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

Author

Sikkema, R.S. (Reina S), Pas, S.D. (Suzan), Nieuwenhuijse, D.F. (David F.), O'Toole, Á. (Áine), Verweij, J. (Jaco), Linden, A. van der, Chestakova, I. (Irina), Schapendonk, C.M.E. (Claudia), Pronk, M.R. (Mark), Lexmond, P. (Pascal), Bestebroer, T.M. (Theo), Overmars, R.J. (Ronald J), Nieuwkoop, S. (Stefan) van, van den Bijllaardt, W. (Wouter), Bentvelsen, R.G. (Robbert G), Rijen, M.M.L. (Miranda) van, Buiting, A.G.M. (Anton), van Oudheusden, A.J.G. (Anne J G), Diederen, B.M.W. (Bram), Bergmans, D.C. (Tom), Eijck, A.A. (Annemiek), Molenkamp, R. (Richard), Rambaut, A. (Andrew), Timen, A. (Aura), Kluytmans, J.A.J.W. (Jan), Oude Munnink, B.B. (Bas B.), Kluytmans-Vandenbergh, M.F.Q. (Marjolein), Koopmans D.V.M., M.P.G. (Marion), Sikkema, R.S. (Reina S), Pas, S.D. (Suzan), Nieuwenhuijse, D.F. (David F.), O'Toole, Á. (Áine), Verweij, J. (Jaco), Linden, A. van der, Chestakova, I. (Irina), Schapendonk, C.M.E. (Claudia), Pronk, M.R. (Mark), Lexmond, P. (Pascal), Bestebroer, T.M. (Theo), Overmars, R.J. (Ronald J), Nieuwkoop, S. (Stefan) van, van den Bijllaardt, W. (Wouter), Bentvelsen, R.G. (Robbert G), Rijen, M.M.L. (Miranda) van, Buiting, A.G.M. (Anton), van Oudheusden, A.J.G. (Anne J G), Diederen, B.M.W. (Bram), Bergmans, D.C. (Tom), Eijck, A.A. (Annemiek), Molenkamp, R. (Richard), Rambaut, A. (Andrew), Timen, A. (Aura), Kluytmans, J.A.J.W. (Jan), Oude Munnink, B.B. (Bas B.), Kluytmans-Vandenbergh, M.F.Q. (Marjolein), and Koopmans D.V.M., M.P.G. (Marion)

Abstract

Background: 10 days after the first reported case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in the Netherlands (on Feb 27, 2020), 55 (4%) of 1497 health-care workers in nine hospitals located in the south of the Netherlands had tested positive for SARS-CoV-2 RNA. We aimed to gain insight in possible sources of infection in health-care workers. Methods: We did a cross-sectional study at three of the nine hospitals located in the south of the Netherlands. We screened health-care workers at the participating hospitals for SARS-CoV-2 infection, based on clinical symptoms (fever or mild respiratory symptoms) in the 10 days before screening. We obtained epidemiological data through structured interviews with health-care workers and combined this information with data from whole-genome sequencing of SARS-CoV-2 in clinical samples taken from health-care workers and patients. We did an in-depth analysis of sources and modes of transmission of SARS-CoV-2 in health-care workers and patients. Findings: Between March 2 and March 12, 2020, 1796 (15%) of 12 022 health-care workers were screened, of whom 96 (5%) tested positive for SARS-CoV-2. We obtained complete and near-complete genome sequences from 50 health-care workers and ten patients. Most sequences were grouped in three clusters, with two clusters showing local circulation within the region. The noted patterns were consistent with multiple introductions into the hospitals through community-acquired infections and local amplification in the community. Interpretation: Although direct transmission in the hospitals cannot be ruled out, our data do not support widespread nosocomial transmission as the source of infection in patients or health-care workers. Funding: EU Horizon 2020 (RECoVer, VEO, and the European Joint Programme One Health METASTAVA), and the National Institute of Allergy and Infectious Diseases, National Institutes of Health.

Published
2020
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2. Virus genomes reveal factors that spread and sustained the Ebola epidemic

Author

Dudas, G. (Gytis), Carvalho, L.M. (Luiz Max), Bedford, T. (Trevor), Tatem, A.J. (Andrew J.), Baele, G. (Guy), Faria, R. (Rui), Park, D.J. (Daniel J.), Ladner, J.T. (Jason T.), Arias, A., Asogun, D. (Danny), Bielejec, F. (Filip), Caddy, S.L., Cotten, M. (Matthew), D'Ambrozio, J. (Jonathan), Dellicour, S. (Simon), Di Caro, A. (Antonino), Diclaro, J.W. (Joseph W.), Duraffour, S. (Sophie), Elmore, M.J. (Michael J.), Fakoli, L.S. (Lawrence S.), Faye, O. (Ousmane), Gilbert, M.L. (Merle L.), Gevao, S.M. (Sahr M.), Gire, S. (Stephen), Gladden-Young, A. (Adrianne), Gnirke, A. (Andreas), Goba, A. (Augustine), Grant, D.S. (Donald S.), Haagmans, B.L. (Bart), Hiscox, J.A. (Julian A.), Jah, U., Kugelman, J.R. (Jeffrey R.), Liu, D. (Di), Lu, J. (Jia), Malboeuf, C.M. (Christine M.), Mate, S. (Suzanne), Matthews, D.A. (David A.), Matranga, C.B. (Christian B.), Meredith, L.W. (Luke W.), Qu, J. (James), Quick, J. (Joshua), Pas, S.D. (Suzan), Phan, M.V.T. (My V. T.), Pollakis, G. (G.), Reusken, C.B.E.M. (Chantal), Sanchez-Lockhart, M. (Mariano), Schaffner, S.F. (Stephen F.), Schieffelin, J.S. (John S.), Sealfon, R.S. (Rachel S.), Simon-Loriere, E. (Etienne), Smits, S.L. (Saskia), Stoecker, K. (Kilian), Thorne, L. (Lucy), Tobin, E.A. (Ekaete Alice), Vandi, M.A. (Mohamed A.), Watson, S.J. (Simon J.), West, K. (Kendra), Whitmer, S. (Shannon), Wiley, M.R. (Michael R.), Winnicki, S.M. (Sarah M.), Wohl, S. (Shirlee), Wölfel, R. (Roman), Yozwiak, N.L. (Nathan L.), Andersen, K.G. (Kristian G.), Blyden, S.O. (Sylvia O.), Bolay, F. (Fatorma), Carroll, M.W. (Miles W.), Dahn, B. (Bernice), Diallo, B. (Boubacar), Formenty, P. (Pierre), Fraser, C. (Christophe), Gao, G.F. (George F.), Garry, R.F. (Robert F.), Goodfellow, I. (Ian), Günther, S. (Stephan), Happi, C.T. (Christian T.), Holmes, E.C. (Edward C.), Kargbo, B. (Brima), Keïta, S. (Sakoba), Kellam, P. (Paul), Koopmans D.V.M., M.P.G. (Marion), Kuhn, J.H. (Jens H.), Loman, N.J. (Nicholas J.), Magassouba, N. (N'Faly), Naidoo, D. (Dhamari), Nichol, S.T. (Stuart T.), Nyenswah, T. (Tolbert), Palacios, G. (Gustavo), Pybus, O. (Oliver), Sabeti, P.C. (Pardis C.), Sall, A. (Amadou), Ströher, U. (Ute), Wurie, I., Suchard, M.A. (Marc), Lemey, P. (Philippe), Rambaut, A. (Andrew), Dudas, G. (Gytis), Carvalho, L.M. (Luiz Max), Bedford, T. (Trevor), Tatem, A.J. (Andrew J.), Baele, G. (Guy), Faria, R. (Rui), Park, D.J. (Daniel J.), Ladner, J.T. (Jason T.), Arias, A., Asogun, D. (Danny), Bielejec, F. (Filip), Caddy, S.L., Cotten, M. (Matthew), D'Ambrozio, J. (Jonathan), Dellicour, S. (Simon), Di Caro, A. (Antonino), Diclaro, J.W. (Joseph W.), Duraffour, S. (Sophie), Elmore, M.J. (Michael J.), Fakoli, L.S. (Lawrence S.), Faye, O. (Ousmane), Gilbert, M.L. (Merle L.), Gevao, S.M. (Sahr M.), Gire, S. (Stephen), Gladden-Young, A. (Adrianne), Gnirke, A. (Andreas), Goba, A. (Augustine), Grant, D.S. (Donald S.), Haagmans, B.L. (Bart), Hiscox, J.A. (Julian A.), Jah, U., Kugelman, J.R. (Jeffrey R.), Liu, D. (Di), Lu, J. (Jia), Malboeuf, C.M. (Christine M.), Mate, S. (Suzanne), Matthews, D.A. (David A.), Matranga, C.B. (Christian B.), Meredith, L.W. (Luke W.), Qu, J. (James), Quick, J. (Joshua), Pas, S.D. (Suzan), Phan, M.V.T. (My V. T.), Pollakis, G. (G.), Reusken, C.B.E.M. (Chantal), Sanchez-Lockhart, M. (Mariano), Schaffner, S.F. (Stephen F.), Schieffelin, J.S. (John S.), Sealfon, R.S. (Rachel S.), Simon-Loriere, E. (Etienne), Smits, S.L. (Saskia), Stoecker, K. (Kilian), Thorne, L. (Lucy), Tobin, E.A. (Ekaete Alice), Vandi, M.A. (Mohamed A.), Watson, S.J. (Simon J.), West, K. (Kendra), Whitmer, S. (Shannon), Wiley, M.R. (Michael R.), Winnicki, S.M. (Sarah M.), Wohl, S. (Shirlee), Wölfel, R. (Roman), Yozwiak, N.L. (Nathan L.), Andersen, K.G. (Kristian G.), Blyden, S.O. (Sylvia O.), Bolay, F. (Fatorma), Carroll, M.W. (Miles W.), Dahn, B. (Bernice), Diallo, B. (Boubacar), Formenty, P. (Pierre), Fraser, C. (Christophe), Gao, G.F. (George F.), Garry, R.F. (Robert F.), Goodfellow, I. (Ian), Günther, S. (Stephan), Happi, C.T. (Christian T.), Holmes, E.C. (Edward C.), Kargbo, B. (Brima), Keïta, S. (Sakoba), Kellam, P. (Paul), Koopmans D.V.M., M.P.G. (Marion), Kuhn, J.H. (Jens H.), Loman, N.J. (Nicholas J.), Magassouba, N. (N'Faly), Naidoo, D. (Dhamari), Nichol, S.T. (Stuart T.), Nyenswah, T. (Tolbert), Palacios, G. (Gustavo), Pybus, O. (Oliver), Sabeti, P.C. (Pardis C.), Sall, A. (Amadou), Ströher, U. (Ute), Wurie, I., Suchard, M.A. (Marc), Lemey, P. (Philippe), and Rambaut, A. (Andrew)

Abstract

The 2013-2016 West African epidemic caused by the Ebola virus was of unprecedented magnitude, duration and impact. Here we reconstruct the dispersal, proliferation and decline of Ebola virus throughout the region by analysing 1,610 Ebola virus genomes, which represent over 5% of the known cases. We test the association of geography, climate and demography with viral movement among administrative regions, inferring a classic 'gravity' model, with intense dispersal between larger and closer populations. Despite attenuation of international dispersal after border closures, cross-border transmission had already sown the seeds for an international epidemic, rendering these measures ineffective at curbing the epidemic. We address why the epidemic did not spread into neighbouring countries, showing that these countries were susceptible to substantial outbreaks but at lower risk of introductions. Finally, we reveal that this large epidemic was a heterogeneous and spatially dissociated collection of transmission clusters of varying size, duration and connectivity. These insights will help to inform interventions in future epidemics.

Published
2017
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3. Genome sequences of a novel vietnamese bat bunyavirus

Author

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), Tham, N.T.H. (Nguyen Thi Hong), Tien, N.T.H. (Nguyen Thi Hong), Chuc, N.T.K. (Nguyen Thi Kim), Ngoc, N.T.L. (Nguyen Thi Le), Ha, N.T.L. (Nguyen Thi Lien), Lien, N.T.N. (Nguyen Thi Nam), Diep, N.T.N. (Nguyen Thi Ngoc), Nhung, N.T. (Nguyen Thi), Chau, N.T.S. (Nguyen Thi Song), Chi, N.T.Y. (Nguyen Thi Yen), Trinh, N.T. (Nguyen Thieu), Van, N.T. (Nguyen Thu), Van Cuong, N. (Nguyen), Van Hung, N. (Nguyen), Kinh, N. (Nguyen) van, Hoang, N.V.M. (Nguyen Van Minh), Van My, N. (Nguyen), Van Thang, N. (Nguyen), Van Thanh, N. (Nguyen), Van Vinh Chau, N. (Nguyen), Van Xang, N. (Nguyen), My, P.H. (Pham Ha), Anh, P.H. (Pham Hong), Khoa, P.T.M. (Pham Thi Minh), Tam, P.T.T. (Pham Thi Thanh), Van Lao, P. (Pham), Van Minh, P. (Pham), Van Be Bay, P. (Phan), My, P.V.T. (Phan Vu Tra), Rabaa, M.A. (Maia A.), Rahman, M. (Motiur), Thompson, C. (Corinne), Thwaites, G. (Guy), Ngan, T.T.D. (Ta Thi Dieu), Nhu, T.D.H. (Tran Do Hoang), Chau, T.H.M. (Tran Hoang Minh), Toan, T.K. (Tran Khanh), Phuc, T.M. (Tran My), Hong, T.T.K. (Tran Thi Kim), Dung, T.T.N. (Tran Thi Ngoc), Thanh, T.T.T. (Tran Thi Thanh), Minh, T.T.T. (Tran Thi Thuy), Nguyen, T.T. (Tran Thua), Hien, T.T. (Tran Tinh), Tri, T.Q. (Trinh Quang), Hien, V.B. (Vo Be), Tai, V.N. (Vo Nhut), Cuong, V.Q. (Vo Quoc), Phat, V.V. (Voong Vinh), Huong, V.U.T.L. (V.U. Thi Lan), Hang, V.T.T. (Vu Thi Ty), Wertheim, H.F.L. (Heiman), Bogaardt, C. (Carlijn), Chase-Topping, M. (Margo), Ivens, A.L., Lu, L. (Lu), Nyugen, D. (Dung), Rambaut, A. (Andrew), Simmonds, P. (Peter), Woolhouse, M. (Mark), Deijs, M. (Martin), Jebbink, M.F. (Maarten F.), Jazaeri Farsani, S.M. (Seyed Mohammad), Dodd, K. (Kimberly), Euren, J. (Jason), Lucas, A. (Ashley), Ortiz, N. (Nancy), Pennacchio, L.A. (Len), Rubin, E. (Edward), Saylors, K.E. (Karen E.), Hai, T.M. (Tran Minh), Wolfe, N.D. (Nathan D.), 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), Tham, N.T.H. (Nguyen Thi Hong), Tien, N.T.H. (Nguyen Thi Hong), Chuc, N.T.K. (Nguyen Thi Kim), Ngoc, N.T.L. (Nguyen Thi Le), Ha, N.T.L. (Nguyen Thi Lien), Lien, N.T.N. (Nguyen Thi Nam), Diep, N.T.N. (Nguyen Thi Ngoc), Nhung, N.T. (Nguyen Thi), Chau, N.T.S. (Nguyen Thi Song), Chi, N.T.Y. (Nguyen Thi Yen), Trinh, N.T. (Nguyen Thieu), Van, N.T. (Nguyen Thu), Van Cuong, N. (Nguyen), Van Hung, N. (Nguyen), Kinh, N. (Nguyen) van, Hoang, N.V.M. (Nguyen Van Minh), Van My, N. (Nguyen), Van Thang, N. (Nguyen), Van Thanh, N. (Nguyen), Van Vinh Chau, N. (Nguyen), Van Xang, N. (Nguyen), My, P.H. (Pham Ha), Anh, P.H. (Pham Hong), Khoa, P.T.M. (Pham Thi Minh), Tam, P.T.T. (Pham Thi Thanh), Van Lao, P. (Pham), Van Minh, P. (Pham), Van Be Bay, P. (Phan), My, P.V.T. (Phan Vu Tra), Rabaa, M.A. (Maia A.), Rahman, M. (Motiur), Thompson, C. (Corinne), Thwaites, G. (Guy), Ngan, T.T.D. (Ta Thi Dieu), Nhu, T.D.H. (Tran Do Hoang), Chau, T.H.M. (Tran Hoang Minh), Toan, T.K. (Tran Khanh), Phuc, T.M. (Tran My), Hong, T.T.K. (Tran Thi Kim), Dung, T.T.N. (Tran Thi Ngoc), Thanh, T.T.T. (Tran Thi Thanh), Minh, T.T.T. (Tran Thi Thuy), Nguyen, T.T. (Tran Thua), Hien, T.T. (Tran Tinh), Tri, T.Q. (Trinh Quang), Hien, V.B. (Vo Be), Tai, V.N. (Vo Nhut), Cuong, V.Q. (Vo Quoc), Phat, V.V. (Voong Vinh), Huong, V.U.T.L. (V.U. Thi Lan), Hang, V.T.T. (Vu Thi Ty), Wertheim, H.F.L. (Heiman), Bogaardt, C. (Carlijn), Chase-Topping, M. (Margo), Ivens, A.L., Lu, L. (Lu), Nyugen, D. (Dung), Rambaut, A. (Andrew), Simmonds, P. (Peter), Woolhouse, M. (Mark), Deijs, M. (Martin), Jebbink, M.F. (Maarten F.), Jazaeri Farsani, S.M. (Seyed Mohammad), Dodd, K. (Kimberly), Euren, J. (Jason), Lucas, A. (Ashley), Ortiz, N. (Nancy), Pennacchio, L.A. (Len), Rubin, E. (Edward), Saylors, K.E. (Karen E.), Hai, T.M. (Tran Minh), and Wolfe, N.D. (Nathan D.)

Abstract

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.

Published
2016
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4. Global circulation patterns of seasonal influenza viruses vary with antigenic drift

Author

Bedford, T. (Trevor), Riley, S. (Steven), Barr, I.G. (Ian), Broor, S. (Shobha), Chadha, M. (Mandeep), Cox, N.J. (Nancy), Daniels, R.S. (Rodney S.), Gunasekaran, C.P. (C. Palani), Hurt, A.C. (Aeron), Kelso, A., Klimov, A. (Alexander), Lewis, N.S. (Nicola), Li, X. (Xiyan), McCauley, J. (John William), Odagiri, T. (Takato), Potdar, V. (Varsha), Rambaut, A. (Andrew), Shu, Y. (Yuelong), Skepner, E. (Eugene), Smith, D.J. (Derek James), Suchard, M.A. (Marc), Tashiro, M. (Masato), Wang, D. (Dayan), Xu, X. (Xiyan), Lemey, P. (Philippe), Russell, C.A. (Colin), Bedford, T. (Trevor), Riley, S. (Steven), Barr, I.G. (Ian), Broor, S. (Shobha), Chadha, M. (Mandeep), Cox, N.J. (Nancy), Daniels, R.S. (Rodney S.), Gunasekaran, C.P. (C. Palani), Hurt, A.C. (Aeron), Kelso, A., Klimov, A. (Alexander), Lewis, N.S. (Nicola), Li, X. (Xiyan), McCauley, J. (John William), Odagiri, T. (Takato), Potdar, V. (Varsha), Rambaut, A. (Andrew), Shu, Y. (Yuelong), Skepner, E. (Eugene), Smith, D.J. (Derek James), Suchard, M.A. (Marc), Tashiro, M. (Masato), Wang, D. (Dayan), Xu, X. (Xiyan), Lemey, P. (Philippe), and Russell, C.A. (Colin)

Abstract

Understanding the spatiotemporal patterns of emergence and circulation of new human seasonal influenza virus variants is a key scientific and public health challenge. The global circulation patterns of influenza A/H3N2 viruses are well characterized, but the patterns of A/H1N1 and B viruses have remained largely unexplored. Here we show that the global circulation patterns of A/H1N1 (up to 2009), B/Victoria, and B/Yamagata viruses differ substantially from those of A/H3N2 viruses, on the basis of analyses of 9,604 haemagglutinin sequences of human seasonal influenza viruses from 2000 to 2012. Whereas genetic variants of A/H3N2 viruses did not persist locally between epidemics and were reseeded from East and Southeast Asia, genetic variants of A/H1N1 and B viruses persisted across several seasons and exhibited complex global dynamics with East and Southeast Asia playing a limited role in disseminating new variants. The less frequent global movement of influenza A/H1N1 and B viruses coincided with slower rates of antigenic evolution, lower ages of infection, and smaller, less frequent epidemics compared to A/H3N2 viruses. Detailed epidemic models support differences in age of infection, combined with the less frequent travel of children, as probable drivers of the differences in the patterns of global circulation, suggesting a complex interaction between virus evolution, epidemiology, and human behaviour.

Published
2015
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5. Unifying Viral Genetics and Human Transportation Data to Predict the Global Transmission Dynamics of Human Influenza H3N2

Author

Lemey, P. (Philippe), Rambaut, A. (Andrew), Bedford, T. (Trevor), Faria, R. (Rui), Bielejec, F. (Filip), Baele, G. (Guy), Russell, C.A. (Colin), Smith, D.J. (Derek James), Pybus, O. (Oliver), Brockmann, K., Suchard, M.A. (Marc), Lemey, P. (Philippe), Rambaut, A. (Andrew), Bedford, T. (Trevor), Faria, R. (Rui), Bielejec, F. (Filip), Baele, G. (Guy), Russell, C.A. (Colin), Smith, D.J. (Derek James), Pybus, O. (Oliver), Brockmann, K., and Suchard, M.A. (Marc)

Abstract

Information on global human movement patterns is central to spatial epidemiological models used to predict the behavior of influenza and other infectious diseases. Yet it remains difficult to test which modes of dispersal drive pathogen spread at various geographic scales using standard epidemiological data alone. Evolutionary analyses of pathogen genome sequences increasingly provide insights into the spatial dynamics of influenza viruses, but to date they have largely neglected the wealth of information on human mobility, mainly because no statistical framework exists within which viral gene sequences and empirical data on host movement can be combined. Here, we address this problem by applying a phylogeographic approach to elucidate the global spread of human influenza subtype H3N2 and assess its ability to predict the spatial spread of human influenza A viruses worldwide. Using a framework that estimates the migration history of human influenza while simultaneously testing and quantifying a range of potential predictive variables of spatial spread, we show that the global dynamics of influenza H3N2 are driven by air passenger flows, whereas at more local scales spread is also determined by processes that correlate with geographic distance. Our analyses further confirm a central role

Published
2014
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6. Phylodynamic reconstruction reveals norovirus GII.4 epidemic expansions and their molecular determinants

Author

Siebenga, J.J. (Joukje), Lemey, P. (Philippe), Pond, S.L.K. (Sergei), Rambaut, A. (Andrew), Vennema, H. (Harry), Koopmans D.V.M., M.P.G. (Marion), Siebenga, J.J. (Joukje), Lemey, P. (Philippe), Pond, S.L.K. (Sergei), Rambaut, A. (Andrew), Vennema, H. (Harry), and Koopmans D.V.M., M.P.G. (Marion)

Abstract

Noroviruses are the most common cause of viral gastroenteritis. An increase in the number of globally reported norovirus outbreaks was seen the past decade, especially for outbreaks caused by successive genogroup II genotype 4 (GII.4) variants. Whether this observed increase was due to an upswing in the number of infections, or to a surveillance artifact caused by heightened awareness and concomitant improved reporting, remained unclear. Therefore, we set out to study the population structu

Published
2010
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