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Novel astrovirus and calicivirus identified in migratory birds in Brazil
Abstracts / International Journal of Infectious Diseases 53S (2016) 4–163
03.006
03.007
Novel astrovirus and calicivirus identified in migratory birds in Brazil
Crimean congo hemorrhagic fever, 2013 and 2014 Sudan
W.M. Souza a,∗ , M.F. Romeiro b , M.J. Fumagalli a , J. Araujo b , L. La Serra a , L.C. Vieira a , E.L. Durigon b , P.R. Murcia c , L.T.M. Figueiredo a
C. Kohl a,∗ , M. Eldegail b , I. Mahmoud b , L. Schrick a , A. Radonic a , P. Emmerich c , T. Rieger c , S. Gunther c , A. Nitsche a , A.A. Osman b
a
a
University of São Paulo, Virology Research Center, Ribeirão Preto/BR b University of São Paulo, Institute of Biomedical Sciences, São Paulo/BR c MRC- University of Glasgow Centre for Virus Research, College of Medical, Veterinary and Life Sciences, Glasgow/UK Purpose: Examining the viral diversity present in domestic and wild birds in Brazil. To this end we applied a metagenomic approach to clinical specimens derived from different birds species in various geographical locations. Methods & Materials: We sampled 100 individuals that represented eight different birds species. The samples of poultry (Gallus gallus, Cairina monchata) were collected in Breves city, Pará State, whereas samples from migratory birds (Arenaria interpres, Thalasseus sandvicensis, Calidris pusilla) were collected in Coroa do Avião Island, Pernambuco State, and wild residents birds (Hilophilus amaurocephalus, Sarkesphorus cristapus and Coryphospingus pileatus) in São José do Egito, Paraíba State. Samples were distributed in pools based on species, sample type (i.e. cloacal swabs and sera), date and capture location. Viral RNA was extracted and followed by synthesis of double-stranded cDNA prior to Illumina sequencing. Sequence reads were quality-filtered, removed the adapter sequences and remaining reads were assembled de novo. Obtained contigs were submitted to BLAST-based searches to identify viruses and further subject to phylogenetic analyses. Results: We found nine viruses that showed similarity to known caliciviruses and astroviruses. A complete genome and two partial genomes of astrovirus were obtained from two pools of Arenaria interpres. The genome organization of Arenaria interpres astrovirus (AiAstV) was similar to that of other Astrovirus, and phylogenetic analysis reveals that the AiAstV is a member of Avastrovirus genus. AiAstV was most closely related to a recently characterized chicken avastrovirus with their genomes sharing ∼60% amino acid identity. On another hand, four contigs and a complete genome of a calivirus were obtained in four pools from Cairina monchata, Arenaria interpres and Hilophilus amaurocephalus. A complete full-length genome sequence of approximately 8 kb in length was obtained from samples from Arenaria interpres, showing a genomic organization typical of caliciviruses. Phylogenetic analysis reveals that Arenaria interpres calicivirus is a potential member of Nacovirus genus. Interestingly, both novel viruses were detected exclusively from cloacals swab, strongly suggesting the excretion of these viruses in nature. Conclusion: Based on our results we found two novel astrovirus and calicivirus species in the Avastrovirus and Nacovirus genera, respectively. Further studies should aim to characterize their host range and pathogenic potential.
Robert Koch Institute; Center for Biological Threats and Special Pathogens 1 (ZBS-1), Berlin/DE b National Public Health Laboratory, NPHL, Karthoum/SD c Bernhard-Nocht-Institute for Tropical Medicine, Virology, Hamburg/DE Purpose: The German Partnership Program for Excellence in Biological and Health Security was launched in 2013 and is funded by the German Federal Foreign Office. Currently, the program funds projects in 18 countries in the fields of infectious disease surveillance, detection & diagnostics, biosafety & biosecurity, capacity building and networking. In Sudan one focus of the partnership is the detection of highly pathogenic viruses and identification of known and yet unknown etiological agents in outbreak situations. Methods & Materials: In 2014 an outbreak of hemorrhagic fever in humans was reported from different states of Sudan (South Darfur, West Kordofan, South Kordofan). The NPHL investigated the cases and forwarded 29 sera samples from patients suffering from hemorrhagic fever to the RKI. The sample-set included a panel of 10 sera collected during former hemorrhagic fever outbreaks in the same region in 2013. All sera were tested with qPCR assays for Marburg virus, Ebola virus and CCHFV. Additionally all samples were subjected to metagenomic deep sequencing on an Illumina MiSeq sequencer. Results: CCHF was identified by two independent qPCR assays in a sample from November 2013 and November 2014, respectively. Deep sequencing confirmed these results. Based on the available sequences the novel CCHFV strain ‘Sudan 2014’ shares 96% identity (na) with its closest relative CCHFV SPU 187/90 from South Africa. Conclusion: CCHFV is reported to be transmitted by ticks in Europe, Asia and Africa and known as etiological agent of severe hemorrhagic fever in humans and livestock. Beside insect-repellent no preventive measures are available. The pathogenicity and characteristics of this novel strain have yet to be determined by cell-culture isolation and serology. Further molecular analysis will contribute to clarify the divergence of the CCHFV strains detected in 2013 and 2014. First results including possible co-infections will be presented. http://dx.doi.org/10.1016/j.ijid.2016.11.027 03.008 An epidemiological investigation of a multisource outbreak of Crimean-Congo hemorrhagic fever in Karachi, from January– 15th September 2016 M.A. Syed a,∗ , H. Jhatyal b a
http://dx.doi.org/10.1016/j.ijid.2016.11.026
9
b
FELTP-Pakistan, Health, Karachi, SINDH/PK FELTP-PAKISTAN, Health, Karachi/PK
Purpose: In Pakistan Crimean–Congo haemorrhagic fever (CCHF) is an emerging life-threatening viral disease with case fatality rates up to 50%. With the increase in number of CCHF confirmed cases in the Karachi by December 2015, we decided to focus attention on disease in 2016. An epidemiological investigation was
03.006
03.007
Novel astrovirus and calicivirus identified in migratory birds in Brazil
Crimean congo hemorrhagic fever, 2013 and 2014 Sudan
W.M. Souza a,∗ , M.F. Romeiro b , M.J. Fumagalli a , J. Araujo b , L. La Serra a , L.C. Vieira a , E.L. Durigon b , P.R. Murcia c , L.T.M. Figueiredo a
C. Kohl a,∗ , M. Eldegail b , I. Mahmoud b , L. Schrick a , A. Radonic a , P. Emmerich c , T. Rieger c , S. Gunther c , A. Nitsche a , A.A. Osman b
a
a
University of São Paulo, Virology Research Center, Ribeirão Preto/BR b University of São Paulo, Institute of Biomedical Sciences, São Paulo/BR c MRC- University of Glasgow Centre for Virus Research, College of Medical, Veterinary and Life Sciences, Glasgow/UK Purpose: Examining the viral diversity present in domestic and wild birds in Brazil. To this end we applied a metagenomic approach to clinical specimens derived from different birds species in various geographical locations. Methods & Materials: We sampled 100 individuals that represented eight different birds species. The samples of poultry (Gallus gallus, Cairina monchata) were collected in Breves city, Pará State, whereas samples from migratory birds (Arenaria interpres, Thalasseus sandvicensis, Calidris pusilla) were collected in Coroa do Avião Island, Pernambuco State, and wild residents birds (Hilophilus amaurocephalus, Sarkesphorus cristapus and Coryphospingus pileatus) in São José do Egito, Paraíba State. Samples were distributed in pools based on species, sample type (i.e. cloacal swabs and sera), date and capture location. Viral RNA was extracted and followed by synthesis of double-stranded cDNA prior to Illumina sequencing. Sequence reads were quality-filtered, removed the adapter sequences and remaining reads were assembled de novo. Obtained contigs were submitted to BLAST-based searches to identify viruses and further subject to phylogenetic analyses. Results: We found nine viruses that showed similarity to known caliciviruses and astroviruses. A complete genome and two partial genomes of astrovirus were obtained from two pools of Arenaria interpres. The genome organization of Arenaria interpres astrovirus (AiAstV) was similar to that of other Astrovirus, and phylogenetic analysis reveals that the AiAstV is a member of Avastrovirus genus. AiAstV was most closely related to a recently characterized chicken avastrovirus with their genomes sharing ∼60% amino acid identity. On another hand, four contigs and a complete genome of a calivirus were obtained in four pools from Cairina monchata, Arenaria interpres and Hilophilus amaurocephalus. A complete full-length genome sequence of approximately 8 kb in length was obtained from samples from Arenaria interpres, showing a genomic organization typical of caliciviruses. Phylogenetic analysis reveals that Arenaria interpres calicivirus is a potential member of Nacovirus genus. Interestingly, both novel viruses were detected exclusively from cloacals swab, strongly suggesting the excretion of these viruses in nature. Conclusion: Based on our results we found two novel astrovirus and calicivirus species in the Avastrovirus and Nacovirus genera, respectively. Further studies should aim to characterize their host range and pathogenic potential.
Robert Koch Institute; Center for Biological Threats and Special Pathogens 1 (ZBS-1), Berlin/DE b National Public Health Laboratory, NPHL, Karthoum/SD c Bernhard-Nocht-Institute for Tropical Medicine, Virology, Hamburg/DE Purpose: The German Partnership Program for Excellence in Biological and Health Security was launched in 2013 and is funded by the German Federal Foreign Office. Currently, the program funds projects in 18 countries in the fields of infectious disease surveillance, detection & diagnostics, biosafety & biosecurity, capacity building and networking. In Sudan one focus of the partnership is the detection of highly pathogenic viruses and identification of known and yet unknown etiological agents in outbreak situations. Methods & Materials: In 2014 an outbreak of hemorrhagic fever in humans was reported from different states of Sudan (South Darfur, West Kordofan, South Kordofan). The NPHL investigated the cases and forwarded 29 sera samples from patients suffering from hemorrhagic fever to the RKI. The sample-set included a panel of 10 sera collected during former hemorrhagic fever outbreaks in the same region in 2013. All sera were tested with qPCR assays for Marburg virus, Ebola virus and CCHFV. Additionally all samples were subjected to metagenomic deep sequencing on an Illumina MiSeq sequencer. Results: CCHF was identified by two independent qPCR assays in a sample from November 2013 and November 2014, respectively. Deep sequencing confirmed these results. Based on the available sequences the novel CCHFV strain ‘Sudan 2014’ shares 96% identity (na) with its closest relative CCHFV SPU 187/90 from South Africa. Conclusion: CCHFV is reported to be transmitted by ticks in Europe, Asia and Africa and known as etiological agent of severe hemorrhagic fever in humans and livestock. Beside insect-repellent no preventive measures are available. The pathogenicity and characteristics of this novel strain have yet to be determined by cell-culture isolation and serology. Further molecular analysis will contribute to clarify the divergence of the CCHFV strains detected in 2013 and 2014. First results including possible co-infections will be presented. http://dx.doi.org/10.1016/j.ijid.2016.11.027 03.008 An epidemiological investigation of a multisource outbreak of Crimean-Congo hemorrhagic fever in Karachi, from January– 15th September 2016 M.A. Syed a,∗ , H. Jhatyal b a
http://dx.doi.org/10.1016/j.ijid.2016.11.026
9
b
FELTP-Pakistan, Health, Karachi, SINDH/PK FELTP-PAKISTAN, Health, Karachi/PK
Purpose: In Pakistan Crimean–Congo haemorrhagic fever (CCHF) is an emerging life-threatening viral disease with case fatality rates up to 50%. With the increase in number of CCHF confirmed cases in the Karachi by December 2015, we decided to focus attention on disease in 2016. An epidemiological investigation was