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Publications

HAVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences

Author(s): Phuoc Thien Truong Nguyen, Ilya Plyusnin, Tarja Sironen, Olli Vapalahti, Ravi Kant, Teemu Smura
Published in: BMC Bioinformatics, 22/1, 2021, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-021-04294-2

SARS-CoV-2 Infection and Disease Modelling Using Stem Cell Technology and Organoids

Author(s): Marta Trevisan, Silvia Riccetti, Alessandro Sinigaglia, Luisa Barzon
Published in: International Journal of Molecular Sciences, 22/5, 2021, Page(s) 2356, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms22052356

Monitoring SARS-CoV-2 Circulation and Diversity through Community Wastewater Sequencing, the Netherlands and Belgium

Author(s): Ray Izquierdo-Lara, Goffe Elsinga, Leo Heijnen, Bas B. Oude Munnink, Claudia M.E. Schapendonk, David Nieuwenhuijse, Matthijs Kon, Lu Lu, Frank M. Aarestrup, Samantha Lycett, Gertjan Medema, Marion P.G. Koopmans, Miranda de Graaf
Published in: Emerging Infectious Diseases, 27/5, 2021, Page(s) 1405-1415, ISSN 1080-6040
Publisher: US National Center for Infectious Diseases
DOI: 10.3201/eid2705.204410

Experimental Infection and Genetic Characterization of Two Different Capripox Virus Isolates in Small Ruminants

Author(s): Janika Wolff, Jacqueline King, Tom Moritz, Anne Pohlmann, Donata Hoffmann, Martin Beer, Bernd Hoffmann
Published in: Viruses, 12/10, 2020, Page(s) 1098, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v12101098

Experimental SARS-CoV-2 Infection of Bank Voles

Author(s): Lorenz Ulrich, Anna Michelitsch, Nico Halwe, Kerstin Wernike, Donata Hoffmann, Martin Beer
Published in: Emerging Infectious Diseases, 27/4, 2021, Page(s) 1193-1195, ISSN 1080-6040
Publisher: US National Center for Infectious Diseases
DOI: 10.3201/eid2704.204945

Phylogenetic Investigation of Norovirus Transmission between Humans and Animals

Author(s): Nele Villabruna, Ray W. Izquierdo Lara, Judit Szarvas, Marion P. G. Koopmans, Miranda de Graaf
Published in: Viruses, 12/11, 2020, Page(s) 1287, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v12111287

COVID-19 in health-care workers in three hospitals in the south of the Netherlands: a cross-sectional study

Author(s): Reina S Sikkema, Suzan D Pas, David F Nieuwenhuijse, Áine O'Toole, Jaco Verweij, Anne van der Linden, Irina Chestakova, Claudia Schapendonk, Mark Pronk, Pascal Lexmond, Theo Bestebroer, Ronald J Overmars, Stefan van Nieuwkoop, Wouter van den Bijllaardt, Robbert G Bentvelsen, Miranda M L van Rijen, Anton G M Buiting, Anne J G van Oudheusden, Bram M Diederen, Anneke M C Bergmans, Annemiek van der E
Published in: The Lancet Infectious Diseases, 20/11, 2020, Page(s) 1273-1280, ISSN 1473-3099
Publisher: The Lancet Publishing Group
DOI: 10.1016/s1473-3099(20)30527-2

The genetics of highly pathogenic avian influenza viruses of subtype H5 in Germany, 2006–2020

Author(s): Jacqueline King, Timm Harder, Franz J. Conraths, Martin Beer, Anne Pohlmann
Published in: Transboundary and Emerging Diseases, 68/3, 2021, Page(s) 1136-1150, ISSN 1865-1674
Publisher: Blackwell-Wiss.-Verl
DOI: 10.1111/tbed.13843

Human West Nile Virus Lineage 2 Infection: Epidemiological, Clinical, and Virological Findings

Author(s): Monia Pacenti, Alessandro Sinigaglia, Elisa Franchin, Silvana Pagni, Enrico Lavezzo, Fabrizio Montarsi, Gioia Capelli, Luisa Barzon
Published in: Viruses, 12/4, 2020, Page(s) 458, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v12040458

Suppression of a SARS-CoV-2 outbreak in the Italian municipality of Vo’

Author(s): Enrico Lavezzo, Elisa Franchin, Constanze Ciavarella, Gina Cuomo-Dannenburg, Luisa Barzon, Claudia Del Vecchio, Lucia Rossi, Riccardo Manganelli, Arianna Loregian, Nicolò Navarin, Davide Abate, Manuela Sciro, Stefano Merigliano, Ettore De Canale, Maria Cristina Vanuzzo, Valeria Besutti, Francesca Saluzzo, Francesco Onelia, Monia Pacenti, Saverio G. Parisi, Giovanni Carretta, Daniele Donato, Lucia
Published in: Nature, 584/7821, 2020, Page(s) 425-429, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-020-2488-1

Filling the gaps in the global prevalence map of clinical antimicrobial resistance

Author(s): Rik Oldenkamp, Constance Schultsz, Emiliano Mancini, Antonio Cappuccio
Published in: Proceedings of the National Academy of Sciences, 118/1, 2020, Page(s) e2013515118, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.2013515118

Next-generation diagnostics: virus capture facilitates a sensitive viral diagnosis for epizootic and zoonotic pathogens including SARS-CoV-2

Author(s): Claudia Wylezich, Sten Calvelage, Kore Schlottau, Ute Ziegler, Anne Pohlmann, Dirk Höper, Martin Beer
Published in: Microbiome, 9/1, 2021, ISSN 2049-2618
Publisher: BMC
DOI: 10.1186/s40168-020-00973-z

SARS-CoV-2 spike D614G change enhances replication and transmission

Author(s): Bin Zhou, Tran Thi Nhu Thao, Donata Hoffmann, Adriano Taddeo, Nadine Ebert, Fabien Labroussaa, Anne Pohlmann, Jacqueline King, Silvio Steiner, Jenna N. Kelly, Jasmine Portmann, Nico Joel Halwe, Lorenz Ulrich, Bettina Salome Trüeb, Xiaoyu Fan, Bernd Hoffmann, Li Wang, Lisa Thomann, Xudong Lin, Hanspeter Stalder, Berta Pozzi, Simone de Brot, Nannan Jiang, Dan Cui, Jaber Hossain, Malania M. Wilson,
Published in: Nature, 592/7852, 2021, Page(s) 122-127, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-021-03361-1

Co‐infections: Simultaneous detections of West Nile virus and Usutu virus in birds from Germany

Author(s): Pauline Dianne Santos, Friederike Michel, Claudia Wylezich, Dirk Höper, Markus Keller, Cora M. Holicki, Claudia A. Szentiks, Martin Eiden, Aemero Muluneh, Antonie Neubauer‐Juric, Sabine Thalheim, Anja Globig, Martin Beer, Martin H. Groschup, Ute Ziegler
Published in: Transboundary and Emerging Diseases, 2021, ISSN 1865-1674
Publisher: Blackwell-Wiss.-Verl
DOI: 10.1111/tbed.14050

Deep learning identification for citizen science surveillance of tiger mosquitoes

Author(s): Balint Armin Pataki, Joan Garriga, Roger Eritja, John R. B. Palmer, Frederic Bartumeus, Istvan Csabai
Published in: Scientific Reports, 11/1, 2021, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-021-83657-4

West Nile fever upsurge in a Greek regional unit, 2020

Author(s): Anna Papa, Katerina Tsioka, Sandra Gewehr, Stella Kalaitzopouou, Danai Pervanidou, Anna Vakali, Chrysovalantou Kefaloudi, Styliani Pappa, Xanthoula Louka, Spiros Mourelatos
Published in: Acta Tropica, 221, 2021, Page(s) 106010, ISSN 0001-706X
Publisher: Elsevier BV
DOI: 10.1016/j.actatropica.2021.106010

Rapid SARS-CoV-2 whole-genome sequencing and analysis for informed public health decision-making in the Netherlands

Author(s): Bas B. Oude Munnink, David F. Nieuwenhuijse, Mart Stein, Áine O’Toole, Manon Haverkate, Madelief Mollers, Sandra K. Kamga, Claudia Schapendonk, Mark Pronk, Pascal Lexmond, Anne van der Linden, Theo Bestebroer, Irina Chestakova, Ronald J. Overmars, Stefan van Nieuwkoop, Richard Molenkamp, Annemiek A. van der Eijk, Corine GeurtsvanKessel, Harry Vennema, Adam Meijer, Andrew Rambaut, Jaap van Disse
Published in: Nature Medicine, 26/9, 2020, Page(s) 1405-1410, ISSN 1078-8956
Publisher: Nature Publishing Group
DOI: 10.1038/s41591-020-0997-y

Multi‐species ELISA for the detection of antibodies against SARS‐CoV‐2 in animals

Author(s): Kerstin Wernike, Andrea Aebischer, Anna Michelitsch, Donata Hoffmann, Conrad Freuling, Anne Balkema‐Buschmann, Annika Graaf, Thomas Müller, Nikolaus Osterrieder, Melanie Rissmann, Dennis Rubbenstroth, Jacob Schön, Claudia Schulz, Jakob Trimpert, Lorenz Ulrich, Asisa Volz, Thomas Mettenleiter, Martin Beer
Published in: Transboundary and Emerging Diseases, 68/4, 2021, Page(s) 1779-1785, ISSN 1865-1674
Publisher: Blackwell-Wiss.-Verl
DOI: 10.1111/tbed.13926

CRHP Finder, a webtool for the detection of clarithromycin resistance in Helicobacter pylori from whole‐genome sequencing data

Author(s): Melodi Yusibova, Henrik Hasman, Philip Thomas Lanken Conradsen Clausen, Frank Imkamp, Karoline Wagner, Leif Percival Andersen
Published in: Helicobacter, 25/6, 2020, ISSN 1083-4389
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/hel.12752

Rapid multiplex MinION nanopore sequencing workflow for Influenza A viruses

Author(s): Jacqueline King, Timm Harder, Martin Beer, Anne Pohlmann
Published in: BMC Infectious Diseases, 20/1, 2020, ISSN 1471-2334
Publisher: BioMed Central
DOI: 10.1186/s12879-020-05367-y

Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types

Author(s): Ilya Plyusnin, Ravi Kant, Anne J Jääskeläinen, Tarja Sironen, Liisa Holm, Olli Vapalahti, Teemu Smura
Published in: Virus Evolution, 6/2, 2020, ISSN 2057-1577
Publisher: Oxford Academic
DOI: 10.1093/ve/veaa091

Predicting Spatial Patterns of Sindbis Virus (SINV) Infection Risk in Finland Using Vector, Host and Environmental Data

Author(s): Ruut Uusitalo, Mika Siljander, C. Lorna Culverwell, Guy Hendrickx, Andreas Lindén, Timothée Dub, Juha Aalto, Jussi Sane, Cedric Marsboom, Maija T. Suvanto, Andrea Vajda, Hilppa Gregow, Essi M. Korhonen, Eili Huhtamo, Petri Pellikka, Olli Vapalahti
Published in: International Journal of Environmental Research and Public Health, 18/13, 2021, Page(s) 7064, ISSN 1660-4601
Publisher: IJERPH
DOI: 10.3390/ijerph18137064

Transmission of SARS-CoV-2 on mink farms between humans and mink and back to humans

Author(s): Bas B. Oude Munnink, Reina S. Sikkema, David F. Nieuwenhuijse, Robert Jan Molenaar, Emmanuelle Munger, Richard Molenkamp, Arco van der Spek, Paulien Tolsma, Ariene Rietveld, Miranda Brouwer, Noortje Bouwmeester-Vincken, Frank Harders, Renate Hakze-van der Honing, Marjolein C. A. Wegdam-Blans, Ruth J. Bouwstra, Corine GeurtsvanKessel, Annemiek A. van der Eijk, Francisca C. Velkers, Lidwien A. M. Sm
Published in: Science, 371/6525, 2021, Page(s) 172-177, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.abe5901

Modelling West Nile Virus and Usutu Virus Pathogenicity in Human Neural Stem Cells

Author(s): Silvia Riccetti, Alessandro Sinigaglia, Giovanna Desole, Norbert Nowotny, Marta Trevisan, Luisa Barzon
Published in: Viruses, 12/8, 2020, Page(s) 882, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v12080882

A glimpse of antimicrobial resistance gene diversity in kefir and yoghurt

Author(s): Adrienn Gréta Tóth, István Csabai, Gergely Maróti, Ákos Jerzsele, Attila Dubecz, Árpád V. Patai, Maura Fiona Judge, Sára Ágnes Nagy, László Makrai, Krisztián Bányai, Géza Szita, Norbert Solymosi
Published in: Scientific Reports, 10/1, 2020, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-020-80444-5

Autochthonous dengue outbreak in Italy 2020: Clinical, virological and entomological findings

Author(s): Luisa Barzon, Federico Gobbi, Gioia Capelli, Fabrizio Montarsi, Simone Martini, Silvia Riccetti, Alessandro Sinigaglia, Monia Pacenti, Giacomina Pavan, Mario Rassu, Maria Teresa Padovan, Vinicio Manfrin, Francesca Zanella, Francesca Russo, Felice Foglia, Luca Lazzarini
Published in: Journal of Travel Medicine, 2021, ISSN 1195-1982
Publisher: B.C. Decker Inc.
DOI: 10.1093/jtm/taab130

Neuropilin-1 facilitates SARS-CoV-2 cell entry and infectivity

Author(s): Ludovico Cantuti-Castelvetri, Ravi Ojha, Liliana D. Pedro, Minou Djannatian, Jonas Franz, Suvi Kuivanen, Franziska van der Meer, Katri Kallio, Tuğberk Kaya, Maria Anastasina, Teemu Smura, Lev Levanov, Leonora Szirovicza, Allan Tobi, Hannimari Kallio-Kokko, Pamela Österlund, Merja Joensuu, Frédéric A. Meunier, Sarah J. Butcher, Martin Sebastian Winkler, Brit Mollenhauer, Ari Helenius, Ozgun Gok
Published in: Science, 370/6518, 2020, Page(s) 856-860, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.abd2985

Susceptibility of Raccoon Dogs for Experimental SARS-CoV-2 Infection

Author(s): Conrad M. Freuling, Angele Breithaupt, Thomas Müller, Julia Sehl, Anne Balkema-Buschmann, Melanie Rissmann, Antonia Klein, Claudia Wylezich, Dirk Höper, Kerstin Wernike, Andrea Aebischer, Donata Hoffmann, Virginia Friedrichs, Anca Dorhoi, Martin H. Groschup, Martin Beer, Thomas C. Mettenleiter
Published in: Emerging Infectious Diseases, 26/12, 2020, Page(s) 2982-2985, ISSN 1080-6040
Publisher: US National Center for Infectious Diseases
DOI: 10.3201/eid2612.203733

At the tip of an iceberg: citizen science and active surveillance collaborating to broaden the known distribution of Aedes japonicus in Spain

Author(s): Roger Eritja, Sarah Delacour-Estrella, Ignacio Ruiz-Arrondo, Mikel A. González, Carlos Barceló, Ana L. García-Pérez, Javier Lucientes, Miguel Á. Miranda, Frederic Bartumeus
Published in: Parasites & Vectors, 14/1, 2021, ISSN 1756-3305
Publisher: BioMed Central
DOI: 10.1186/s13071-021-04874-4

Automated download and clean-up of family-specific databases for kmer-based virus identification

Author(s): Rosa L Allesøe, Camilla K Lemvigh, My V T Phan, Philip T L C Clausen, Alfred F Florensa, Marion P G Koopmans, Ole Lund, Matthew Cotten
Published in: Bioinformatics, 37/5, 2020, Page(s) 705-710, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btaa857

Comparative pathogenesis of COVID-19, MERS, and SARS in a nonhuman primate model

Author(s): Barry Rockx, Thijs Kuiken, Sander Herfst, Theo Bestebroer, Mart M. Lamers, Bas B. Oude Munnink, Dennis de Meulder, Geert van Amerongen, Judith van den Brand, Nisreen M. A. Okba, Debby Schipper, Peter van Run, Lonneke Leijten, Reina Sikkema, Ernst Verschoor, Babs Verstrepen, Willy Bogers, Jan Langermans, Christian Drosten, Martje Fentener van Vlissingen, Ron Fouchier, Rik de Swart, Marion Koopmans,
Published in: Science, 368/6494, 2020, Page(s) 1012-1015, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.abb7314

Genomic monitoring of SARS-CoV-2 uncovers an Nsp1 deletion variant that modulates type I interferon response

Author(s): Jing-wen Lin, Chao Tang, Han-cheng Wei, Baowen Du, Chuan Chen, Minjin Wang, Yongzhao Zhou, Ming-xia Yu, Lu Cheng, Suvi Kuivanen, Natacha S. Ogando, Lev Levanov, Yuancun Zhao, Chang-ling Li, Ran Zhou, Zhidan Li, Yiming Zhang, Ke Sun, Chengdi Wang, Li Chen, Xia Xiao, Xiuran Zheng, Sha-sha Chen, Zhen Zhou, Ruirui Yang, Dan Zhang, Mengying Xu, Junwei Song, Danrui Wang, Yupeng Li, ShiKun Lei, Wanqin Ze
Published in: Cell Host & Microbe, 29/3, 2021, Page(s) 489-502.e8, ISSN 1931-3128
Publisher: Cell Press
DOI: 10.1016/j.chom.2021.01.015

Occurrence of Antibodies against SARS-CoV-2 in the Domestic Cat Population of Germany

Author(s): Anna Michelitsch, Donata Hoffmann, Kerstin Wernike, Martin Beer
Published in: Vaccines, 8/4, 2020, Page(s) 772, ISSN 2076-393X
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/vaccines8040772

Novel HPAIV H5N8 Reassortant (Clade 2.3.4.4b) Detected in Germany

Author(s): Jacqueline King, Christoph Schulze, Andreas Engelhardt, Andreas Hlinak, Sara-Lisa Lennermann, Kerstin Rigbers, Jasmin Skuballa, Christoph Staubach, Thomas C. Mettenleiter, Timm Harder, Martin Beer, Anne Pohlmann
Published in: Viruses, 12/3, 2020, Page(s) 281, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v12030281

MINTyper: an outbreak-detection method for accurate and rapid SNP typing of clonal clusters with noisy long reads

Author(s): Malte B Hallgren, Søren Overballe-Petersen, Ole Lund, Henrik Hasman, Philip T L C Clausen
Published in: Biology Methods and Protocols, 6/1, 2021, ISSN 2396-8923
Publisher: Oxford Academic
DOI: 10.1093/biomethods/bpab008

SARS-CoV-2 Neutralizing Human Antibodies Protect Against Lower Respiratory Tract Disease in a Hamster Model

Author(s): Bart L Haagmans, Danny Noack, Nisreen M A Okba, Wentao Li, Chunyan Wang, Theo Bestebroer, Rory de Vries, Sander Herfst, Dennis de Meulder, Elwin Verveer, Peter van Run, Mart M Lamers, Bart Rijnders, Casper Rokx, Frank van Kuppeveld, Frank Grosveld, Dubravka Drabek, Corine Geurts van Kessel, Marion Koopmans, Berend Jan Bosch, Thijs Kuiken, Barry Rockx
Published in: The Journal of Infectious Diseases, 223/12, 2021, Page(s) 2020-2028, ISSN 0022-1899
Publisher: University of Chicago Press
DOI: 10.1093/infdis/jiab289