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Deployment of Dutch mobile laboratories in the West African Ebola virus response
Abstracts / Journal of Clinical Virology 70 (2015) S1–S126
Abstract No: 1596 Presentation at ESCV 2015: Oral 5 Virological characterisation of influenza viruses in Portugal during 2014/2015 season P. Pechirra 1,∗ , P. Cristóvão 1 , I. Costa 1 , C. Roque 2 , P. Barreiro 3 , S. Duarte 3 , A. Machado 4 , A.P. Rodrigues 4 , B. Nunes 4 , R. Guiomar 5
S3
genetic clade 3. Most influenza A (H3) viruses clustered into the subgroup 3C.2a and are distinct from the vaccine strain A/Texas/50/2012, however not all of them are similar to A/Switzerland/9715293/2013 (the strain chosen to integrate the influenza vaccine in 2015/2016). http://dx.doi.org/10.1016/j.jcv.2015.07.015 Abstract No: 1674
1
Portuguese Influenza Reference Laboratory, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal 2 Cell Culture Unit, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal 3 Technology and Innovation Unit, Human Genetic Department, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal 4 Department of Epidemiology, National Institute of Health Dr Ricardo Jorge, Lisbon, Portugal 5 Portuguese Influenza Reference Laboratory, National Institute of Health Dr. Ricardo Jorge, IP, Portugal Background: Continuous monitoring of the antigenic and genetic changes in circulating influenza viruses is essential for the selection of different vaccine candidates or changes in antiviral recommendations. This study reports antigenic and genetic characterisations of influenza viruses isolated in Portugal during the 2014/2015 influenza season. Methods: During the 2014/2015, in the context of influenza virological surveillance, 903 nasopharyngeal swabs were obtained through the National Influenza Surveillance Programme (NISP) and 190 from the Portuguese Laboratory Network for the Influenza Diagnosis. National Influenza Reference Laboratory has characterised antigenically, by hemagglutination-inhibition assays, 204 influenza strains after isolation on MDCK-Siat1 cell culture. A sample of 118 influenza viruses was selected for HA1 genetic characterisation. Results: Among 903 ILI cases from NISP tested for influenza, 328 (36%) were influenza B/Yamagata viruses, 149 (17%) influenza A (H3) viruses and 21 (2%) pandemic influenza A(H1) viruses. Only 2 from 178 influenza B isolates were antigenically similar to the 2014/2015 vaccine strain B/Massachusetts/2/2012. Most type B viruses (139; 78%) were similar to B/Phuket/3073/2013, the vaccine strain selected for 2015/2016 season in northern hemisphere. The remaining 37 isolates were poorly recognized by antisera raised against these vaccine strains. Genetically, all characterised influenza B viruses belong to Yamagata phylogenetic clade 3. Regarding influenza A (H3) viruses, their antigenic characterisation has been hampered due to a decreasing ability of the viruses to agglutinate red blood cells. For this reason, only 19 A(H3) isolates were antigenically characterised, 16 of them reacted poorly with any antiserum, and 3 were antigenically similar to the next season vaccine strain A/Switzerland/9715293/2013. Genetically, A(H3) viruses clustered in 2 subgroups: 37 viruses into subgroup 3C.2a (with A/Hong Kong/5738/2014 as reference strain of this group) while 17 viruses belong to subgroup 3C.3 (represented by A/Samara/73/2013). Antigenic and genetic characterisations were performed on 7 and 9 influenza A (H1)pdm09 viruses, respectively. All of them remain antigenically similar to the vaccine strain A/California/7/2009 and are part of the genetic group 6B, represented by the reference strain A/South Africa/3626/2013. Conclusion: Unlike the observed in most European countries, in Portugal, type B viruses were dominant amongst circulating influenza viruses in 2014/2015 winter. They revealed antigenic heterogeneity although all belong to B/Phuket/3073/2013
Presentation at ESCV 2015: Oral 6 Deployment of Dutch mobile laboratories in the West African Ebola virus response S.D. Pas ∗ , C. Reusken, B.L. Haagmans, M.P. Koopmans Erasmus MC, Netherlands Background: The Ebola virus disease (EVD) epidemic in WestAfrica is the worst ever, with 27,049 probable, suspected and confirmed cases, including 11,149 deaths up to June. One of the pillars in the EVD response has been the deployment of 27 temporary (mobile) laboratories of the international community (in coordination with the local authorities) to provide rapid testing capacity for Ebola virus (EBOV) and malaria. Short turn-around-times (TAT) for diagnostic samples (WHO target: <24 hours) are an absolute necessity to control the epidemic. Methods: Three BSL2 laboratories were built, in two 20-foot and one 40-foot sea container and equipped with an BSL3 glovebox, nucleic acid extraction machine and a real-time thermocycler to provide EBOV molecular diagnostics for whole blood, EDTA-plasma and throat swabs and Plasmodium falciparum lateral flow assay for whole blood samples. Based on a literature review and alignment of the outbreak strain (Ebola Makona virus) with published primer sets, we selected an available dual target (NP and L gen) internally controlled qPCR EBOV assay, with a commercially method (Altona Filoscreen) as back-up system. The in-house method is fully quality controlled (according to ISO15189), and checked with the WHO external quality control panel prior to operation. Teams of four experienced volunteer laboratory workers were selected on level and combination of expertise, and trained on more than 10 aspects, including biosafety training and acculturation and security and changed every 4–5 weeks. Results: The three mobile laboratories were deployed in December, January and February to Koidu, Sierra Leone, Sinje, Liberia and Freetown, Sierra Leone respectively. The lead time for the first laboratory was 2.5 months since the request. In total 3623 samples have been processed, in which 48 samples (38 blood and 10 swabs) EBOV RNA was detected with a median Ct-value of 21.0 (range 14.7-36.4). In 39.8% of 1733 EDTA-blood samples malaria was detected. Median TAT (sample receipt to result) was 6.1 hours (2.6–30.4), with 99% of the sample results reported within 24 hours. Important challenges were power failures, sensitivity of equipment to local climate conditions, expensive logistic chains and the lack of overall coordination of the Ebola response effort. Conclusion: The deployment of the Dutch mobile laboratories showed that rapid development of core laboratory capacity is possible. Nevertheless, the laboratory capacity building started late in the outbreak, and considering the costs of such ad hoc deployment, investing in longer term sustainable laboratory capacity should be a top priority. http://dx.doi.org/10.1016/j.jcv.2015.07.016
Abstract No: 1596 Presentation at ESCV 2015: Oral 5 Virological characterisation of influenza viruses in Portugal during 2014/2015 season P. Pechirra 1,∗ , P. Cristóvão 1 , I. Costa 1 , C. Roque 2 , P. Barreiro 3 , S. Duarte 3 , A. Machado 4 , A.P. Rodrigues 4 , B. Nunes 4 , R. Guiomar 5
S3
genetic clade 3. Most influenza A (H3) viruses clustered into the subgroup 3C.2a and are distinct from the vaccine strain A/Texas/50/2012, however not all of them are similar to A/Switzerland/9715293/2013 (the strain chosen to integrate the influenza vaccine in 2015/2016). http://dx.doi.org/10.1016/j.jcv.2015.07.015 Abstract No: 1674
1
Portuguese Influenza Reference Laboratory, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal 2 Cell Culture Unit, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal 3 Technology and Innovation Unit, Human Genetic Department, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal 4 Department of Epidemiology, National Institute of Health Dr Ricardo Jorge, Lisbon, Portugal 5 Portuguese Influenza Reference Laboratory, National Institute of Health Dr. Ricardo Jorge, IP, Portugal Background: Continuous monitoring of the antigenic and genetic changes in circulating influenza viruses is essential for the selection of different vaccine candidates or changes in antiviral recommendations. This study reports antigenic and genetic characterisations of influenza viruses isolated in Portugal during the 2014/2015 influenza season. Methods: During the 2014/2015, in the context of influenza virological surveillance, 903 nasopharyngeal swabs were obtained through the National Influenza Surveillance Programme (NISP) and 190 from the Portuguese Laboratory Network for the Influenza Diagnosis. National Influenza Reference Laboratory has characterised antigenically, by hemagglutination-inhibition assays, 204 influenza strains after isolation on MDCK-Siat1 cell culture. A sample of 118 influenza viruses was selected for HA1 genetic characterisation. Results: Among 903 ILI cases from NISP tested for influenza, 328 (36%) were influenza B/Yamagata viruses, 149 (17%) influenza A (H3) viruses and 21 (2%) pandemic influenza A(H1) viruses. Only 2 from 178 influenza B isolates were antigenically similar to the 2014/2015 vaccine strain B/Massachusetts/2/2012. Most type B viruses (139; 78%) were similar to B/Phuket/3073/2013, the vaccine strain selected for 2015/2016 season in northern hemisphere. The remaining 37 isolates were poorly recognized by antisera raised against these vaccine strains. Genetically, all characterised influenza B viruses belong to Yamagata phylogenetic clade 3. Regarding influenza A (H3) viruses, their antigenic characterisation has been hampered due to a decreasing ability of the viruses to agglutinate red blood cells. For this reason, only 19 A(H3) isolates were antigenically characterised, 16 of them reacted poorly with any antiserum, and 3 were antigenically similar to the next season vaccine strain A/Switzerland/9715293/2013. Genetically, A(H3) viruses clustered in 2 subgroups: 37 viruses into subgroup 3C.2a (with A/Hong Kong/5738/2014 as reference strain of this group) while 17 viruses belong to subgroup 3C.3 (represented by A/Samara/73/2013). Antigenic and genetic characterisations were performed on 7 and 9 influenza A (H1)pdm09 viruses, respectively. All of them remain antigenically similar to the vaccine strain A/California/7/2009 and are part of the genetic group 6B, represented by the reference strain A/South Africa/3626/2013. Conclusion: Unlike the observed in most European countries, in Portugal, type B viruses were dominant amongst circulating influenza viruses in 2014/2015 winter. They revealed antigenic heterogeneity although all belong to B/Phuket/3073/2013
Presentation at ESCV 2015: Oral 6 Deployment of Dutch mobile laboratories in the West African Ebola virus response S.D. Pas ∗ , C. Reusken, B.L. Haagmans, M.P. Koopmans Erasmus MC, Netherlands Background: The Ebola virus disease (EVD) epidemic in WestAfrica is the worst ever, with 27,049 probable, suspected and confirmed cases, including 11,149 deaths up to June. One of the pillars in the EVD response has been the deployment of 27 temporary (mobile) laboratories of the international community (in coordination with the local authorities) to provide rapid testing capacity for Ebola virus (EBOV) and malaria. Short turn-around-times (TAT) for diagnostic samples (WHO target: <24 hours) are an absolute necessity to control the epidemic. Methods: Three BSL2 laboratories were built, in two 20-foot and one 40-foot sea container and equipped with an BSL3 glovebox, nucleic acid extraction machine and a real-time thermocycler to provide EBOV molecular diagnostics for whole blood, EDTA-plasma and throat swabs and Plasmodium falciparum lateral flow assay for whole blood samples. Based on a literature review and alignment of the outbreak strain (Ebola Makona virus) with published primer sets, we selected an available dual target (NP and L gen) internally controlled qPCR EBOV assay, with a commercially method (Altona Filoscreen) as back-up system. The in-house method is fully quality controlled (according to ISO15189), and checked with the WHO external quality control panel prior to operation. Teams of four experienced volunteer laboratory workers were selected on level and combination of expertise, and trained on more than 10 aspects, including biosafety training and acculturation and security and changed every 4–5 weeks. Results: The three mobile laboratories were deployed in December, January and February to Koidu, Sierra Leone, Sinje, Liberia and Freetown, Sierra Leone respectively. The lead time for the first laboratory was 2.5 months since the request. In total 3623 samples have been processed, in which 48 samples (38 blood and 10 swabs) EBOV RNA was detected with a median Ct-value of 21.0 (range 14.7-36.4). In 39.8% of 1733 EDTA-blood samples malaria was detected. Median TAT (sample receipt to result) was 6.1 hours (2.6–30.4), with 99% of the sample results reported within 24 hours. Important challenges were power failures, sensitivity of equipment to local climate conditions, expensive logistic chains and the lack of overall coordination of the Ebola response effort. Conclusion: The deployment of the Dutch mobile laboratories showed that rapid development of core laboratory capacity is possible. Nevertheless, the laboratory capacity building started late in the outbreak, and considering the costs of such ad hoc deployment, investing in longer term sustainable laboratory capacity should be a top priority. http://dx.doi.org/10.1016/j.jcv.2015.07.016