Versatile Emerging infectious disease Observatory

Publications

SARS-CoV-2 and Type 1 Diabetes in Finnish Children

Author(s): Knip M, Parviainen A, Turtinen M, But A, Härkönen T, Hepojoki J, Sironen T, Iheozor-Ejiofor R, Uğurlu H, Saksela K, Lempainen J, Ilonen J, Vapalahti O, Register FPD
Published in: Social Science Research Network, 2022, ISSN 1556-5068
Publisher: Elsevier
DOI: 10.2139/ssrn.4237744

SARS-CoV-2 infections among healthcare workers at Helsinki University Hospital, Finland, spring 2020: Serosurvey, symptoms and risk factors

Author(s): Anu Kantele, Tinja Lääveri, Lauri Kareinen, Sari H. Pakkanen, Karin Blomgren, Sointu Mero, Anu Patjas, Jenni Virtanen, Ruut Uusitalo, Maija Lappalainen, Asko Järvinen, Satu Kurkela, Anne J. Jääskeläinen, Olli Vapalahti, Tarja Sironen
Published in: Travel Medicine and Infectious Disease, Issue 39, 2021, ISSN 1477-8939
Publisher: Elsevier BV
DOI: 10.1016/j.tmaid.2020.101949

Canine Saliva as a Possible Source of Antimicrobial Resistance Genes

Author(s): Adrienn Gréta Tóth, Imre Tóth, Bernadett Rózsa, Attila Dubecz, Árpád V. Patai, Tibor Németh, Selçuk Kaplan, Eszter Gabriella Kovács, László Makrai, Norbert Solymosi
Published in: Antibiotics, Issue 11/11, 2022, ISSN 2078-2489
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/antibiotics11111490

Impact of antigenic evolution and original antigenic sin on SARS-CoV-2 immunity

Author(s): Muriel Aguilar-Bretones, Ron Am Fouchier, Marion Pg Koopmans, Gijsbert P van Nierop
Published in: The Journal of Clinical Investigation, Issue 133/1, 2023, ISSN 0021-9738
Publisher: American Society for Clinical Investigation
DOI: 10.1172/jci162192

Rise and fall of SARS-CoV-2 variants in Rotterdam: Comparison of wastewater and clinical surveillance

Author(s): Ray W Izquierdo-Lara, Leo Heijnen, Bas B Oude Munnink, Claudia M E Schapendonk, Goffe Elsinga, Jeroen Langeveld, Johan Post, Divyae K Prasad, Christian Carrizosa, Frederic Been, Janko van Beek, Remy Schilperoort, Rianne Vriend, Ewout Fanoy, Evelien I T de Schepper, Reina S Sikkema, Richard Molenkamp, Frank M Aarestrup, Gertjan Medema, Marion P G Koopmans and Miranda de Graaf
Published in: Science of the Total Environment, Issue 873, 2023, ISSN 0048-9697
Publisher: Elsevier BV
DOI: 10.1016/j.scitotenv.2023.162209

Case Report: The Carotid Body in COVID-19: Histopathological and Virological Analyses of an Autopsy Case Series

Author(s): Andrea Porzionato, Aron Emmi, Martina Contran, Elena Stocco, Silvia Riccetti, Alessandro Sinigaglia, Veronica Macchi, Luisa Barzon and Raffaele De Caro
Published in: Frontiers in Immunology, Issue 12, 2021, ISSN 1664-3224
Publisher: Frontiers Media SA
DOI: 10.3389/fimmu.2021.736529

Has Epizootic Become Enzootic? Evidence for a Fundamental Change in the Infection Dynamics of Highly Pathogenic Avian Influenza in Europe, 2021

Author(s): Anne Pohlmann, Jacqueline King, Alice Fusaro, Bianca Zecchin, Ashley C Banyard, Ian H Brown, Alexander M P Byrne, Nancy Beerens, Yuan Liang, Rene Heutink, Frank Harders, Joe James, Scott M Reid, Rowena D E Hansen, Nicola S Lewis, Charlotte Hjulsager, Lars E Larsen, Siamak Zohari, Kristofer Anderson, Caroline Bröjer, Alexander Nagy, Vladimir Savič, Steven van Borm, Mieke Steensels, Francois-Xavie
Published in: mBio, Issue 13/4, 2022, ISSN 2161-2129
Publisher: American Society for Microbiology
DOI: 10.1128/mbio.00609-22

One Day in Denmark: Nationwide point-prevalence survey of human bacterial isolates and comparison of classical and whole-genome sequence-based species identification methods

Author(s): Ana Rita Rebelo,Tobias Ibfelt, Valeria Bortolaia, Pimlapas Leekitcharoenphon, Dennis Schrøder Hansen, Hans Linde Nielsen, Svend Ellermann-Eriksen, Michael Kemp, Bent Løwe Røder, Niels Frimodt-Møller, Turid Snekloth Søndergaard, John Eugenio Coia, Claus Østergaard, Michael Pedersen, Henrik Westh and Frank Møller Aarestrup
Published in: PLOS ONE, 2022, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0261999

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, Issue 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, Issue 22/5, 2021, Page(s) 2356, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms22052356

Hypopharyngeal Ulcers in COVID-19: Histopathological and Virological Analyses – A Case Report

Author(s): Andrea Porzionato, Elena Stocco1, Aron Emmi, Martina Contran, Veronica Macchi, Silvia Riccetti, Alessandro Sinigaglia, Luisa Barzon and Raffaele De Caro
Published in: Frontiers in Immunology, Issue 12, 2021, ISSN 1664-3224
Publisher: Frontiers Media SA
DOI: 10.3389/fimmu.2021.676828

Sindbis virus neutralising antibodies detected in Swedish horses

Author(s): Agnes Björnström, Anne-Lie Blomström, Manish Chandra Singh, Jenny C Hesson
Published in: One Health, Issue 12, 2021, ISSN 2352-7714
Publisher: Elsevier BV
DOI: 10.1016/j.onehlt.2021.100242

An advanced sequence clustering and designation workflow reveals the enzootic maintenance of a dominant West Nile virus subclade in Germany

Author(s): Pauline Dianne Santos, Anne Günther, Markus Keller, Timo Homeier-Bachmann, Martin H. Groschup, Martin Beer, Dirk Höper and Ute Ziegler
Published in: BioRxiv, 2022, ISSN 2692-8205
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1101/2022.10.05.509209

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, Issue 27/5, 2021, Page(s) 1405-1415, ISSN 1080-6040
Publisher: US National Center for Infectious Diseases
DOI: 10.3201/eid2705.204410

Prevalence, Infectious Characteristics and Genetic Diversity of Staphylococcus aureus and Methicillin-Resistant Staphylococcus aureus (MRSA) in Two Raw-Meat Processing Establishments in Northern Greece

Author(s): Dimitrios Komodromos, Charalampos Kotzamanidis, Virginia Giantzi, Styliani Pappa, Anna Papa, Antonios Zdragas, Apostolos Angelidis, Daniel Sergelidis
Published in: Pathogens, Issue 11/11, 2022, ISSN 2076-0817
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/pathogens11111370

Integrating Global Citizen Science Platforms to Enable Next-Generation Surveillance of Invasive and Vector Mosquitoes

Author(s): Ryan M. Carney, Connor Mapes, Russanne D. Low, Alex Long, Anne Bowser, David Durieux, Karlene Rivera, Berj Dekramanjian, Frederic Bartumeus, Daniel Guerrero, Carrie E. Seltzer, Farhat Azam, Sriram Chellappan and John R. B. Palmer
Published in: Insects, Issue 13/8, 2022, ISSN 2075-4450
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/insects13080675

Normalisation of SARS-CoV-2 concentrations in wastewater: The use of flow, electrical conductivity and crAssphage

Author(s): Jeroen Langeveld, Remy Schilperoort, Leo Heijnen, Goffe Elsinga, Claudia E.M. Schapendonk, Ewout Fanoy, Evelien I.T. de Schepper, Marion P.G. Koopmans, Miranda de Graaf and Gertjan Medema
Published in: Science of the Total Environment, Issue 865, 2022, ISSN 0048-9697
Publisher: Elsevier BV
DOI: 10.1016/j.scitotenv.2022.161196

Timeliness of online COVID-19 reports from official sources

Author(s): Laura Espinosa, Olesia Altunina, and Marcel Salathé
Published in: Frontiers in Public Health, Issue 10, 2023, ISSN 2296-2565
Publisher: Future Biologics
DOI: 10.3389/fpubh.2022.1027812

Kinetics of Neutralizing Antibodies of COVID-19 Patients Tested Using Clinical D614G, B.1.1.7, and B 1.351 Isolates in Microneutralization Assays

Author(s): Jenni Virtanen, Ruut Uusitalo, Essi M. Korhonen, Kirsi Aaltonen, Teemu Smura, Suvi Kuivanen, Sari H. Pakkanen, Sointu Mero, Anu Patjas, Marianna Riekkinen, Anu Kantele, Visa Nurmi, Klaus Hedman, Jussi Hepojoki,Tarja Sironen, Eili Huhtamo and Olli Vapalahti
Published in: Viruses, Issue 13/6, 2021, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v13060996

ClusTRace, a bioinformatic pipeline for analyzing clusters in virus phylogenies

Author(s): Ilya Plyusnin1, Phuoc Thien Truong Nguyen, Tarja Sironen, Olli Vapalahti, Teemu Smura and Ravi Kant
Published in: BMC Bioinformatics, Issue 23/196, 2022, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-022-04709-8

Nanobody engineering for SARS-CoV-2 neutralization and detection

Author(s): Liina Hannula, Suvi Kuivanen, Jonathan Lasham, Ravi Kant, Lauri Kareinen, Mariia Bogacheva, Tomas Strandin, Tarja Sironen, Vivek Sharma, Petri Saviranta, Anja Kipar, Olli Vapalahti, Juha T. Huiskonen, Ilona Rissanen
Published in: BioRxiv, 2022, ISSN 2692-8205
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1101/2022.09.14.507920

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, Issue 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, Issue 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, Issue 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, Issue 20/11, 2020, Page(s) 1273-1280, ISSN 1473-3099
Publisher: The Lancet Publishing Group
DOI: 10.1016/s1473-3099(20)30527-2

Diagnostic Potential of a Luminex-Based Coronavirus Disease 2019 Suspension Immunoassay (COVID-19 SIA) for the Detection of Antibodies against SARS-CoV-2

Author(s): Tove Hoffman, Linda Kolstad, Johanna F. Lindahl, Bo Albinsson, Anders Bergqvist, Bengt Rönnberg and Åke Lundkvist
Published in: Viruses, Issue 13/993, 2021, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v13060993

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, Issue 68/3, 2021, Page(s) 1136-1150, ISSN 1865-1674
Publisher: Blackwell-Wiss.-Verl
DOI: 10.1111/tbed.13843

Human Virus Genomes Are Enriched in Conserved Adenine/Thymine/Uracil Multiple Tracts That Pause Polymerase Progression

Author(s): Emanuela Ruggiero, Enrico Lavezzo, Marco Grazioli, Irene Zanin, Maja Marušič, Janez Plavec, Sara N. Richter and Stefano Toppo
Published in: Frontiers in Microbiology, Issue 13, 2022, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2022.915069

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, Issue 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, Issue 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, Issue 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, Issue 9/1, 2021, ISSN 2049-2618
Publisher: BMC
DOI: 10.1186/s40168-020-00973-z

Targeting the NS2B-NS3 protease of tick-borne encephalitis virus withpan-flaviviral protease inhibitors

Author(s): Dario Akaberi, Amanda Båhlström, Praveen K. Chinthakindi, Tomas Nyman, Anja Sandström, Josef D. Järhult, Navaneethan Palanisamy, Åke Lundkvist and Johan Lennerstrand
Published in: Antiviral Research, Issue 190, 2021, ISSN 0166-3542
Publisher: Elsevier BV
DOI: 10.1016/j.antiviral.2021.105074

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, Issue 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

Neutralising reactivity against SARS-CoV-2 Delta and Omicron variants by vaccination and infection history

Author(s): Enrico Lavezzo, Monia Pacenti, Laura Manuto, Caterina Boldrin, Margherita Cattai, Marco Grazioli, Federico Bianca, Margherita Sartori, Federico Caldart, Gioele Castelli, Michele Nicoletti, Eleonora Nieddu, Elisa Salvadoretti, Beatrice Labella, Ludovico Fava, Maria Cristina Vanuzzo, Vittoria Lisi, Maria Antonello, Carmela Ileana Grimaldi, Chiara Zulian, Claudia Del Vecchio, Mario Plebani, Andrea Pa
Published in: Genome Medicine, Issue 14/61, 2022, ISSN 1756-994X
Publisher: BioMed Central
DOI: 10.1186/s13073-022-01066-2

Highly pathogenic avian influenza virus incursions of subtype H5N8, H5N5, H5N1, H5N4, and H5N3 in Germany during 2020-21

Author(s): Jacqueline King, Timm Harder, Anja Globig, Lina Stacker, Anne Günther, Christian Grund, Martin Beer, Anne Pohlmann
Published in: Virus Evolution, Issue 8/1, 2022, ISSN 2057-1577
Publisher: Oxford University Press
DOI: 10.1093/ve/veac035

The next phase of SARS-CoV-2 surveillance: real-time molecular epidemiology

Author(s): Bas B Oude Munnink, Nathalie Worp, David F Nieuwenhuijse, Reina S Sikkema, Bart Haagmans, Ron A M Fouchier, Marion Koopmans
Published in: Nature Medicine, Issue 27/9, 2021, ISSN 1078-8956
Publisher: Nature Publishing Group
DOI: 10.1038/s41591-021-01472-w

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, Issue 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, Issue 221, 2021, Page(s) 106010, ISSN 0001-706X
Publisher: Elsevier BV
DOI: 10.1016/j.actatropica.2021.106010

Transatlantic spread of highly pathogenic avian influenza H5N1 by wild birds from Europe to North America in 2021

Author(s): V. Caliendo; N. S. Lewis; A. Pohlmann; S.R. Baillie; A.C. Banyard; M. Beer; I.H. Brown; R.A.M. Fouchier; R.D.E. Hansen; T.K. Lameris; A.S. Lang; S. Laurendeau; O. Lung; G. Robertson; H. van der Jeugd; T.N. Alkie; K. Thorup; M.L. van Toor; J. Waldenström; C. Yason; T. Kuiken; Y. Berhane
Published in: Scientific Reports, Issue 45, 2022, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1101/2022.01.13.476155

A 10-Minute “Mix and Read” Antibody Assay for SARS-CoV-2

Author(s): Juuso Rusanen, Lauri Kareinen, Lev Levanov, Sointu Mero, Sari H. Pakkanen, Anu Kantele, Fatima Amanat, Florian Krammer, Klaus Hedman, Olli Vapalahti and Jussi Hepojoki
Published in: Viruses, Issue 13/2, 2021, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v13020143

Introduction and Rapid Spread of SARS-CoV-2 Omicron Variant and Dynamics of BA.1 and BA.1.1 Sublineages, Finland, December 2021

Author(s): Hanna Vauhkonen, Phuoc Truong Nguyen, Ravi Kant, Ilja Plyusnin, Mert Erdin, Satu Kurkela, Hanna Liimatainen, Niina Ikonen, Soile Blomqvist, Kirsi Liitsola, Erika Lindh, Otto Helve, Hanna Jarva, Raisa Loginov, Aino Palva, Tiina Hannunen, Sari Hannula, Mikko Parry, Paula Kauppi, Antti Vaheri, Tarja Sironen, Maija Lappalainen, Carita Savolainen-Kopra, Teemu Smura, Olli Vapalahti
Published in: Emerging Infectious Diseases, Issue 28/6, 2022, ISSN 1080-6040
Publisher: US National Center for Infectious Diseases
DOI: 10.3201/eid2806.220515

Common Laboratory Mice Are Susceptible to Infection with the SARS-CoV-2 Beta Variant

Author(s): Ravi Kant, Lauri Kareinen, Teemu Smura, Tobias L. Freitag, Sawan Kumar Jha, Kari Alitalo, Seppo Meri, Tarja Sironen, Kalle Saksela, Tomas Strandin, Anja Kipar and Olli Vapalahti
Published in: Viruses, Issue 13/11, 2021, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v13112263

Evaluation of Production Lots of a Rapid Point-of-Care Lateral Flow Serological Test Intended for Identification of IgM and IgG against the N-Terminal Part of the Spike Protein (S1) of SARS-CoV-2

Author(s): Tove Hoffman, Linda Kolstad, Bengt Rönnberg and Åke Lundkvist
Published in: Viruses, Issue 13/6, 2021, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v13061043

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, Issue 26/9, 2020, Page(s) 1405-1410, ISSN 1078-8956
Publisher: Nature Publishing Group
DOI: 10.1038/s41591-020-0997-y

Temporal Dynamics of Influenza A(H5N1) Subtype before and after the Emergence of H5N8.

Author(s): Amer F, Li R, Rabie N, El-Husseiny MH, Yehia N, Hagag NM, Samy M, Selim A, Hassan MK, Hassan WMM, Arafa AS, Lundkvist Å, Shahein MA, Naguib MM.
Published in: Viruses, Issue 13/8, 2021, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v13081565

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, Issue 68/4, 2021, Page(s) 1779-1785, ISSN 1865-1674
Publisher: Blackwell-Wiss.-Verl
DOI: 10.1111/tbed.13926

Genetic data in the fight against pandemics

Author(s): Ágnes Becsei, Orsolya Anna Pipek, Péter Pollner, István Csabai
Published in: AK Journals, Issue 2/1, 2021, Page(s) 12-16, ISSN 2732-2688
Publisher: Scientia et Securitas
DOI: 10.1556/112.2021.00006

One Day in Denmark: Comparison of Phenotypic and Genotypic Antimicrobial Susceptibility Testing in Bacterial Isolates From Clinical Settings

Author(s): Ana Rita Rebelo, Valeria Bortolaia, Pimlapas Leekitcharoenphon, Dennis Schrøder Hansen, Hans Linde Nielsen, Svend Ellermann-Eriksen, Michael Kemp, Bent Løwe Røder, Niels Frimodt-Møller, Turid Snekloth Søndergaard, John Eugenio Coia, Claus Østergaard, Henrik Westh and Frank M. Aarestrup
Published in: Frontiers in Microbiology, Issue 13, 2022, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2022.804627

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, Issue 25/6, 2020, ISSN 1083-4389
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/hel.12752

Clusters of science and health related Twitter users become more isolated during the COVID-19 pandemic

Author(s): Francesco Durazzi, Martin Müller, Marcel Salathé & Daniel Remondini
Published in: Scientific Reports volume, Issue 11/19655, 2021, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-021-99301-0

Wolbachia prevalence in the vector species Culex pipiens and Culex torrentium in a Sindbis virus-endemic region of Sweden

Author(s): Alexander Bergman; Jenny C. Hesson
Published in: Parasites & Vectors, 2021, ISSN 1756-3305
Publisher: BioMed Central
DOI: 10.1186/s13071-021-04937-6

Sindbis Virus Infection in Non-Blood-Fed Hibernating Culex pipiens Mosquitoes in Sweden

Author(s): Alexander Bergman, Emma Dahl, Åke Lundkvist and Jenny C. Hesson
Published in: Viruses, Issue 12/12, 2020, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v12121441

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, Issue 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, Issue 6/2, 2020, ISSN 2057-1577
Publisher: Oxford Academic
DOI: 10.1093/ve/veaa091

Modeling the impact of surveillance activities combined with physical distancing interventions on COVID-19 epidemics at a local level

Author(s): Guan-Jhou Chen, John R B Palmer, Frederic Bartumeus and Ana Alba-Casals
Published in: Infectious Disease Modelling, Issue 7, 2022, ISSN 2468-0427
Publisher: Elsevier
DOI: 10.1016/j.idm.2022.11.001

Circulating microRNA signatures associated with disease severity and outcome in COVID-19 patients

Author(s): Alessandra Giannella, Silvia Riccetti, Alessandro Sinigaglia, Chiara Piubelli, Elisa Razzaboni, Piero Di Battista, Matteo Agostini, Emanuela Dal Molin, Riccardo Manganelli, Federico Gobbi, Giulio Ceolotto, Luisa Barzon
Published in: Frontiers in Immunology, 2022, ISSN 1664-3224
Publisher: Frontiers Media SA
DOI: 10.3389/fimmu.2022.968991

ResFinder – an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes

Author(s): Alfred Ferrer Florensa, Rolf Sommer Kaas, Philip Thomas Lanken Conradsen Clausen, Derya Aytan-Aktug and Frank M. Aarestrup
Published in: Microbial Genomics, Issue 8/1, 2022, ISSN 2057-5858
Publisher: The Microbiology Society
DOI: 10.1099/mgen.0.000748

Image-based & machine learning-guided multiplexed serology test for SARS-CoV-2

Author(s): Vilja Pietiäinen, Minttu Polso, Ede Migh, Christian Guckelsberger, Maria Harmati, Akos Diosdi, Laura Turunen, Antti Hassinen, Swapnil Potdar, Annika Koponen, Edina Gyukity Sebestyen, Ferenc Kovacs, Andras Kriston, Reka Hollandi, Katalin Burian, Gabriella Terhes, Adam Visnyovszki, Eszter Fodor, Zsombor Lacza, Anu Kantele, Pekka Kolehmainen, Laura Kakkola, Tomas Strandin, Lev Levanov, Olli Kallion
Published in: medRxiv, 2022, ISSN 1756-1833
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2022.09.08.22279729

Incidence Trends for SARS-CoV-2 Alpha and Beta Variants, Finland, Spring 2021

Author(s): Ravi Kant, Phuoc Truong Nguyen, Soile Blomqvist, Mert Erdin, Hussein Alburkat, Maija Suvanto, Fathiah Zakham, Veera Salminen, Viktor Olander, Minna Paloniemi, Leena Huhti, Sara Lehtinen, Bruno Luukinen, Hanna Jarva, Hannimari Kallio-Kokko, Satu Kurkela, Maija Lappalainen, Hanna Liimatainen, Sari Hannula, Jani Halkilahti, Jonna Ikonen, Niina Ikonen, Otto Helve, Marianne Gunell, Tytti Vuorinen, Ilya
Published in: Emerging Infectious Diseases, Issue 27/12, 2021, ISSN 1080-6040
Publisher: US National Center for Infectious Diseases
DOI: 10.3201/eid2712.211631

Mis-tweeting communication: a Vaccine Hesitancy analysis among twitter users in Italy

Author(s): Davide Gori, Francesco Durazzi, Marco Montalti, Zeno Di Valerio, Chiara Reno, Maria Pia Fantini, Daniel Remondini
Published in: Acta Biomedica, Issue 92/6, 2021, ISSN 0392-4203
Publisher: Mattioli 1885 SpA
DOI: 10.23750/abm.v92is6.12251

SARS-CoV-2 in hospital indoor environments is predominantly non-infectious

Author(s): Janina Krambrich, Dario Akaberi, Jiaxin Ling, Tove Hofman, Lennart Svensson, Marie Hagbom and Åke Lundkvist
Published in: Virology Journal, Issue 18/109, 2021, ISSN 1743-422x
Publisher: BioMed Central
DOI: 10.1186/s12985-021-01556-6

Emergence of ST39 carbapenem-resistant Klebsiella pneumoniae producing VIM-1 and KPC-2

Author(s): Theodoros Karampatakis, Charalampos Zarras, Styliani Pappa, Eleni Vagdatli, Elias Iosifidis, Emmanuel Roilides, Anna Papa
Published in: Microbial Pathofenesis, Issue 162, 2022, ISSN 0882-4010
Publisher: Elsevier BV
DOI: 10.1016/j.micpath.2021.105373

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, Issue 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, Issue 371/6525, 2021, Page(s) 172-177, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.abe5901

A curated data resource of 214K metagenomes for characterization of the global antimicrobial resistome

Author(s): Hannah-Marie Martiny, Patrick Munk,Christian Brinch, Frank M. Aarestrup and Thomas N. Petersen
Published in: PLOS Biology, 2022, ISSN 1544-9173
Publisher: Public Library of Science
DOI: 10.1371/journal.pbio.3001792

Mosquito alert: leveraging citizen science to create a GBIF mosquito occurrence dataset

Author(s): Živko Južnič-Zonta, Isis Sanpera-Calbet, Roger Eritja, John R.B. Palmer, Agustí Escobar, Joan Garriga, Aitana Oltra, Alex Richter-Boix, Francis Schaffner, Alessandra della Torre, Miguel Ángel Miranda, Marion Koopmans, Luisa Barzon, Frederic Bartumeus Ferre
Published in: GigaByte, Issue 1/13, 2022, ISSN 2709-4715
Publisher: GigaScience Press
DOI: 10.5281/zenodo.6379002

Differential plasmacytoid dendritic cell phenotype and type I Interferon response in asymptomatic and severe COVID-19 infection

Author(s): Martina Severa, Roberta A. Diotti, Marilena P. Etna, Fabiana Rizzo, Stefano Fiore, Daniela Ricci, Marco Iannetta, Alessandro Sinigaglia, Alessandra Lodi, Nicasio Mancini, Elena Criscuolo, Massimo Clementi, Massimo Andreoni, Stefano Balducci, Luisa Barzon, Paola Stefanelli, Nicola Clementi, Eliana M. Coccia
Published in: PLOS Pathogens, Issue 17/9, 2021, ISSN 1553-7366
Publisher: Public Library of Science
DOI: 10.1371/journal.ppat.1009878

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, Issue 12/8, 2020, Page(s) 882, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v12080882

Adaptation, spread and transmission of SARS-CoV-2 in farmed minks and associated humans in the Netherlands

Author(s): Lu Lu, Reina S Sikkema, Francisca C Velkers, David F Nieuwenhuijse, Egil A J Fischer, Paola A Meijer, Noortje Bouwmeester-Vincken, Ariene Rietveld, Marjolijn C A Wegdam-Blans, Paulien Tolsma, Marco Koppelman, Lidwien A M Smit, Renate W Hakze-van der Honing , Wim H M van der Poel, Arco N van der Spek, Marcel A H Spierenburg, Robert Jan Molenaar, Jan de Rond, Marieke Augustijn, Mark Woolhouse, J Arj
Published in: Nature Communications, Issue 12/1, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-27096-9

Connect to Protect: Dynamics and Genetic Connections of Highly Pathogenic Avian Influenza Outbreaks in Poultry from 2016 to 2021 in Germany

Author(s): King, Jacqueline, Christoph Staubach, Christiane Lüder, Susanne Koethe, Anne Günther, Lina Stacker, Dennis Rubbenstroth, Klaas Dietze, Christian Grund, Franz J. Conraths, Timm Harder, Martin Beer, and Anne Pohlmann
Published in: Viruses, Issue 14, 2022, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v14091849

Detection of antimicrobial resistance genes in urban air

Author(s): Ágnes Becsei, Norbert Solymosi, István Csabai, Donát Magyar
Published in: Microbiology Open, 2021, ISSN 2045-8827
Publisher: John Wiley and Sons Inc.
DOI: 10.1002/mbo3.1248

Rapid SARS-CoV-2 Intra-Host and Within-Household Emergence of Novel Haplotypes

Author(s): Manuto, Laura, Marco Grazioli, Andrea Spitaleri, Paolo Fontana, Luca Bianco, Luigi Bertolotti, Martina Bado, Giorgia Mazzotti, Federico Bianca, Francesco Onelia, Giovanni Lorenzin, Fabio Simeoni, Dejan Lazarevic, Elisa Franchin, Claudia Del Vecchio, Ilaria Dorigatti, Giovanni Tonon, Daniela Maria Cirillo, Enrico Lavezzo, Andrea Crisanti, and Stefano Toppo
Published in: Viruses, Issue 14/2, 2022, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v14020399

Early initiation of the respiratory syncytial virus season in 2021-2022, Greece

Author(s): Styliani Pappa, Katerina Haidopoulou, Charalampos Zarras, Eleni Theodorakou, Eleni Papadimitriou, Elias Iosifidis, Ioanna Gkeka, Konstantina Stoikou, Eleni Vagdatli, Lemonia Skoura and Anna Papa
Published in: Journal of Medical Virology, 2022, ISSN 0146-6615
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/jmv.27671

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, Issue 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, Issue 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, Issue 26/12, 2020, Page(s) 2982-2985, ISSN 1080-6040
Publisher: US National Center for Infectious Diseases
DOI: 10.3201/eid2612.203733

Highly Divergent SARS-CoV-2 Alpha Variant in Chronically Infected Immunocompromised Person

Author(s): Bas B Oude Munnink, Roel H T Nijhuis, Nathalie Worp, Marjan Boter, Babette Weller, Babs E Verstrepen, Corine GeurtsvanKessel, Maarten F Corsten, Anne Russcher and Marion Koopmans
Published in: Emerging Infectious Diseases, Issue 28/9, 2022, ISSN 1080-6040
Publisher: US National Center for Infectious Diseases
DOI: 10.3201/eid2809.220875

Global Distribution of mcr Gene Variants in 214K Metagenomic Samples

Author(s): Hannah-Marie Martiny, Patrick Munk, Christian Brinch, Judit Szarvas, Frank M Aarestrup, Thomas Nordahl Petersen
Published in: mSystems, Issue 7/2, 2022, ISSN 2379-5077
Publisher: American Society for Microbiology
DOI: 10.1128/msystems.00105-22

Early start of seasonal transmission and co-circulation of West Nile virus lineage 2 and a newly introduced lineage 1 strain in northern Italy, June 2022

Author(s): Barzon L, Montarsi F, Quaranta E, Monne I, Pacenti M, Michelutti A, Toniolo F, Danesi P, Marchetti G, Gobbo F, Sinigaglia A, Riccetti S, Dal Molin E, Favero L, Russo F, Capelli G.
Published in: Eurosurveillance, Issue 27/29/21, 2022, ISSN 1560-7917
Publisher: ECDC
DOI: 10.2807/1560-7917.es.2022.27.29.2200548

The phylodynamics of SARS-CoV-2 during 2020 in Finland

Author(s): Phuoc Truong Nguyen, Ravi Kant, Frederik Van den Broeck, Maija T. Suvanto, Hussein Alburkat, Jenni Virtanen, Ella Ahvenainen, Robert Castren, Samuel L. Hong, Guy Baele, Maarit J. Ahava, Hanna Jarva, Suvi Tuulia Jokiranta, Hannimari Kallio-Kokko, Eliisa Kekäläinen, Vesa Kirjavainen, Elisa Kortela, Satu Kurkela, Maija Lappalainen, Hanna Liimatainen, Marc A. Suchard, Sari Hannula, Pekka Ellonen, Ta
Published in: Communications Medicine, Issue 2/65, 2022, ISSN 2730-664X
Publisher: Nature Portfolio publishing
DOI: 10.1038/s43856-022-00130-7

West Nile Virus in Culex Mosquitoes in Central Macedonia, Greece, 2022

Author(s): Katerina Tsioka, Sandra Gewehr, Styliani Pappa, Stella Kalaitzopoulou, Konstantina Stoikou, Spiros Mourelatos and Anna Papa
Published in: Viruses, Issue 15/1, 2023, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v15010224

Synergistic Block of SARS-CoV-2 Infection by Combined Drug Inhibition of the Host Entry Factors PIKfyve Kinase and TMPRSS2 Protease

Author(s): Alex J B Kreutzberger, Anwesha Sanyal, Ravi Ojha, Jesse D Pyle, Olli Vapalahti, Giuseppe Balistreri, Tom Kirchhausen
Published in: Journal of Virology, Issue 95/21, 2021, ISSN 0022-538X
Publisher: American Society for Microbiology
DOI: 10.1128/jvi.00975-21

Scaling neighbor joining to one million taxa with dynamic and heuristic neighbor joining

Author(s): Philip T L C Clausen
Published in: Bioinformatics, Issue 39/1, 2023, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btac774

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, Issue 14/1, 2021, ISSN 1756-3305
Publisher: BioMed Central
DOI: 10.1186/s13071-021-04874-4

The central role of Italy in the spatial spread of USUTU virus in Europe

Author(s): B Zecchin, A Fusaro, A Milani, A Schivo, S Ravagnan, S Ormelli, C Mavian, A Michelutti, F Toniolo, L Barzon, I Monne, G Capelli
Published in: Virus Evolution, Issue 7/1, 2021, ISSN 2057-1577
Publisher: Oxford University Press
DOI: 10.1093/ve/veab048

Infections with highly pathogenic avian influenza A virus (HPAIV) H5N8 in harbor seals at the German North Sea coast, 2021

Author(s): Alexander Postel, Jacqueline King, Franziska K Kaiser, Johanna Kennedy, Mara Sophie Lombardo, Wencke Reineking, Madeleine de le Roi, Timm Harder, Anne Pohlmann, Thomas Gerlach, Guus Rimmelzwaan, Simon Rohner, Lotte C Striewe, Stephanie Gross, Luca A Schick, Jana C Klink, Katharina Kramer, Albert D M E Osterhaus, Martin Beer, Wolfgang Baumgärtner, Ursula Siebert and Paul Becher
Published in: Emerging Microbes & Infections, Issue 11/1, 2022, ISSN 2222-1751
Publisher: Nature Publishing Group
DOI: 10.1080/22221751.2022.2043726

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, Issue 37/5, 2020, Page(s) 705-710, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btaa857

Antimicrobial resistance determinants in silage

Author(s): Sára Ágnes Nagy, Adrienn Gréta Tóth, Márton Papp, Selçuk Kaplan & Norbert Solymosi
Published in: Scientific Reports, Issue 12/5243, 2022, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-022-09296-5

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, Issue 368/6494, 2020, Page(s) 1012-1015, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.abb7314

History and classification of Aigai virus (formerly Crimean-Congo haemorrhagic fever virus genotype VI)

Author(s): Anna Papa, Marco Marklewitz, Sofia Paraskevopoulou, Aura R. Garrison, Sergey V. Alkhovsky, Tatjana Avšič-Županc, Dennis A. Bente, Éric Bergeron, Felicity Burt, Nicholas Di Paola, Koray Ergünay, Roger Hewson, Ali Mirazimi, Amadou Alpha Sall, Jessica R. Spengler, Thomas S. Postler, Gustavo Palacios, and Jens H. Kuhn
Published in: The Journal of General Virology, Issue 103/4, 2022, ISSN 1465-2099
Publisher: Microbiology Society
DOI: 10.1099/jgv.0.001734

Identification of mutations in SARS-CoV-2 PCR primer regions

Author(s): Anikó Mentes, Krisztián Papp, Dávid Visontai, József Stéger, VEO Technical Working Group, István Csabai, Anna Medgyes-Horváth and Orsolya Anna Pipek
Published in: Scientific Reports, Issue 12, 2022, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-022-21953-3

COVID-19 Neuropathology: evidence for SARS-CoV-2 invasion of Human Brainstem Nuclei

Author(s): Aron Emmi, Stefania Rizzo, Luisa Barzon, Michele Sandre, Elisa Carturan, Alessandro Sinigaglia, Silvia Riccetti, Mila della Barbera, Rafael Boscolo-Berto, Patrizia Cocco, Veronica Macchi, Angelo Antonini, Monica De Gaspari, Cristina Basso, Raffaele De Caro, Andrea Porzionato
Published in: BioRxiv, 2022, ISSN 2692-8205
Publisher: Cold Spring Habor Laboratory Press
DOI: 10.1101/2022.06.29.498117

Natural diversity of the honey bee (Apis mellifera) gut bacteriome in various climatic and seasonal states

Author(s): Márton Papp, László Békési, Róbert Farkas, László Makrai, Maura Fiona Judge, Gergely Maróti, Dóra Tőzsér, Norbert Solymosi
Published in: PLOS ONE, Issue 17/9, 2022, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0273844

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, Issue 29/3, 2021, Page(s) 489-502.e8, ISSN 1931-3128
Publisher: Cell Press
DOI: 10.1016/j.chom.2021.01.015

Sindbis virus outbreak and evidence for geographical expansion in Finland, 2021

Author(s): Maija T Suvanto, Ruut Uusitalo, Eveline Otte im Kampe, Tytti Vuorinen, Satu Kurkela, Olli Vapalahti, Timothée Dub, Eili Huhtamo and Essi M Korhonen
Published in: Euro Surveillance, Issue 27/31, 2022, ISSN 1025-496X
Publisher: Centre Europeen pour la Surveillance Epidemiologique du SIDA
DOI: 10.2807/1560-7917.es.2022.27.31.2200580

Mobile Antimicrobial Resistance Genes in Probiotics

Author(s): Adrienn Gréta Tóth, István Csabai, Maura Fiona Judge, Gergely Maróti, Ágnes Becsei, Sándor Spisák, and Norbert Solymosi
Published in: Antibiotics, Issue 10/11, 2021, ISSN 2078-2489
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/antibiotics10111287

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, Issue 8/4, 2020, Page(s) 772, ISSN 2076-393X
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/vaccines8040772

Association between guilds of birds in the African-Western Palaearctic region and the tick species Hyalomma rufipes, one of the main vectors of Crimean-Congo hemorrhagic fever virus

Author(s): Tove Hoffman, Laura G. Carra, Patrik Öhagen, Thord Fransson, Christos Barboutis, Dario Piacentini, Jordi Figuerola, Yosef Kiat, Alejandro Onrubia, Thomas G.T. Jaenson, Kenneth Nilsson, Åke Lundkvist, and Björn Olsen
Published in: One Health, 2021, ISSN 2352-7714
Publisher: Elsevier
DOI: 10.1016/j.onehlt.2021.100349

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, Issue 12/3, 2020, Page(s) 281, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v12030281

Seasonal coronavirus-specific B cells with limited SARS-CoV-2 cross-reactivity dominate the IgG response in severe COVID-19.

Author(s): Muriel Aguilar-Bretones; Brenda M. Westerhuis; Matthijs P. Raadsen; Erwin de Bruin; Felicity D. Chandler; Nisreen M.A. Okba; Bart L. Haagmans; Thomas Langerak; Henrik Endeman; Johannes P. C. van den Akker; Diederik Gommers; Eric C. M. van Gorp; Corine H. GeurtsvanKessel; Rory D. de Vries; Ron A. M. Fouchier; Barry Rockx; Marion Koopmans; Gijsbert P. van Nierop
Published in: Journal of Clinical Investigation, Issue 51, 2021, ISSN 1558-8238
Publisher: American Society for Clinical Investigation
DOI: 10.1172/jci150613

Antigenic cartography of SARS-CoV-2 reveals that Omicron BA.1 and BA.2 are antigenically distinct.

Author(s): Mykytyn, Anna Z; Rissmann, Melanie; Kok, Adinda; Rosu, Miruna E; Schipper, Debby; Breugem, Tim I; van den Doel, Petra B; Chandler, Felicity; Bestebroer, Theo; de Wit, Maurice; van Royen, Martin E; Molenkamp, Richard; Oude Munnink, Bas B; de Vries, Rory D; GeurtsvanKessel, Corine; Smith, Derek J; Koopmans, Marion P G; Rockx, Barry; Lamers, Mart M; Fouchier, Ron A M; Haagmans, Bart L.
Published in: Science Immunology, Issue 7/75, 2022, ISSN 2470-9468
Publisher: AAAS
DOI: 10.1126/sciimmunol.abq4450

Longitudinal analysis of T cell receptor repertoires reveals shared patterns of antigen-specific response to SARS-CoV-2 infection

Author(s): Rachel M Gittelman, Enrico Lavezzo, Thomas M Snyder, H Jabran Zahid, Cara L Carty, Rebecca Elyanow, Sudeb Dalai, Ilan Kirsch, Lance Baldo, Laura Manuto, Elisa Franchin, Claudia Del Vecchio, Monia Pacenti, Caterina Boldrin, Margherita Cattai, Francesca Saluzzo, Andrea Padoan, Mario Plebani, Fabio Simeoni, Jessica Bordini, Nicola I Lorè, Dejan Lazarević, Daniela M Cirillo, Paolo Ghia, Stefano Topp
Published in: JCI Insight, 2022, ISSN 2077-0383
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.1172/jci.insight.151849

Evaluation of the use of alternative sample types for mosquito-borne flavivirus surveillance: Using Usutu virus as a model

Author(s): Nnomzie C. Atama, Irina V. Chestakova, Erwin de Bruin, Tijs J. van den Berg, Emmanuelle Munger, Chantal Reusken, Bas B. Oude Munnink, Henk van der Jeugd, Judith M.A. van den Brand, Marion P.G. Koopmans and Reina S. Sikkema
Published in: One Health, Issue 15, 2022, ISSN 2352-7714
Publisher: Elsevier
DOI: 10.1016/j.onehlt.2022.100456

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, Issue 6/1, 2021, ISSN 2396-8923
Publisher: Oxford Academic
DOI: 10.1093/biomethods/bpab008

Experimental Infection of Mink with SARS-COV-2 Omicron Variant and Subsequent Clinical Disease

Author(s): Jenni Virtanen, Kirsi Aaltonen, Kristel Kegler, Vinaya Venkat, Thanakorn Niamsap, Lauri Kareinen, Rasmus Malmgren, Olga Kivelä, Nina Atanasova, Pamela Österlund, Teemu Smura, Antti Sukura, Tomas Strandin, Lara Dutra, Olli Vapalahti, Heli Nordgren, Ravi Kant and Tarja Sironen
Published in: Emerging Infectious Diseases, Issue 28/6, 2022, ISSN 1080-6040
Publisher: US National Center for Infectious Diseases
DOI: 10.3201/eid2806.220328

Intranasal inhibitor broadly blocks SARS-CoV-2 including recent highly immunoevasive Omicron subvariants

Author(s): Anna R. Mäkelä, Hasan Uğurlu, Liina Hannula, Ravi Kant, Petja Salminen, Riku Fagerlund, Sanna Mäki, Anu Haveri, Tomas Strandin, Lauri Kareinen, Jussi Hepojoki, Suvi Kuivanen, Lev Levanov, Arja Pasternack, Rauno A. Naves, Olli Ritvos, Pamela Österlund, Tarja Sironen, Olli Vapalahti, Anja Kipar, Juha T. Huiskonen, Ilona Rissanen and Kalle Saksela
Published in: BioRxiv, 2022, ISSN 2692-8205
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1101/2021.12.28.474326

Iceland as Stepping Stone for Spread of Highly Pathogenic Avian Influenza Virus between Europe and North America

Author(s): Anne Günther, Oliver Krone, Vilhjalmur Svansson, Anne Pohlmann, Jacqueline King, Gunnar Thor Hallgrimsson, Kristinn Haukur Skarphéðinsson, Heiða Sigurðardóttir, Stefán Ragnar Jónsson, Martin Beer, Brigitte Brugger, Timm Harder
Published in: Emerging Infectious Diseases, Issue 28/12, 2022, ISSN 1080-6040
Publisher: US National Center for Infectious Diseases
DOI: 10.3201/eid2812.221086

West Nile Virus spread in Europe - phylogeographic pattern analysis and key drivers

Author(s): Lu Lu, Feifei Zhang, Bas B. Oude Munnink, Emmanuelle Munger, Reina S. Sikkema, Styliani Pappa, Katerina Tsioka, Alessandro Sinigaglia, Emanuela Dal Molin, Barbara B. Shih, Anne Günther, Anne Pohlmann, Martin Beer, Rachel A. Taylor, Frederic Bartumeus, Mark Woolhouse, Frank M. Aarestrup, Luisa Barzon, Anna Papa and Samantha Lycett
Published in: BioRxiv, 2022, ISSN 2692-8205
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1101/2022.11.10.515886

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, Issue 223/12, 2021, Page(s) 2020-2028, ISSN 0022-1899
Publisher: University of Chicago Press
DOI: 10.1093/infdis/jiab289

Spa diversity and genetic characterization of t127 methicillin-resistant Staphylococcus aureus in a tertiary Greek hospital

Author(s): Katerina Tsergouli, Theodoros Karampatakis, Konstantina Kontopoulou, Styliani Pappa, Parthena Kampouridou, Georgia Kallasidou, Katerina Tsioka, Sophia Zotou, Εleftheria-Eugenia Farmaki, Charalampos Kotzamanidis and Anna Papa
Published in: Acta Microbiologica et immunologica Hungarica, Issue 69/3, 2022, ISSN 1217-8950
Publisher: Akademiai Kiado
DOI: 10.1556/030.2022.01825

Risks of SARS-CoV-2 transmission between free-ranging animals and captive mink in the Netherlands

Author(s): Reina S. Sikkema, Lineke Begeman, René Janssen, Wendy J. Wolters, Corine Geurtsvankessel, Erwin de Bruin, Renate W. Hakze-van der Honing, Phaedra Eblé, Wim H.M. van der Poel, Judith M.A. van den Brand, Roy Slaterus, Maurice La Haye, Marion P.G. Koopmans, Francisca Velkers and Thijs Kuiken
Published in: Transboundary and Emerging Diseases, 2022, ISSN 1865-1674
Publisher: Blackwell-Wiss.-Verl
DOI: 10.1111/tbed.14686

Rapid spread of a new West Nile virus lineage 1 associated with increased risk of neuroinvasive disease during a large outbreak in northern Italy, 2022: One Health analysis.

Author(s): Barzon L, Pacenti M, Montarsi F, Fornasiero D, Gobbo F, Quaranta E, Monne I, Fusaro A, Volpe A, Sinigaglia A, Riccetti S, Molin ED, Satto S, Lisi V, Gobbi F, Galante S, Feltrin G, Valeriano V, Favero L, Russo F, Mazzucato M, Bortolami A, Mulatti P, Terregino C, Capelli G.
Published in: Journal of Travel Medicine, 2022, ISSN 1195-1982
Publisher: B.C. Decker Inc.
DOI: 10.1093/jtm/taac125

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