To document the viral zoonotic risks in Vietnam, fecal samples were systematically collected from a number of mammals in southern Vietnam and subjected to agnostic deep sequencing. We describe here novel Vietnamese bunyavirus sequences detected in bat feces. The complete L and S segments from 14 viruses were determined

Bach, TK

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Berto, A

Bogaardt, C

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          To document the viral zoonotic risks in Vietnam, fecal samples were systematically collected from a number of mammals in southern Vietnam and subjected to agnostic deep sequencing. We describe here novel Vietnamese bunyavirus sequences detected in bat feces. The complete L and S segments from 14 viruses were determined.</jats:p

Bas B. Oude Munnink

My V. T. Phan

Lia van der Hoek

Paul Kellam

Matthew Cotten

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Genome Sequences of a Novel Vietnamese Bat Bunyavirus

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     Edinburgh Research Explorer                                      Genome sequences of a novel vietnamese bat bunyavirusCitation for published version:Oude Munnink, BB, Phan, MVT, Hoek, LVD, Kellam, P, Cotten, M, Kiet, BT, Baker, S, Berto, A, Boni, MF,Bryant, JE, Phu, BD, Campbell, JI, Carrique-Mas, J, Hung, DM, Huong, DT, Oanh, DT, Day, JN, Van Tan,D, van Doorn, HR, Han, DA, Farrar, JJ, Trang, HTT, Nghia, HDT, Long, HB, Van Duong, H, Thu, HTK,Cuong, LC, Hung, LM, Phuong, LT, Phuc, LT, Phuong, LT, Luat, LX, Thu Ha, LT, Van Chuong, L, Loan,MTP, Nadjm, B, Bao, NT, Hoa, NT, Tue, NT, Tu, NC, Thuan, ND, Dong, N, Chuyen, NK, An, NN, Vinh, NN,Hung, NQ, Dung, NT, Minh, NT, Binh, NT, Tham, NTH, Tien, NTH, Chuc, NTK, Ngoc, NTL, Ha, NTL, Lien,NTN, Diep, NTN, Nhung, NT, Chau, NTS, Chi, NTY, Trinh, NT, Van, NT, Van Cuong, N, Van Hung, N, VanKinh, N, Hoang, NVM, Van My, N, Van Thang, N, Van Thanh, N, Van Vinh Chau, N, Van Xang, N, My, PH,Anh, PH, Khoa, PTM, Tam, PTT, Van Lao, P, Van Minh, P, Van Be Bay, P, My, PVT, Rabaa, MA, Rahman,M, Thompson, C, Thwaites, G, Ngan, TTD, Nhu, TDH, Chau, THM, Toan, TK, Phuc, TM, Hong, TTK, Dung,TTN, Thanh, TTT, Minh, TTT, Nguyen, TT, Hien, TT, Tri, TQ, Hien, VB, Tai, VN, Cuong, VQ, Phat, VV,Huong, VUTL, Hang, VTT, Wertheim, H, Bogaardt, C, Chase-Topping, M, Ivens, AL, Lu, L, Nyugen, D,Rambaut, A, Simmonds, P, Woolhouse, M, Deijs, M, Jebbink, MF, Jazaeri Farsani, SM, Dodd, K, Euren, J,Lucas, A, Ortiz, N, Pennacchio, L, Rubin, E, Saylors, KE, Hai, TM & Wolfe, ND 2016, 'Genome sequencesof a novel vietnamese bat bunyavirus' Genome announcements, vol. 4, no. 6, e0136616. DOI:10.1128/genomeA.01366-16Digital Object Identifier (DOI):10.1128/genomeA.01366-16Link:Link to publication record in Edinburgh Research ExplorerDocument Version:Publisher's PDF, also known as Version of recordPublished In:Genome announcementsPublisher Rights Statement:© 2016 Oude Munnink et al. This is an open-access article distributed under the terms of the Creative CommonsAttribution 4.0 International licenseGeneral rightsCopyright for the publications made accessible via the Edinburgh Research Explorer is retained by the author(s)and / or other copyright owners and it is a condition of accessing these publications that users recognise andabide by the legal requirements associated with these rights.Take down policyThe University of Edinburgh has made every reasonable effort to ensure that Edinburgh Research Explorercontent complies with UK legislation. If you believe that the public display of this file breaches copyright pleasecontact openaccess@ed.ac.uk providing details, and we will remove access to the work immediately andinvestigate your claim.Download date: 05. Apr. 2019Genome Sequences of a Novel Vietnamese Bat BunyavirusBas B. Oude Munnink,a,b My V. T. Phan,a Lia van der Hoek,c Paul Kellam,a,d Matthew Cotten,a,b the VIZIONS ConsortiumWellcome Trust Sanger Institute, Hinxton, Englanda; Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlandsb; Laboratory of ExperimentalVirology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlandsc; Imperial College London, London, United KingdomdTo document the viral zoonotic risks in Vietnam, fecal samples were systematically collected from a number of mammals insouthern Vietnam and subjected to agnostic deep sequencing. We describe here novel Vietnamese bunyavirus sequences de-tected in bat feces. The complete L and S segments from 14 viruses were determined.Received 25 October 2016 Accepted 28 October 2016 Published 22 December 2016Citation Oude Munnink BB, Phan MVT, van der Hoek L, Kellam P, Cotten M, the VIZIONS Consortium. 2016. Genome sequences of a novel Vietnamese bat bunyavirus. GenomeAnnounc 4(6):e01366-16. doi:10.1128/genomeA.01366-16.Copyright © 2016 Oude Munnink et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.Address correspondence to Matthew Cotten, mc13@sanger.ac.uk.The Bunyaviridae is a diverse viral family comprising five gen-era. Some members are notorious for their zoonotic potential(hantavirus and Rift Valley fever virus), one can cause severeproblems in cattle (Smallenberg virus), and another infects plants(tomato spotted wilt virus).Members of the envelopedBunyaviri-dae typically enclose a segmented negative-sense single-strandedRNA genome, with the L segment encoding an RNA-dependentRNA polymerase (RdRp), theM segment encoding glycoproteins,and the S segment encoding the nucleoprotein. The combinedgenomic length of the three segments is 11 to 19 kb (1).We searched for novel members of the Bunyaviridae in 135 batfecal samples collected from roosting sites using an agnostic deep-sequencing approach (2). Fecal samples were processed as previ-ously described (3), followed by sequencing on an Illumina HiSeqplatform yielding 3 to 4 million 250-nucleotide (nt) paired-endreads per sample, which were de novo assembled using SPAdesversion 3.5.0 (4), followed by improve_assembly (5). The result-ing reads were subjected to a modified protein blast search usingusearch (6) to identify Bunyaviridae-related sequences.Fourteen of 135 samples (10%) yielded sequences with 51%amino acid identity to a small part of the RdRp of a Rhinolophuspearsoni bunyavirus. The M and S segments of this new Vietnam-ese bat bunyavirus could not be identified using simple homologysearching. Therefore, Uclust (6) was used to cluster all consensussequences of the bunyavirus-positive samples. Contigs present inover 70% of the samples were submitted to a conserved domainsearch (7), which yielded a putative S segment of the novel bun-yavirus showing similarities to a conserved tenuivirus/phlebovi-rus nucleocapsid protein domain; however, no amino acid iden-tity to known bunyaviruses could be identified. The genomelengths of the L segment of the novel Vietnamese bat bunyaviruseswere 6,484 to 6,713 nucleotides (average sequence coverage, 78- to2,619-fold). The nucleotide sequence of the L segment of the 14isolates differed at 21 to 124 positions (98% to 100% nucleotideidentity), while the S segments differed at 5 to 54 positions (97% to100% nucleotide identity). The genome length of the S segmentvaried between 1,464 and 1,578 nucleotides (average sequencecoverage, 47- to 849-fold).Consistentwith other studies (8, 9), no contigswith similaritiesto the BunyaviridaeM segment could be found. Either the M seg-ments exists in these samples with greater sequence divergenceprecluding identification, or these viruses exist without a standardM segment, perhaps by complementation with functions fromother coinfecting viruses.In conclusion, we present the L and S genome segments of anovel Vietnamese bunyavirus. This novel virus was identified in14 bat fecal samples, and for all viruses, the complete genomesequences of the L and S segments were determined. The lengthsof the two segments of this novel unclassified bunyavirus are con-sistent with other members of Phlebovirus and theHantavirus (1);however, additional research is needed to accurately classify thisnovel bunyavirus and resolve the M segment mystery.Accession number(s). The complete genome sequences of theVietnamese bat bunyaviruses are deposited in GenBank under theaccession numbers KX886759 to KX886786.ACKNOWLEDGMENTSThe VIZIONS Consortium members (alphabetical order by surname)from the Oxford University Clinical Research Unit are Bach Tuan Kiet,Stephen Baker, Alessandra Berto,Maciej F. Boni, Juliet E. Bryant, Bui DucPhu, James I. Campbell, Juan Carrique-Mas, Dang Manh Hung, DangThaoHuong, Dang TramOanh, JeremyN.Day, DinhVanTan,H. Rogiervan Doorn, Duong An Han, Jeremy J. Farrar, Hau Thi Thu Trang, HoDang Trung Nghia, Hoang Bao Long, Hoang Van Duong, Huynh ThiKim Thu, Lam Chi Cuong, Le Manh Hung, Le Thanh Phuong, Le ThiPhuc, Le Thi Phuong, Le Xuan Luat, Luu Thi Thu Ha, Ly Van Chuong,Mai Thi Phuoc Loan, Behzad Nadjm, Ngo Thanh Bao, Ngo Thi Hoa, NgoTri Tue, Nguyen Canh Tu, Nguyen Dac Thuan, Nguyen Dong, NguyenKhac Chuyen, Nguyen Ngoc An, Nguyen Ngoc Vinh, Nguyen QuocHung, Nguyen Thanh Dung, Nguyen Thanh Minh, Nguyen Thi Binh,Nguyen Thi Hong Tham, Nguyen Thi Hong Tien, Nguyen Thi KimChuc, Nguyen Thi Le Ngoc, Nguyen Thi Lien Ha, Nguyen Thi Nam Lien,Nguyen Thi Ngoc Diep, Nguyen Thi Nhung, Nguyen Thi Song Chau,Nguyen Thi Yen Chi, Nguyen Thieu Trinh, Nguyen Thu Van, NguyenVan Cuong, Nguyen Van Hung, Nguyen Van Kinh, Nguyen Van MinhHoang, Nguyen Van My, Nguyen Van Thang, Nguyen Van Thanh,Nguyen Van Vinh Chau, Nguyen Van Xang, Pham Ha My, Pham HongAnh, PhamThiMinhKhoa, PhamThi ThanhTam, PhamVan Lao, PhamVan Minh, Phan Van Be Bay, Phan Vu Tra My, Maia A. Rabaa, MotiurRahman, Corinne Thompson, Guy Thwaites, Ta Thi DieuNgan, TranDocrossmarkGenome AnnouncementsNovember/December 2016 Volume 4 Issue 6 e01366-16 genomea.asm.org 1 on February 14, 2017 by UNIVERSITY OF EDINBURGHhttp://genomea.asm.org/Downloaded from Hoang Nhu, Tran HoangMinh Chau, Tran Khanh Toan, TranMy Phuc,Tran Thi KimHong, Tran Thi Ngoc Dung, Tran Thi Thanh Thanh, TranThi Thuy Minh, Tran Thua Nguyen, Tran Tinh Hien, Trinh Quang Tri,Vo Be Hien, Vo Nhut Tai, Vo Quoc Cuong, Voong Vinh Phat, V. U. ThiLanHuong, andVuThi TyHang,HeimanWertheim; from theCentre forImmunity, Infection and Evolution, University of Edinburgh: Carlijn Bo-gaardt, Margo Chase-Topping, A. L. Ivens, Lu Lu, DungNyugen, AndrewRambaut, Peter Simmonds, and Mark Woolhouse; from the WellcomeTrust Sanger Institute, Hinxton, United Kingdom: Matthew Cotten, BasOude Munnink, Paul Kellam, andMy Vu Tra Phan; from the Laboratoryof Experimental Virology, Department of Medical Microbiology, Centerfor Infection and Immunity Amsterdam (CINIMA), Academic MedicalCenter of the University of Amsterdam, Amsterdam, The Netherlands:Martin Deijs, Lia van der Hoek, Maarten F. Jebbink, and Seyed Moham-mad Jazaeri Farsani; and from Metabiota, Inc., San Francisco, CA: Kim-berly Dodd, Jason Euren, Ashley Lucas, Nancy Ortiz, Len Pennacchio,Edward Rubin, Karen E. Saylors, Tran Minh Hai, and Nathan D. Wolfe.FUNDING INFORMATIONThis work was supported by the Wellcome Trust of the United Kingdomthrough the VIZIONS strategic award WT/093724. M.C. and B.B.O.M.were additionally funded by the EuropeanUnion’sHorizon 2020 researchand innovation program under grant agreements 643476 (COMPARE)and 634650 (Virogenesis).REFERENCES1. King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ. 2012. Virustaxonomy: classification and nomenclature of viruses, 9th ed. ElsevierAcademic, San Diego, CA.2. Cotten M, Oude Munnink B, Canuti M, Deijs M, Watson SJ, Kellam P,van der Hoek L. 2014. Full genome virus detection in fecal samples usingsensitive nucleic acid preparation, deep sequencing, and a novel iterativesequence classification algorithm. PLoS One 9:e93269. http://dx.doi.org/10.1371/journal.pone.0093269.3. de Vries M, Oude Munnink BB, Deijs M, Canuti M, Koekkoek SM,Molenkamp R, Bakker M, Jurriaans S, van Schaik BD, Luyf AC,Olabarriaga SD, van Kampen AH, van der Hoek L. 2012. Performanceof VIDISCA-454 in feces-suspensions and serum. Viruses 4:1328–1334.http://dx.doi.org/10.3390/v4081328.4. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, KulikovAS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV,Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012.SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. http://dx.doi.org/10.1089/cmb.2012.0021.5. Page AJ. 2012. Improve_assembly. https://metacpan.org/pod/distribution/Bio_AssemblyImprovement/bin/improve_assembly.6. Edgar RC. 2010. Search and clustering orders of magnitude faster thanBLAST. Bioinformatics 26:2460 –2461. http://dx.doi.org/10.1093/bioinformatics/btq461.7. Marchler-Bauer A, Derbyshire MK, Gonzales NR, Lu S, Chitsaz F, GeerLY, Geer RC, He J, Gwadz M, Hurwitz DI, Lanczycki CJ, Lu F, MarchlerGH, Song JS, Thanki N, Wang Z, Yamashita RA, Zhang D, Zheng C,Bryant SH. 2015. CDD: NCBI’s conserved domain database. Nucleic Ac-ids Res 43:D222–D226. http://dx.doi.org/10.1093/nar/gku1221.8. Tokarz R, Williams SH, Sameroff S, Sanchez Leon M, Jain K, LipkinWI. 2014. Virome analysis of Amblyomma americanum, Dermacentorvariabilis, and Ixodes scapularis ticks reveals novel highly divergent verte-brate and invertebrate viruses. J Virol 88:11480–11492. http://dx.doi.org/10.1128/JVI.01858-14.9. Sakamoto JM, Ng TF, Suzuki Y, Tsujimoto H, Deng X, Delwart E,Rasgon JL. 2016. Bunyaviruses are common in male and female Ixodesscapularis ticks in central Pennsylvania. PeerJ 4:e2324. http://dx.doi.org/10.7717/peerj.2324.Oude Munnink et al.Genome Announcements2 genomea.asm.org November/December 2016 Volume 4 Issue 6 e01366-16 on February 14, 2017 by UNIVERSITY OF EDINBURGHhttp://genomea.asm.org/Downloaded from 

Oude Munnink, Bas B.

Phan, My V.T.

van der Hoek, Lia

Kellam, Paul

Cotten, Matthew

VIZIONS Consortium,

Enlighten

Genome Sequences of a Novel Vietnamese Bat BunyavirusBas B. Oude Munnink,a,b My V. T. Phan,a Lia van der Hoek,c Paul Kellam,a,d Matthew Cotten,a,b the VIZIONS ConsortiumWellcome Trust Sanger Institute, Hinxton, Englanda; Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlandsb; Laboratory of ExperimentalVirology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlandsc; Imperial College London, London, United KingdomdTo document the viral zoonotic risks in Vietnam, fecal samples were systematically collected from a number of mammals insouthern Vietnam and subjected to agnostic deep sequencing. We describe here novel Vietnamese bunyavirus sequences de-tected in bat feces. The complete L and S segments from 14 viruses were determined.Received 25 October 2016 Accepted 28 October 2016 Published 22 December 2016Citation Oude Munnink BB, Phan MVT, van der Hoek L, Kellam P, Cotten M, the VIZIONS Consortium. 2016. Genome sequences of a novel Vietnamese bat bunyavirus. GenomeAnnounc 4(6):e01366-16. doi:10.1128/genomeA.01366-16.Copyright © 2016 Oude Munnink et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.Address correspondence to Matthew Cotten, mc13@sanger.ac.uk.The Bunyaviridae is a diverse viral family comprising five gen-era. Some members are notorious for their zoonotic potential(hantavirus and Rift Valley fever virus), one can cause severeproblems in cattle (Smallenberg virus), and another infects plants(tomato spotted wilt virus).Members of the envelopedBunyaviri-dae typically enclose a segmented negative-sense single-strandedRNA genome, with the L segment encoding an RNA-dependentRNA polymerase (RdRp), theM segment encoding glycoproteins,and the S segment encoding the nucleoprotein. The combinedgenomic length of the three segments is 11 to 19 kb (1).We searched for novel members of the Bunyaviridae in 135 batfecal samples collected from roosting sites using an agnostic deep-sequencing approach (2). Fecal samples were processed as previ-ously described (3), followed by sequencing on an Illumina HiSeqplatform yielding 3 to 4 million 250-nucleotide (nt) paired-endreads per sample, which were de novo assembled using SPAdesversion 3.5.0 (4), followed by improve_assembly (5). The result-ing reads were subjected to a modified protein blast search usingusearch (6) to identify Bunyaviridae-related sequences.Fourteen of 135 samples (10%) yielded sequences with 51%amino acid identity to a small part of the RdRp of a Rhinolophuspearsoni bunyavirus. The M and S segments of this new Vietnam-ese bat bunyavirus could not be identified using simple homologysearching. Therefore, Uclust (6) was used to cluster all consensussequences of the bunyavirus-positive samples. Contigs present inover 70% of the samples were submitted to a conserved domainsearch (7), which yielded a putative S segment of the novel bun-yavirus showing similarities to a conserved tenuivirus/phlebovi-rus nucleocapsid protein domain; however, no amino acid iden-tity to known bunyaviruses could be identified. The genomelengths of the L segment of the novel Vietnamese bat bunyaviruseswere 6,484 to 6,713 nucleotides (average sequence coverage, 78- to2,619-fold). The nucleotide sequence of the L segment of the 14isolates differed at 21 to 124 positions (98% to 100% nucleotideidentity), while the S segments differed at 5 to 54 positions (97% to100% nucleotide identity). The genome length of the S segmentvaried between 1,464 and 1,578 nucleotides (average sequencecoverage, 47- to 849-fold).Consistentwith other studies (8, 9), no contigswith similaritiesto the BunyaviridaeM segment could be found. Either the M seg-ments exists in these samples with greater sequence divergenceprecluding identification, or these viruses exist without a standardM segment, perhaps by complementation with functions fromother coinfecting viruses.In conclusion, we present the L and S genome segments of anovel Vietnamese bunyavirus. This novel virus was identified in14 bat fecal samples, and for all viruses, the complete genomesequences of the L and S segments were determined. The lengthsof the two segments of this novel unclassified bunyavirus are con-sistent with other members of Phlebovirus and theHantavirus (1);however, additional research is needed to accurately classify thisnovel bunyavirus and resolve the M segment mystery.Accession number(s). The complete genome sequences of theVietnamese bat bunyaviruses are deposited in GenBank under theaccession numbers KX886759 to KX886786.ACKNOWLEDGMENTSThe VIZIONS Consortium members (alphabetical order by surname)from the Oxford University Clinical Research Unit are Bach Tuan Kiet,Stephen Baker, Alessandra Berto,Maciej F. Boni, Juliet E. Bryant, Bui DucPhu, James I. Campbell, Juan Carrique-Mas, Dang Manh Hung, DangThaoHuong, Dang TramOanh, JeremyN.Day, DinhVanTan,H. Rogiervan Doorn, Duong An Han, Jeremy J. Farrar, Hau Thi Thu Trang, HoDang Trung Nghia, Hoang Bao Long, Hoang Van Duong, Huynh ThiKim Thu, Lam Chi Cuong, Le Manh Hung, Le Thanh Phuong, Le ThiPhuc, Le Thi Phuong, Le Xuan Luat, Luu Thi Thu Ha, Ly Van Chuong,Mai Thi Phuoc Loan, Behzad Nadjm, Ngo Thanh Bao, Ngo Thi Hoa, NgoTri Tue, Nguyen Canh Tu, Nguyen Dac Thuan, Nguyen Dong, NguyenKhac Chuyen, Nguyen Ngoc An, Nguyen Ngoc Vinh, Nguyen QuocHung, Nguyen Thanh Dung, Nguyen Thanh Minh, Nguyen Thi Binh,Nguyen Thi Hong Tham, Nguyen Thi Hong Tien, Nguyen Thi KimChuc, Nguyen Thi Le Ngoc, Nguyen Thi Lien Ha, Nguyen Thi Nam Lien,Nguyen Thi Ngoc Diep, Nguyen Thi Nhung, Nguyen Thi Song Chau,Nguyen Thi Yen Chi, Nguyen Thieu Trinh, Nguyen Thu Van, NguyenVan Cuong, Nguyen Van Hung, Nguyen Van Kinh, Nguyen Van MinhHoang, Nguyen Van My, Nguyen Van Thang, Nguyen Van Thanh,Nguyen Van Vinh Chau, Nguyen Van Xang, Pham Ha My, Pham HongAnh, PhamThiMinhKhoa, PhamThi ThanhTam, PhamVan Lao, PhamVan Minh, Phan Van Be Bay, Phan Vu Tra My, Maia A. Rabaa, MotiurRahman, Corinne Thompson, Guy Thwaites, Ta Thi DieuNgan, TranDocrossmarkGenome AnnouncementsNovember/December 2016 Volume 4 Issue 6 e01366-16 genomea.asm.org 1 on October 23, 2019 at SWETS SUBSCRIPTION SERVICEhttp://mra.asm.org/Downloaded from Hoang Nhu, Tran HoangMinh Chau, Tran Khanh Toan, TranMy Phuc,Tran Thi KimHong, Tran Thi Ngoc Dung, Tran Thi Thanh Thanh, TranThi Thuy Minh, Tran Thua Nguyen, Tran Tinh Hien, Trinh Quang Tri,Vo Be Hien, Vo Nhut Tai, Vo Quoc Cuong, Voong Vinh Phat, V. U. ThiLanHuong, andVuThi TyHang,HeimanWertheim; from theCentre forImmunity, Infection and Evolution, University of Edinburgh: Carlijn Bo-gaardt, Margo Chase-Topping, A. L. Ivens, Lu Lu, DungNyugen, AndrewRambaut, Peter Simmonds, and Mark Woolhouse; from the WellcomeTrust Sanger Institute, Hinxton, United Kingdom: Matthew Cotten, BasOude Munnink, Paul Kellam, andMy Vu Tra Phan; from the Laboratoryof Experimental Virology, Department of Medical Microbiology, Centerfor Infection and Immunity Amsterdam (CINIMA), Academic MedicalCenter of the University of Amsterdam, Amsterdam, The Netherlands:Martin Deijs, Lia van der Hoek, Maarten F. Jebbink, and Seyed Moham-mad Jazaeri Farsani; and from Metabiota, Inc., San Francisco, CA: Kim-berly Dodd, Jason Euren, Ashley Lucas, Nancy Ortiz, Len Pennacchio,Edward Rubin, Karen E. Saylors, Tran Minh Hai, and Nathan D. Wolfe.FUNDING INFORMATIONThis work was supported by the Wellcome Trust of the United Kingdomthrough the VIZIONS strategic award WT/093724. M.C. and B.B.O.M.were additionally funded by the EuropeanUnion’sHorizon 2020 researchand innovation program under grant agreements 643476 (COMPARE)and 634650 (Virogenesis).REFERENCES1. King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ. 2012. Virustaxonomy: classification and nomenclature of viruses, 9th ed. ElsevierAcademic, San Diego, CA.2. Cotten M, Oude Munnink B, Canuti M, Deijs M, Watson SJ, Kellam P,van der Hoek L. 2014. Full genome virus detection in fecal samples usingsensitive nucleic acid preparation, deep sequencing, and a novel iterativesequence classification algorithm. PLoS One 9:e93269. http://dx.doi.org/10.1371/journal.pone.0093269.3. de Vries M, Oude Munnink BB, Deijs M, Canuti M, Koekkoek SM,Molenkamp R, Bakker M, Jurriaans S, van Schaik BD, Luyf AC,Olabarriaga SD, van Kampen AH, van der Hoek L. 2012. Performanceof VIDISCA-454 in feces-suspensions and serum. Viruses 4:1328–1334.http://dx.doi.org/10.3390/v4081328.4. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, KulikovAS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV,Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012.SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. http://dx.doi.org/10.1089/cmb.2012.0021.5. Page AJ. 2012. Improve_assembly. https://metacpan.org/pod/distribution/Bio_AssemblyImprovement/bin/improve_assembly.6. Edgar RC. 2010. Search and clustering orders of magnitude faster thanBLAST. Bioinformatics 26:2460 –2461. http://dx.doi.org/10.1093/bioinformatics/btq461.7. Marchler-Bauer A, Derbyshire MK, Gonzales NR, Lu S, Chitsaz F, GeerLY, Geer RC, He J, Gwadz M, Hurwitz DI, Lanczycki CJ, Lu F, MarchlerGH, Song JS, Thanki N, Wang Z, Yamashita RA, Zhang D, Zheng C,Bryant SH. 2015. CDD: NCBI’s conserved domain database. Nucleic Ac-ids Res 43:D222–D226. http://dx.doi.org/10.1093/nar/gku1221.8. Tokarz R, Williams SH, Sameroff S, Sanchez Leon M, Jain K, LipkinWI. 2014. Virome analysis of Amblyomma americanum, Dermacentorvariabilis, and Ixodes scapularis ticks reveals novel highly divergent verte-brate and invertebrate viruses. J Virol 88:11480–11492. http://dx.doi.org/10.1128/JVI.01858-14.9. Sakamoto JM, Ng TF, Suzuki Y, Tsujimoto H, Deng X, Delwart E,Rasgon JL. 2016. Bunyaviruses are common in male and female Ixodesscapularis ticks in central Pennsylvania. PeerJ 4:e2324. http://dx.doi.org/10.7717/peerj.2324.Oude Munnink et al.Genome Announcements2 genomea.asm.org November/December 2016 Volume 4 Issue 6 e01366-16 on October 23, 2019 at SWETS SUBSCRIPTION SERVICEhttp://mra.asm.org/Downloaded from 

English

Genome sequences of a novel Vietnamese bat bunyavirus

Van der Hoek, L

Van Doorn, HR

Thompson, C

Thwaites, G

Ta, TDN

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Tran, KT

Tran, MP

Tran, TKH

Tran, TND

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Trinh, QT

Vo, BH

Vo, NT

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Voong, VP

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Genome Sequences of a Novel Vietnamese Bat BunyavirusBas B. Oude Munnink,a,b My V. T. Phan,a Lia van der Hoek,c Paul Kellam,a,d Matthew Cotten,a,b the VIZIONS ConsortiumWellcome Trust Sanger Institute, Hinxton, Englanda; Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlandsb; Laboratory of ExperimentalVirology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlandsc; Imperial College London, London, United KingdomdTo document the viral zoonotic risks in Vietnam, fecal samples were systematically collected from a number of mammals insouthern Vietnam and subjected to agnostic deep sequencing. We describe here novel Vietnamese bunyavirus sequences de-tected in bat feces. The complete L and S segments from 14 viruses were determined.Received 25 October 2016 Accepted 28 October 2016 Published 22 December 2016Citation Oude Munnink BB, Phan MVT, van der Hoek L, Kellam P, Cotten M, the VIZIONS Consortium. 2016. Genome sequences of a novel Vietnamese bat bunyavirus. GenomeAnnounc 4(6):e01366-16. doi:10.1128/genomeA.01366-16.Copyright © 2016 Oude Munnink et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.Address correspondence to Matthew Cotten, mc13@sanger.ac.uk.The Bunyaviridae is a diverse viral family comprising five gen-era. Some members are notorious for their zoonotic potential(hantavirus and Rift Valley fever virus), one can cause severeproblems in cattle (Smallenberg virus), and another infects plants(tomato spotted wilt virus). Members of the enveloped Bunyaviri-dae typically enclose a segmented negative-sense single-strandedRNA genome, with the L segment encoding an RNA-dependentRNA polymerase (RdRp), the M segment encoding glycoproteins,and the S segment encoding the nucleoprotein. The combinedgenomic length of the three segments is 11 to 19 kb (1).We searched for novel members of the Bunyaviridae in 135 batfecal samples collected from roosting sites using an agnostic deep-sequencing approach (2). Fecal samples were processed as previ-ously described (3), followed by sequencing on an Illumina HiSeqplatform yielding 3 to 4 million 250-nucleotide (nt) paired-endreads per sample, which were de novo assembled using SPAdesversion 3.5.0 (4), followed by improve_assembly (5). The result-ing reads were subjected to a modified protein blast search usingusearch (6) to identify Bunyaviridae-related sequences.Fourteen of 135 samples (10%) yielded sequences with 51%amino acid identity to a small part of the RdRp of a Rhinolophuspearsoni bunyavirus. The M and S segments of this new Vietnam-ese bat bunyavirus could not be identified using simple homologysearching. Therefore, Uclust (6) was used to cluster all consensussequences of the bunyavirus-positive samples. Contigs present inover 70% of the samples were submitted to a conserved domainsearch (7), which yielded a putative S segment of the novel bun-yavirus showing similarities to a conserved tenuivirus/phlebovi-rus nucleocapsid protein domain; however, no amino acid iden-tity to known bunyaviruses could be identified. The genomelengths of the L segment of the novel Vietnamese bat bunyaviruseswere 6,484 to 6,713 nucleotides (average sequence coverage, 78- to2,619-fold). The nucleotide sequence of the L segment of the 14isolates differed at 21 to 124 positions (98% to 100% nucleotideidentity), while the S segments differed at 5 to 54 positions (97% to100% nucleotide identity). The genome length of the S segmentvaried between 1,464 and 1,578 nucleotides (average sequencecoverage, 47- to 849-fold).Consistent with other studies (8, 9), no contigs with similaritiesto the Bunyaviridae M segment could be found. Either the M seg-ments exists in these samples with greater sequence divergenceprecluding identification, or these viruses exist without a standardM segment, perhaps by complementation with functions fromother coinfecting viruses.In conclusion, we present the L and S genome segments of anovel Vietnamese bunyavirus. This novel virus was identified in14 bat fecal samples, and for all viruses, the complete genomesequences of the L and S segments were determined. The lengthsof the two segments of this novel unclassified bunyavirus are con-sistent with other members of Phlebovirus and the Hantavirus (1);however, additional research is needed to accurately classify thisnovel bunyavirus and resolve the M segment mystery.Accession number(s). The complete genome sequences of theVietnamese bat bunyaviruses are deposited in GenBank under theaccession numbers KX886759 to KX886786.ACKNOWLEDGMENTSThe VIZIONS Consortium members (alphabetical order by surname)from the Oxford University Clinical Research Unit are Bach Tuan Kiet,Stephen Baker, Alessandra Berto, Maciej F. Boni, Juliet E. Bryant, Bui DucPhu, James I. Campbell, Juan Carrique-Mas, Dang Manh Hung, DangThao Huong, Dang Tram Oanh, Jeremy N. Day, Dinh Van Tan, H. Rogiervan Doorn, Duong An Han, Jeremy J. Farrar, Hau Thi Thu Trang, HoDang Trung Nghia, Hoang Bao Long, Hoang Van Duong, Huynh ThiKim Thu, Lam Chi Cuong, Le Manh Hung, Le Thanh Phuong, Le ThiPhuc, Le Thi Phuong, Le Xuan Luat, Luu Thi Thu Ha, Ly Van Chuong,Mai Thi Phuoc Loan, Behzad Nadjm, Ngo Thanh Bao, Ngo Thi Hoa, NgoTri Tue, Nguyen Canh Tu, Nguyen Dac Thuan, Nguyen Dong, NguyenKhac Chuyen, Nguyen Ngoc An, Nguyen Ngoc Vinh, Nguyen QuocHung, Nguyen Thanh Dung, Nguyen Thanh Minh, Nguyen Thi Binh,Nguyen Thi Hong Tham, Nguyen Thi Hong Tien, Nguyen Thi KimChuc, Nguyen Thi Le Ngoc, Nguyen Thi Lien Ha, Nguyen Thi Nam Lien,Nguyen Thi Ngoc Diep, Nguyen Thi Nhung, Nguyen Thi Song Chau,Nguyen Thi Yen Chi, Nguyen Thieu Trinh, Nguyen Thu Van, NguyenVan Cuong, Nguyen Van Hung, Nguyen Van Kinh, Nguyen Van MinhHoang, Nguyen Van My, Nguyen Van Thang, Nguyen Van Thanh,Nguyen Van Vinh Chau, Nguyen Van Xang, Pham Ha My, Pham HongAnh, Pham Thi Minh Khoa, Pham Thi Thanh Tam, Pham Van Lao, PhamVan Minh, Phan Van Be Bay, Phan Vu Tra My, Maia A. Rabaa, MotiurRahman, Corinne Thompson, Guy Thwaites, Ta Thi Dieu Ngan, Tran DocrossmarkGenome AnnouncementsNovember/December 2016 Volume 4 Issue 6 e01366-16 genomea.asm.org 1Hoang Nhu, Tran Hoang Minh Chau, Tran Khanh Toan, Tran My Phuc,Tran Thi Kim Hong, Tran Thi Ngoc Dung, Tran Thi Thanh Thanh, TranThi Thuy Minh, Tran Thua Nguyen, Tran Tinh Hien, Trinh Quang Tri,Vo Be Hien, Vo Nhut Tai, Vo Quoc Cuong, Voong Vinh Phat, V. U. ThiLan Huong, and Vu Thi Ty Hang, Heiman Wertheim; from the Centre forImmunity, Infection and Evolution, University of Edinburgh: Carlijn Bo-gaardt, Margo Chase-Topping, A. L. Ivens, Lu Lu, Dung Nyugen, AndrewRambaut, Peter Simmonds, and Mark Woolhouse; from the WellcomeTrust Sanger Institute, Hinxton, United Kingdom: Matthew Cotten, BasOude Munnink, Paul Kellam, and My Vu Tra Phan; from the Laboratoryof Experimental Virology, Department of Medical Microbiology, Centerfor Infection and Immunity Amsterdam (CINIMA), Academic MedicalCenter of the University of Amsterdam, Amsterdam, The Netherlands:Martin Deijs, Lia van der Hoek, Maarten F. Jebbink, and Seyed Moham-mad Jazaeri Farsani; and from Metabiota, Inc., San Francisco, CA: Kim-berly Dodd, Jason Euren, Ashley Lucas, Nancy Ortiz, Len Pennacchio,Edward Rubin, Karen E. Saylors, Tran Minh Hai, and Nathan D. Wolfe.FUNDING INFORMATIONThis work was supported by the Wellcome Trust of the United Kingdomthrough the VIZIONS strategic award WT/093724. M.C. and B.B.O.M.were additionally funded by the European Union’s Horizon 2020 researchand innovation program under grant agreements 643476 (COMPARE)and 634650 (Virogenesis).REFERENCES1. King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ. 2012. Virustaxonomy: classification and nomenclature of viruses, 9th ed. ElsevierAcademic, San Diego, CA.2. Cotten M, Oude Munnink B, Canuti M, Deijs M, Watson SJ, Kellam P,van der Hoek L. 2014. Full genome virus detection in fecal samples usingsensitive nucleic acid preparation, deep sequencing, and a novel iterativesequence classification algorithm. PLoS One 9:e93269. http://dx.doi.org/10.1371/journal.pone.0093269.3. de Vries M, Oude Munnink BB, Deijs M, Canuti M, Koekkoek SM,Molenkamp R, Bakker M, Jurriaans S, van Schaik BD, Luyf AC,Olabarriaga SD, van Kampen AH, van der Hoek L. 2012. Performanceof VIDISCA-454 in feces-suspensions and serum. Viruses 4:1328 –1334.http://dx.doi.org/10.3390/v4081328.4. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, KulikovAS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV,Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012.SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455– 477. http://dx.doi.org/10.1089/cmb.2012.0021.5. Page AJ. 2012. Improve_assembly. https://metacpan.org/pod/distribution/Bio_AssemblyImprovement/bin/improve_assembly.6. Edgar RC. 2010. Search and clustering orders of magnitude faster thanBLAST. Bioinformatics 26:2460 –2461. http://dx.doi.org/10.1093/bioinformatics/btq461.7. Marchler-Bauer A, Derbyshire MK, Gonzales NR, Lu S, Chitsaz F, GeerLY, Geer RC, He J, Gwadz M, Hurwitz DI, Lanczycki CJ, Lu F, MarchlerGH, Song JS, Thanki N, Wang Z, Yamashita RA, Zhang D, Zheng C,Bryant SH. 2015. CDD: NCBI’s conserved domain database. Nucleic Ac-ids Res 43:D222–D226. http://dx.doi.org/10.1093/nar/gku1221.8. Tokarz R, Williams SH, Sameroff S, Sanchez Leon M, Jain K, LipkinWI. 2014. Virome analysis of Amblyomma americanum, Dermacentorvariabilis, and Ixodes scapularis ticks reveals novel highly divergent verte-brate and invertebrate viruses. J Virol 88:11480 –11492. http://dx.doi.org/10.1128/JVI.01858-14.9. Sakamoto JM, Ng TF, Suzuki Y, Tsujimoto H, Deng X, Delwart E,Rasgon JL. 2016. Bunyaviruses are common in male and female Ixodesscapularis ticks in central Pennsylvania. PeerJ 4:e2324. http://dx.doi.org/10.7717/peerj.2324.Oude Munnink et al.Genome Announcements2 genomea.asm.org November/December 2016 Volume 4 Issue 6 e01366-16

© 2016 Oude Munnink et al. To document the viral zoonotic risks in Vietnam, fecal samples were systematically collected from a number of mammals in southern Vietnam and subjected to agnostic deep sequencing. We describe here novel Vietnamese bunyavirus sequences detected in bat feces. The complete L and S segments from 14 viruses were determined

Oude Munnink, BB

van der Hoek, L

the VIZIONS Consortium

Oxford University Research Archive (ORA)

Oude Munnink, Bas B

Phan, My VT

VIZIONS Consortium

LSHTM Research Online

Genome Sequences of a Novel Vietnamese Bat Bunyavirus.

Oxford University Research Archive

Oude Munnink, B.B. (Bas B.)

Phan, M.V.T. (My Vu Tra)

Hoek, L. (Lia van der)

Kellam, P. (Paul)

Cotten, M. (Matthew)

Kiet, B.T. (Bach Tuan)

Baker, S. (Stephen)

Berto, A. (Alessandra)

Boni, M.F. (Maciej F.)

Bryant, J.E. (Juliet E.)

Phu, B.D. (Bui Duc)

Campbell, J.I. (James I.)

Carrique-Mas, J. (Juan)

Hung, D.M. (Dang Manh)

Huong, D.T. (Dang Thao)

Oanh, D.T. (Dang Tram)

Day, J.N. (Jeremy N.)

Van Tan, D. (Dinh)

van Doorn, H.R. (H. Rogier)

Han, D.A. (Duong An)

Farrar, J.J. (Jeremy J.)

Trang, H.T.T. (Hau Thi Thu)

Nghia, H.D.T. (Ho Dang Trung)

Long, H.B. (Hoang Bao)

Van Duong, H. (Hoang)

Thu, H.T.K. (Huynh Thi Kim)

Cuong, L.C. (Lam Chi)

Hung, L.M. (Le Manh)

Phuong, L.T. (Le Thanh)

Phuc, L.T. (Le Thi)

Phuong, L.T. (Le Thi)

Luat, L.X. (Le Xuan)

Thu Ha, L.T. (Luu Thi)

Van Chuong, L. (Ly)

Loan, M.T.P. (Mai Thi Phuoc)

Nadjm, B. (Behzad)

Bao, N.T. (Ngo Thanh)

Hoa, N.T. (Ngo Thi)

Tue, N.T. (Ngo Tri)

Tu, N.C. (Nguyen Canh)

Thuan, N.D. (Nguyen Dac)

Dong, N. (Nguyen)

Chuyen, N.K. (Nguyen Khac)

An, N.N. (Nguyen Ngoc)

Vinh, N.N. (Nguyen Ngoc)

Hung, N.Q. (Nguyen Quoc)

Dung, N.T. (Nguyen Thanh)

Minh, N.T. (Nguyen Thanh)

Binh, N.T. (Nguyen Thi)

Genome Sequences of a Novel Vietnamese Bat BunyavirusBas B. Oude Munnink,a,b My V. T. Phan,a Lia van der Hoek,c Paul Kellam,a,d Matthew Cotten,a,b the VIZIONS ConsortiumWellcome Trust Sanger Institute, Hinxton, Englanda; Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlandsb; Laboratory of ExperimentalVirology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlandsc; Imperial College London, London, United KingdomdTo document the viral zoonotic risks in Vietnam, fecal samples were systematically collected from a number of mammals insouthern Vietnam and subjected to agnostic deep sequencing. We describe here novel Vietnamese bunyavirus sequences de-tected in bat feces. The complete L and S segments from 14 viruses were determined.Received 25 October 2016 Accepted 28 October 2016 Published 22 December 2016Citation Oude Munnink BB, Phan MVT, van der Hoek L, Kellam P, Cotten M, the VIZIONS Consortium. 2016. Genome sequences of a novel Vietnamese bat bunyavirus. GenomeAnnounc 4(6):e01366-16. doi:10.1128/genomeA.01366-16.Copyright © 2016 Oude Munnink et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.Address correspondence to Matthew Cotten, mc13@sanger.ac.uk.The Bunyaviridae is a diverse viral family comprising five gen-era. Some members are notorious for their zoonotic potential(hantavirus and Rift Valley fever virus), one can cause severeproblems in cattle (Smallenberg virus), and another infects plants(tomato spotted wilt virus).Members of the envelopedBunyaviri-dae typically enclose a segmented negative-sense single-strandedRNA genome, with the L segment encoding an RNA-dependentRNA polymerase (RdRp), theM segment encoding glycoproteins,and the S segment encoding the nucleoprotein. The combinedgenomic length of the three segments is 11 to 19 kb (1).We searched for novel members of the Bunyaviridae in 135 batfecal samples collected from roosting sites using an agnostic deep-sequencing approach (2). Fecal samples were processed as previ-ously described (3), followed by sequencing on an Illumina HiSeqplatform yielding 3 to 4 million 250-nucleotide (nt) paired-endreads per sample, which were de novo assembled using SPAdesversion 3.5.0 (4), followed by improve_assembly (5). The result-ing reads were subjected to a modified protein blast search usingusearch (6) to identify Bunyaviridae-related sequences.Fourteen of 135 samples (10%) yielded sequences with 51%amino acid identity to a small part of the RdRp of a Rhinolophuspearsoni bunyavirus. The M and S segments of this new Vietnam-ese bat bunyavirus could not be identified using simple homologysearching. Therefore, Uclust (6) was used to cluster all consensussequences of the bunyavirus-positive samples. Contigs present inover 70% of the samples were submitted to a conserved domainsearch (7), which yielded a putative S segment of the novel bun-yavirus showing similarities to a conserved tenuivirus/phlebovi-rus nucleocapsid protein domain; however, no amino acid iden-tity to known bunyaviruses could be identified. The genomelengths of the L segment of the novel Vietnamese bat bunyaviruseswere 6,484 to 6,713 nucleotides (average sequence coverage, 78- to2,619-fold). The nucleotide sequence of the L segment of the 14isolates differed at 21 to 124 positions (98% to 100% nucleotideidentity), while the S segments differed at 5 to 54 positions (97% to100% nucleotide identity). The genome length of the S segmentvaried between 1,464 and 1,578 nucleotides (average sequencecoverage, 47- to 849-fold).Consistentwith other studies (8, 9), no contigswith similaritiesto the BunyaviridaeM segment could be found. Either the M seg-ments exists in these samples with greater sequence divergenceprecluding identification, or these viruses exist without a standardM segment, perhaps by complementation with functions fromother coinfecting viruses.In conclusion, we present the L and S genome segments of anovel Vietnamese bunyavirus. This novel virus was identified in14 bat fecal samples, and for all viruses, the complete genomesequences of the L and S segments were determined. The lengthsof the two segments of this novel unclassified bunyavirus are con-sistent with other members of Phlebovirus and theHantavirus (1);however, additional research is needed to accurately classify thisnovel bunyavirus and resolve the M segment mystery.Accession number(s). The complete genome sequences of theVietnamese bat bunyaviruses are deposited in GenBank under theaccession numbers KX886759 to KX886786.ACKNOWLEDGMENTSThe VIZIONS Consortium members (alphabetical order by surname)from the Oxford University Clinical Research Unit are Bach Tuan Kiet,Stephen Baker, Alessandra Berto,Maciej F. Boni, Juliet E. Bryant, Bui DucPhu, James I. Campbell, Juan Carrique-Mas, Dang Manh Hung, DangThaoHuong, Dang TramOanh, JeremyN.Day, DinhVanTan,H. Rogiervan Doorn, Duong An Han, Jeremy J. Farrar, Hau Thi Thu Trang, HoDang Trung Nghia, Hoang Bao Long, Hoang Van Duong, Huynh ThiKim Thu, Lam Chi Cuong, Le Manh Hung, Le Thanh Phuong, Le ThiPhuc, Le Thi Phuong, Le Xuan Luat, Luu Thi Thu Ha, Ly Van Chuong,Mai Thi Phuoc Loan, Behzad Nadjm, Ngo Thanh Bao, Ngo Thi Hoa, NgoTri Tue, Nguyen Canh Tu, Nguyen Dac Thuan, Nguyen Dong, NguyenKhac Chuyen, Nguyen Ngoc An, Nguyen Ngoc Vinh, Nguyen QuocHung, Nguyen Thanh Dung, Nguyen Thanh Minh, Nguyen Thi Binh,Nguyen Thi Hong Tham, Nguyen Thi Hong Tien, Nguyen Thi KimChuc, Nguyen Thi Le Ngoc, Nguyen Thi Lien Ha, Nguyen Thi Nam Lien,Nguyen Thi Ngoc Diep, Nguyen Thi Nhung, Nguyen Thi Song Chau,Nguyen Thi Yen Chi, Nguyen Thieu Trinh, Nguyen Thu Van, NguyenVan Cuong, Nguyen Van Hung, Nguyen Van Kinh, Nguyen Van MinhHoang, Nguyen Van My, Nguyen Van Thang, Nguyen Van Thanh,Nguyen Van Vinh Chau, Nguyen Van Xang, Pham Ha My, Pham HongAnh, PhamThiMinhKhoa, PhamThi ThanhTam, PhamVan Lao, PhamVan Minh, Phan Van Be Bay, Phan Vu Tra My, Maia A. Rabaa, MotiurRahman, Corinne Thompson, Guy Thwaites, Ta Thi DieuNgan, TranDocrossmarkGenome AnnouncementsNovember/December 2016 Volume 4 Issue 6 e01366-16 genomea.asm.org 1 on February 7, 2017 by Erasmus MC Medical Libraryhttp://genomea.asm.org/Downloaded from Hoang Nhu, Tran HoangMinh Chau, Tran Khanh Toan, TranMy Phuc,Tran Thi KimHong, Tran Thi Ngoc Dung, Tran Thi Thanh Thanh, TranThi Thuy Minh, Tran Thua Nguyen, Tran Tinh Hien, Trinh Quang Tri,Vo Be Hien, Vo Nhut Tai, Vo Quoc Cuong, Voong Vinh Phat, V. U. ThiLanHuong, andVuThi TyHang,HeimanWertheim; from theCentre forImmunity, Infection and Evolution, University of Edinburgh: Carlijn Bo-gaardt, Margo Chase-Topping, A. L. Ivens, Lu Lu, DungNyugen, AndrewRambaut, Peter Simmonds, and Mark Woolhouse; from the WellcomeTrust Sanger Institute, Hinxton, United Kingdom: Matthew Cotten, BasOude Munnink, Paul Kellam, andMy Vu Tra Phan; from the Laboratoryof Experimental Virology, Department of Medical Microbiology, Centerfor Infection and Immunity Amsterdam (CINIMA), Academic MedicalCenter of the University of Amsterdam, Amsterdam, The Netherlands:Martin Deijs, Lia van der Hoek, Maarten F. Jebbink, and Seyed Moham-mad Jazaeri Farsani; and from Metabiota, Inc., San Francisco, CA: Kim-berly Dodd, Jason Euren, Ashley Lucas, Nancy Ortiz, Len Pennacchio,Edward Rubin, Karen E. Saylors, Tran Minh Hai, and Nathan D. Wolfe.FUNDING INFORMATIONThis work was supported by the Wellcome Trust of the United Kingdomthrough the VIZIONS strategic award WT/093724. M.C. and B.B.O.M.were additionally funded by the EuropeanUnion’sHorizon 2020 researchand innovation program under grant agreements 643476 (COMPARE)and 634650 (Virogenesis).REFERENCES1. King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ. 2012. Virustaxonomy: classification and nomenclature of viruses, 9th ed. ElsevierAcademic, San Diego, CA.2. Cotten M, Oude Munnink B, Canuti M, Deijs M, Watson SJ, Kellam P,van der Hoek L. 2014. Full genome virus detection in fecal samples usingsensitive nucleic acid preparation, deep sequencing, and a novel iterativesequence classification algorithm. PLoS One 9:e93269. http://dx.doi.org/10.1371/journal.pone.0093269.3. de Vries M, Oude Munnink BB, Deijs M, Canuti M, Koekkoek SM,Molenkamp R, Bakker M, Jurriaans S, van Schaik BD, Luyf AC,Olabarriaga SD, van Kampen AH, van der Hoek L. 2012. Performanceof VIDISCA-454 in feces-suspensions and serum. Viruses 4:1328–1334.http://dx.doi.org/10.3390/v4081328.4. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, KulikovAS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV,Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012.SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. http://dx.doi.org/10.1089/cmb.2012.0021.5. Page AJ. 2012. Improve_assembly. https://metacpan.org/pod/distribution/Bio_AssemblyImprovement/bin/improve_assembly.6. Edgar RC. 2010. Search and clustering orders of magnitude faster thanBLAST. Bioinformatics 26:2460 –2461. http://dx.doi.org/10.1093/bioinformatics/btq461.7. Marchler-Bauer A, Derbyshire MK, Gonzales NR, Lu S, Chitsaz F, GeerLY, Geer RC, He J, Gwadz M, Hurwitz DI, Lanczycki CJ, Lu F, MarchlerGH, Song JS, Thanki N, Wang Z, Yamashita RA, Zhang D, Zheng C,Bryant SH. 2015. CDD: NCBI’s conserved domain database. Nucleic Ac-ids Res 43:D222–D226. http://dx.doi.org/10.1093/nar/gku1221.8. Tokarz R, Williams SH, Sameroff S, Sanchez Leon M, Jain K, LipkinWI. 2014. Virome analysis of Amblyomma americanum, Dermacentorvariabilis, and Ixodes scapularis ticks reveals novel highly divergent verte-brate and invertebrate viruses. J Virol 88:11480–11492. http://dx.doi.org/10.1128/JVI.01858-14.9. Sakamoto JM, Ng TF, Suzuki Y, Tsujimoto H, Deng X, Delwart E,Rasgon JL. 2016. Bunyaviruses are common in male and female Ixodesscapularis ticks in central Pennsylvania. PeerJ 4:e2324. http://dx.doi.org/10.7717/peerj.2324.Oude Munnink et al.Genome Announcements2 genomea.asm.org November/December 2016 Volume 4 Issue 6 e01366-16 on February 7, 2017 by Erasmus MC Medical Libraryhttp://genomea.asm.org/Downloaded from 

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Genome sequences of a novel Vietnamese bat bunyavirus

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