PMC:7029448 / 10280-15417 JSON TXT

Annnotations TAB JSON ListView MergeView

LitCovid-PubTator

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T16","span":{"begin":1802,"end":1806},"obj":"Disease"},{"id":"T17","span":{"begin":2406,"end":2415},"obj":"Disease"},{"id":"T18","span":{"begin":3140,"end":3157},"obj":"Disease"},{"id":"T19","span":{"begin":3140,"end":3149},"obj":"Disease"}],"attributes":[{"id":"A16","pred":"mondo_id","subj":"T16","obj":"http://purl.obolibrary.org/obo/MONDO_0018661"},{"id":"A17","pred":"mondo_id","subj":"T17","obj":"http://purl.obolibrary.org/obo/MONDO_0005812"},{"id":"A18","pred":"mondo_id","subj":"T18","obj":"http://purl.obolibrary.org/obo/MONDO_0005460"},{"id":"A19","pred":"mondo_id","subj":"T19","obj":"http://purl.obolibrary.org/obo/MONDO_0005812"}],"text":"Discussion\nAs at 10 February 2020, 37 confirmed 2019-nCoV cases were reported from eight European countries based on ECDC reporting and testing criteria [3,10]. Multiple modelling studies estimated the risk of 2019-nCoV introduction to Europe as high [11-14]. Pullano et al. indicated the United Kingdom, France and Germany as being at the highest risk, followed by Italy, Spain and the Netherlands [11]. Indeed, all but one country (the Netherlands) have reported cases. The study reported that the occurrence of 2019-nCoV importation from Beijing and Shanghai, both cities with high numbers of travellers to Europe, would likely lead to an even higher and widespread risk for Europe.\nThis rapid assessment of the readiness of EU/EEA laboratories for molecular detection of 2019-nCoV demonstrated a fast implementation of molecular diagnostics by the European specialised laboratory networks with a good geographical coverage for testing. Among both laboratory networks in this study, protocols were shared rapidly and there was an early availability of positive controls and CoV specificity panels via EVAg. Furthermore, the survey indicated a great willingness of laboratories to provide international diagnostic support [10] and to share sequences to contribute to the monitoring of virus evolution and trace transmission chains.\nHowever, although the first protocols suggesting primer/probe sequences were available fast through the WHO website (Figure 1) and validation panels were made available through the EVAg portal soon after [6,7], the availability of primers, probes and positive controls were indicated as most important initial obstacles for test implementation. In addition, lack of sufficient personnel to implement and validate was a barrier, as had been observed in response to the Zika virus (ZIKV) outbreak in the Americas and the related PHEIC [15]. This suggests that the challenges faced by specialised laboratories when responding to emerging events are of structural nature.\nCapacity-wise, the survey indicates that European specialised laboratories are prepared for the current situation, and suggests that a more sensitive case definition than currently in use [10,16] would not create an immediate bottleneck. However, it remains to be seen how realistic the estimates are, particularly in view of the coinciding seasonal epidemic peaks of other respiratory pathogens such as influenza viruses. This will depend on the epidemiological developments in the 2019-nCoV outbreak and on whether the current worldwide control strategy of containment with active case finding [5] will be sustained and the indicated laboratory capacity will suffice. If the outbreak turns into a pandemic, specialised laboratories’ efforts would refocus to reference activities like confirmatory testing, laboratory surveillance including virus characterisation, provision of reference materials and advice, while general testing for 2019-nCoV would shift to first-line hospital laboratories that currently do not have this capacity. This would require a roll-out of tests from the specialised laboratories as was done during the 2009 influenza A(H1N1) pandemic.\nThe survey showed that proper validation of specificity was lacking in a vast majority of the laboratories that had implemented testing while very few laboratories indicated to have implemented tests without availability of a positive control. The important assessment of the clinical sensitivity of the implemented tests was not possible in this very early phase of laboratory response due to the, at the time, absence of positive clinical materials in Europe. The three laboratories without a positive control will also not have assessed the analytical sensitivity of their tests. The legal possibilities (General Data Protection Regulation; GDPR) for sharing and the willingness to share positive clinical material among the network laboratories now that the first 37 cases have been confirmed in the EU/EEA will determine the speed with which laboratories can address the clinical sensitivity of their implemented tests while the number of cases in the EU/EEA is still limited.\nTo properly assess the actual capability of the laboratories to detect (sub)clinical 2019-nCoV cases and to provide directions for corrective actions, proficiency testing by external quality assessment (EQA) is essential and urgently needed. The importance of EQA was illustrated in the European ZIKV response where timely implementation was not matched by an overall good capability [17]. Forty of the 47 responding laboratories in this study indicated that they will participate in such an assessment. Currently activities are ongoing to assess the actual capabilities within both laboratory networks by EQA.\nIn conclusion, while molecular testing for 2019-nCoV was quickly implemented in EU/EEA countries there is still room for improvement especially in the aspect of clinical validation of specificity and sensitivity, as could be expected considering the survey was taken in the very early phase of the laboratory response. Capability testing based on proficiency panels is needed."}

LitCovid-PD-CLO

LitCovid-PD-CHEBI

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T7","span":{"begin":1390,"end":1395},"obj":"Chemical"}],"attributes":[{"id":"A7","pred":"chebi_id","subj":"T7","obj":"http://purl.obolibrary.org/obo/CHEBI_50406"}],"text":"Discussion\nAs at 10 February 2020, 37 confirmed 2019-nCoV cases were reported from eight European countries based on ECDC reporting and testing criteria [3,10]. Multiple modelling studies estimated the risk of 2019-nCoV introduction to Europe as high [11-14]. Pullano et al. indicated the United Kingdom, France and Germany as being at the highest risk, followed by Italy, Spain and the Netherlands [11]. Indeed, all but one country (the Netherlands) have reported cases. The study reported that the occurrence of 2019-nCoV importation from Beijing and Shanghai, both cities with high numbers of travellers to Europe, would likely lead to an even higher and widespread risk for Europe.\nThis rapid assessment of the readiness of EU/EEA laboratories for molecular detection of 2019-nCoV demonstrated a fast implementation of molecular diagnostics by the European specialised laboratory networks with a good geographical coverage for testing. Among both laboratory networks in this study, protocols were shared rapidly and there was an early availability of positive controls and CoV specificity panels via EVAg. Furthermore, the survey indicated a great willingness of laboratories to provide international diagnostic support [10] and to share sequences to contribute to the monitoring of virus evolution and trace transmission chains.\nHowever, although the first protocols suggesting primer/probe sequences were available fast through the WHO website (Figure 1) and validation panels were made available through the EVAg portal soon after [6,7], the availability of primers, probes and positive controls were indicated as most important initial obstacles for test implementation. In addition, lack of sufficient personnel to implement and validate was a barrier, as had been observed in response to the Zika virus (ZIKV) outbreak in the Americas and the related PHEIC [15]. This suggests that the challenges faced by specialised laboratories when responding to emerging events are of structural nature.\nCapacity-wise, the survey indicates that European specialised laboratories are prepared for the current situation, and suggests that a more sensitive case definition than currently in use [10,16] would not create an immediate bottleneck. However, it remains to be seen how realistic the estimates are, particularly in view of the coinciding seasonal epidemic peaks of other respiratory pathogens such as influenza viruses. This will depend on the epidemiological developments in the 2019-nCoV outbreak and on whether the current worldwide control strategy of containment with active case finding [5] will be sustained and the indicated laboratory capacity will suffice. If the outbreak turns into a pandemic, specialised laboratories’ efforts would refocus to reference activities like confirmatory testing, laboratory surveillance including virus characterisation, provision of reference materials and advice, while general testing for 2019-nCoV would shift to first-line hospital laboratories that currently do not have this capacity. This would require a roll-out of tests from the specialised laboratories as was done during the 2009 influenza A(H1N1) pandemic.\nThe survey showed that proper validation of specificity was lacking in a vast majority of the laboratories that had implemented testing while very few laboratories indicated to have implemented tests without availability of a positive control. The important assessment of the clinical sensitivity of the implemented tests was not possible in this very early phase of laboratory response due to the, at the time, absence of positive clinical materials in Europe. The three laboratories without a positive control will also not have assessed the analytical sensitivity of their tests. The legal possibilities (General Data Protection Regulation; GDPR) for sharing and the willingness to share positive clinical material among the network laboratories now that the first 37 cases have been confirmed in the EU/EEA will determine the speed with which laboratories can address the clinical sensitivity of their implemented tests while the number of cases in the EU/EEA is still limited.\nTo properly assess the actual capability of the laboratories to detect (sub)clinical 2019-nCoV cases and to provide directions for corrective actions, proficiency testing by external quality assessment (EQA) is essential and urgently needed. The importance of EQA was illustrated in the European ZIKV response where timely implementation was not matched by an overall good capability [17]. Forty of the 47 responding laboratories in this study indicated that they will participate in such an assessment. Currently activities are ongoing to assess the actual capabilities within both laboratory networks by EQA.\nIn conclusion, while molecular testing for 2019-nCoV was quickly implemented in EU/EEA countries there is still room for improvement especially in the aspect of clinical validation of specificity and sensitivity, as could be expected considering the survey was taken in the very early phase of the laboratory response. Capability testing based on proficiency panels is needed."}

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T2","span":{"begin":3800,"end":3810},"obj":"http://purl.obolibrary.org/obo/GO_0065007"}],"text":"Discussion\nAs at 10 February 2020, 37 confirmed 2019-nCoV cases were reported from eight European countries based on ECDC reporting and testing criteria [3,10]. Multiple modelling studies estimated the risk of 2019-nCoV introduction to Europe as high [11-14]. Pullano et al. indicated the United Kingdom, France and Germany as being at the highest risk, followed by Italy, Spain and the Netherlands [11]. Indeed, all but one country (the Netherlands) have reported cases. The study reported that the occurrence of 2019-nCoV importation from Beijing and Shanghai, both cities with high numbers of travellers to Europe, would likely lead to an even higher and widespread risk for Europe.\nThis rapid assessment of the readiness of EU/EEA laboratories for molecular detection of 2019-nCoV demonstrated a fast implementation of molecular diagnostics by the European specialised laboratory networks with a good geographical coverage for testing. Among both laboratory networks in this study, protocols were shared rapidly and there was an early availability of positive controls and CoV specificity panels via EVAg. Furthermore, the survey indicated a great willingness of laboratories to provide international diagnostic support [10] and to share sequences to contribute to the monitoring of virus evolution and trace transmission chains.\nHowever, although the first protocols suggesting primer/probe sequences were available fast through the WHO website (Figure 1) and validation panels were made available through the EVAg portal soon after [6,7], the availability of primers, probes and positive controls were indicated as most important initial obstacles for test implementation. In addition, lack of sufficient personnel to implement and validate was a barrier, as had been observed in response to the Zika virus (ZIKV) outbreak in the Americas and the related PHEIC [15]. This suggests that the challenges faced by specialised laboratories when responding to emerging events are of structural nature.\nCapacity-wise, the survey indicates that European specialised laboratories are prepared for the current situation, and suggests that a more sensitive case definition than currently in use [10,16] would not create an immediate bottleneck. However, it remains to be seen how realistic the estimates are, particularly in view of the coinciding seasonal epidemic peaks of other respiratory pathogens such as influenza viruses. This will depend on the epidemiological developments in the 2019-nCoV outbreak and on whether the current worldwide control strategy of containment with active case finding [5] will be sustained and the indicated laboratory capacity will suffice. If the outbreak turns into a pandemic, specialised laboratories’ efforts would refocus to reference activities like confirmatory testing, laboratory surveillance including virus characterisation, provision of reference materials and advice, while general testing for 2019-nCoV would shift to first-line hospital laboratories that currently do not have this capacity. This would require a roll-out of tests from the specialised laboratories as was done during the 2009 influenza A(H1N1) pandemic.\nThe survey showed that proper validation of specificity was lacking in a vast majority of the laboratories that had implemented testing while very few laboratories indicated to have implemented tests without availability of a positive control. The important assessment of the clinical sensitivity of the implemented tests was not possible in this very early phase of laboratory response due to the, at the time, absence of positive clinical materials in Europe. The three laboratories without a positive control will also not have assessed the analytical sensitivity of their tests. The legal possibilities (General Data Protection Regulation; GDPR) for sharing and the willingness to share positive clinical material among the network laboratories now that the first 37 cases have been confirmed in the EU/EEA will determine the speed with which laboratories can address the clinical sensitivity of their implemented tests while the number of cases in the EU/EEA is still limited.\nTo properly assess the actual capability of the laboratories to detect (sub)clinical 2019-nCoV cases and to provide directions for corrective actions, proficiency testing by external quality assessment (EQA) is essential and urgently needed. The importance of EQA was illustrated in the European ZIKV response where timely implementation was not matched by an overall good capability [17]. Forty of the 47 responding laboratories in this study indicated that they will participate in such an assessment. Currently activities are ongoing to assess the actual capabilities within both laboratory networks by EQA.\nIn conclusion, while molecular testing for 2019-nCoV was quickly implemented in EU/EEA countries there is still room for improvement especially in the aspect of clinical validation of specificity and sensitivity, as could be expected considering the survey was taken in the very early phase of the laboratory response. Capability testing based on proficiency panels is needed."}

LitCovid-sentences