the laboratory test and X-ray findings. Final confirmation of the aetiology relies on serological tests performed two weeks after the onset of symptoms.