VIZIONS

The rate of infection from emerging and re-emerging pathogens is increasing worldwide. Many emerging infectious diseases have zoonotic origins and could have severe consequences for public health. Specific ‘hotspots’ have been identified where there is greater risk of zoonotic pathogens spilling over into human populations. South-east Asia has been identified as one such area due to close associations between wildlife, livestock and people in countries were the burden of infectious diseases in already high. Vietnam has been at the epicentre of emerging diseases in recent decades, and has a high burden of diseases of unknown origin. Livestock keeping, food production and sociodemographic factors make Vietnam a high risk area for infections of zoonotic origin.

The Vietnam Initiative on Zoonotic Infections (VIZIONS) is a multidisciplinary project involving several international institutions. The project utilises both hospital-based surveillance data and samples from high-risk cohorts to identify diseases of unknown origin and associated pathogens. The overall aims are to: 1) establish an international consortium of institutions using an integrative approach to animal and human health; 2) investigate epidemiology of different clinical syndromes in Vietnam and collect samples from hospital patients with these syndromes; 3) identify diseases of unknown origin from samples collected from patients and members of high-risk cohorts; 4) identify sociodemographic and behavioural factors associated with zoonotic disease transmission 5) create a platform for further research on zoonotic agents.

We are using data from the VIZIONS project to identify hospital patients with diseases of unknown origin for genetic sequencing using multivariate statistical techniques, and to examine spatiotemporal and behavioural data to identify potential cases of zoonotic infection. Additionally, we are using a metagenomics approach to identify any enteric viruses present in human and animal populations in Vietnam. Sequences from virus taxa that are shared between multiple host species are being studied in more detail using phylogenetic methods, to gain insights into how related these viruses are, in the hope of identifying host jumps.

By applying phylogenetic analysis using sequences from PCR or next generating sequencing, we aim to identify the evolution history of viruses and explore spatiotemporal transmission and cross-species transmission pathways during virus evolution.

 

2017 (2)

Detection of potentially novel paramyxovirus and coronavirus viral RNA in bats and rats in the Mekong Delta region of southern Viet Nam. Berto, A.; Anh, P. H.; Carrique-Mas, J. J.; Simmonds, P.; Van Cuong, N.; Tue, N. T.; Van Dung, N.; Woolhouse, M. E.; Smith, I.; Marsh, G. A.; Bryant, J. E.; Thwaites, G. E.; Baker, S.; and Rabaa, M. A. Zoonoses and public health. April 2017.
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A universal genome sequencing method for rotavirus A from human fecal samples which identifies segment reassortment and multi-genotype mixed infection. Dung, T. T. N.; Duy, P. T.; Sessions, O. M.; Sangumathi, U. K.; Phat, V. V.; Tam, P. T. T.; To, N. T. N.; Phuc, T. M.; Hong Chau, T. T.; Chau, N. N. M.; Minh, N. N.; Thwaites, G. E.; Rabaa, M. A.; and Baker, S. BMC genomics, 18(1): 324. April 2017.
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2016 (16)

Unbiased whole-genome deep sequencing of human and porcine stool samples reveals circulation of multiple groups of rotaviruses and a putative zoonotic infection. Phan, M. V. T.; Anh, P. H.; Cuong, N. V.; Munnink, B. B. O.; Hoek, L. v. d.; My, P. T.; Tri, T. N.; Bryant, J. E.; Baker, S.; Thwaites, G.; Woolhouse, M.; Kellam, P.; Rabaa, M. A.; and Cotten, M. L. bioRxiv,058875. June 2016.
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The evolution of Ebola virus: Insights from the 2013-2016 epidemic. Holmes, E. C.; Dudas, G.; Rambaut, A.; and Andersen, K. G. Nature, 538(7624): 193–200. October 2016.
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Temporal and spatial association of Streptococcus suis infection in humans and porcine reproductive and respiratory syndrome outbreaks in pigs in northern Vietnam. Huong, V. T. L.; Thanh, L. V.; Phu, V. D.; Trinh, D. T.; Inui, K.; Tung, N.; Oanh, N. T. K.; Trung, N. V.; Hoa, N. T.; Bryant, J. E.; Horby, P. W.; Kinh, N. V.; and Wertheim, H. F. L. Epidemiology and infection, 144(1): 35–44. January 2016.
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Role for migratory wild birds in the global spread of avian influenza H5N8. Science (New York, N.Y.), 354(6309): 213–217. October 2016.
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Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases. Arias, A.; Watson, S. J.; Asogun, D.; Tobin, E. A.; Lu, J.; Phan, M. V. T.; Jah, U.; Wadoum, R. E. G.; Meredith, L.; Thorne, L.; Caddy, S.; Tarawalie, A.; Langat, P.; Dudas, G.; Faria, N. R.; Dellicour, S.; Kamara, A.; Kargbo, B.; Kamara, B. O.; Gevao, S.; Cooper, D.; Newport, M.; Horby, P.; Dunning, J.; Sahr, F.; Brooks, T.; Simpson, A. J. H.; Groppelli, E.; Liu, G.; Mulakken, N.; Rhodes, K.; Akpablie, J.; Yoti, Z.; Lamunu, M.; Vitto, E.; Otim, P.; Owilli, C.; Boateng, I.; Okoror, L.; Omomoh, E.; Oyakhilome, J.; Omiunu, R.; Yemisis, I.; Adomeh, D.; Ehikhiametalor, S.; Akhilomen, P.; Aire, C.; Kurth, A.; Cook, N.; Baumann, J.; Gabriel, M.; Wölfel, R.; Di Caro, A.; Carroll, M. W.; Günther, S.; Redd, J.; Naidoo, D.; Pybus, O. G.; Rambaut, A.; Kellam, P.; Goodfellow, I.; and Cotten, M. Virus Evolution, 2(1). January 2016.
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Modelling the impact of co-circulating low pathogenic avian influenza viruses on epidemics of highly pathogenic avian influenza in poultry. Nickbakhsh, S.; Hall, M. D.; Dorigatti, I.; Lycett, S. J.; Mulatti, P.; Monne, I.; Fusaro, A.; Woolhouse, M. E. J.; Rambaut, A.; and Kao, R. R. Epidemics, 17: 27–34. December 2016.
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Large-scale screening and characterization of enteroviruses and kobuviruses infecting pigs in Vietnam. Van Dung, N.; Anh, P. H.; Van Cuong, N.; Hoa, N. T.; Carrique-Mas, J.; Hien, V. B.; Sharp, C.; Rabaa, M.; Berto, A.; Campbell, J.; Baker, S.; Farrar, J.; Woolhouse, M. E.; Bryant, J. E.; and Simmonds, P. The Journal of general virology, 97(2): 378–388. February 2016.
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Invasive Non-typhoidal Salmonella Infections in Asia: Clinical Observations, Disease Outcome and Dominant Serovars from an Infectious Disease Hospital in Vietnam. Phu Huong Lan, N.; Le Thi Phuong, T.; Nguyen Huu, H.; Thuy, L.; Mather, A. E.; Park, S. E.; Marks, F.; Thwaites, G. E.; Van Vinh Chau, N.; Thompson, C. N.; and Baker, S. PLoS neglected tropical diseases, 10(8): e0004857. August 2016.
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Human Rhinovirus B and C Genomes from Rural Coastal Kenya. Agoti, C. N.; Kiyuka, P. K.; Kamau, E.; Munywoki, P. K.; Bett, A.; van der Hoek, L.; Kellam, P.; Nokes, D. J.; and Cotten, M. Genome announcements, 4(4). July 2016.
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Global disease burden due to antibiotic resistance - state of the evidence. Woolhouse, M.; Waugh, C.; Perry, M. R.; and Nair, H. Journal of global health, 6(1): 010306. June 2016.
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Genome Sequences of a Novel Vietnamese Bat Bunyavirus. Oude Munnink, B. B.; Phan, M. V. T.; van der Hoek, L.; Kellam, P.; and Cotten, M. Genome announcements, 4(6). December 2016.
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Evolution and phylogeographic dissemination of endemic porcine picornaviruses in Vietnam. Lu, L.; Van Dung, N.; Bryant, J. E.; Carrique-Mas, J.; Van Cuong, N.; Anh, P. H.; Rabaa, M. A.; Baker, S.; Simmonds, P.; and Woolhouse, M. E. Virus evolution, 2(1): vew001. January 2016.
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Evaluation of Luminex xTAG Gastrointestinal Pathogen Panel Assay for Detection of Multiple Diarrheal Pathogens in Fecal Samples in Vietnam. Duong, V. T.; Phat, V. V.; Tuyen, H. T.; Dung, T. T. N.; Trung, P. D.; Minh, P. V.; Tu, L. T. P.; Campbell, J. I.; Le Phuc, H.; Ha, T. T. T.; Ngoc, N. M.; Huong, N. T. T.; Tam, P. T. T.; Huong, D. T.; Xang, N. V.; Dong, N.; Phuong, L. T.; Hung, N. V.; Phu, B. D.; Phuc, T. M.; Thwaites, G. E.; Vi, L. L.; Rabaa, M. A.; Thompson, C. N.; and Baker, S. Journal of clinical microbiology, 54(4): 1094–1100. April 2016.
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Complete Genome Characterization of Two Wild-Type Measles Viruses from Vietnamese Infants during the 2014 Outbreak. Oude Munnink, B. B.; Phan, M. V. T.; Kellam, P.; and Cotten, M. Genome announcements, 4(2). April 2016.
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Assessing the Epidemic Potential of RNA and DNA Viruses. Woolhouse, M. E. J.; Brierley, L.; McCaffery, C.; and Lycett, S. Emerging infectious diseases, 22(12): 2037–2044. December 2016.
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A Clinical and Epidemiological Investigation of the First Reported Human Infection With the Zoonotic Parasite Trypanosoma evansi in Southeast Asia. Van Vinh Chau, N.; Buu Chau, L.; Desquesnes, M.; Herder, S.; Phu Huong Lan, N.; Campbell, J. I.; Van Cuong, N.; Yimming, B.; Chalermwong, P.; Jittapalapong, S.; Ramon Franco, J.; Tri Tue, N.; Rabaa, M. A.; Carrique-Mas, J.; Pham Thi Thanh, T.; Tran Vu Thieu, N.; Berto, A.; Thi Hoa, N.; Van Minh Hoang, N.; Canh Tu, N.; Khac Chuyen, N.; Wills, B.; Tinh Hien, T.; Thwaites, G. E.; Yacoub, S.; and Baker, S. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 62(8): 1002–1008. April 2016.
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2015 (17)

The Vietnam Initiative on Zoonotic Infections (VIZIONS): A Strategic Approach to Studying Emerging Zoonotic Infectious Diseases. Rabaa, M. A.; Tue, N. T.; Phuc, T. M.; Carrique-Mas, J.; Saylors, K.; Cotten, M.; Bryant, J. E.; Nghia, H. D. T.; Cuong, N. V.; Pham, H. A.; Berto, A.; Phat, V. V.; Dung, T. T. N.; Bao, L. H.; Hoa, N. T.; Wertheim, H.; Nadjm, B.; Monagin, C.; van Doorn, H. R.; Rahman, M.; Tra, M. P. V.; Campbell, J. I.; Boni, M. F.; Tam, P. T. T.; van der Hoek, L.; Simmonds, P.; Rambaut, A.; Toan, T. K.; Van Vinh Chau, N.; Hien, T. T.; Wolfe, N.; Farrar, J. J.; Thwaites, G.; Kellam, P.; Woolhouse, M. E. J.; and Baker, S. EcoHealth, 12(4): 726–735. December 2015.
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The impact of environmental and climatic variation on the spatiotemporal trends of hospitalized pediatric diarrhea in Ho Chi Minh City, Vietnam. Thompson, C. N.; Zelner, J. L.; Nhu, T. D. H.; Phan, M. V.; Hoang Le, P.; Nguyen Thanh, H.; Vu Thuy, D.; Minh Nguyen, N.; Ha Manh, T.; Van Hoang Minh, T.; Lu Lan, V.; Nguyen Van Vinh, C.; Tran Tinh, H.; von Clemm, E.; Storch, H.; Thwaites, G.; Grenfell, B. T.; and Baker, S. Health & place, 35: 147–154. September 2015.
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The baseline characteristics and interim analyses of the high-risk sentinel cohort of the Vietnam Initiative on Zoonotic InfectiONS (VIZIONS). Carrique-Mas, J. J.; Tue, N. T.; Bryant, J. E.; Saylors, K.; Cuong, N. V.; Hoa, N. T.; An, N. N.; Hien, V. B.; Lao, P. V.; Tu, N. C.; Chuyen, N. K.; Chuc, N. T. K.; Tan, D. V.; Duong, H. V. V.; Toan, T. K.; Chi, N. T. Y.; Campbell, J.; Rabaa, M. A.; Nadjm, B.; Woolhouse, M.; Wertheim, H.; Thwaites, G.; and Baker, S. Scientific reports, 5: 17965. December 2015.
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Rodents and risk in the Mekong Delta of Vietnam: seroprevalence of selected zoonotic viruses in rodents and humans. Van Cuong, N.; Carrique-Mas, J.; Vo Be, H.; An, N. N.; Tue, N. T.; Anh, N. L.; Anh, P. H.; Phuc, N. T.; Baker, S.; Voutilainen, L.; Jaaskelainen, A.; Huhtamo, E.; Utriainen, M.; Sironen, T.; Vaheri, A.; Henttonen, H.; Vapalahti, O.; Chaval, Y.; Morand, S.; and Bryant, J. E. Vector borne and zoonotic diseases (Larchmont, N.Y.), 15(1): 65–72. January 2015.
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Population susceptibility to a variant swine-origin influenza virus A(H3N2) in Vietnam, 2011-2012. Hoa, L. N. M.; Bryant, J. E.; Choisy, M.; Nguyet, L. A.; Bao, N. T.; Trang, N. H.; Chuc, N. T. K.; Toan, T. K.; Saito, T.; Takemae, N.; Horby, P.; Wertheim, H.; and Fox, A. Epidemiology and infection, 143(14): 2959–2964. October 2015.
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Mobilising community-based research on zoonotic infections: A case study of longitudinal cohorts in Vietnam. Saylors, K.; Tri, T. N.; Khanh, T. T.; Tuan, K. B.; Wertheim, H. F.; Baker, S.; Thi, H. N.; and Bryant, J. E. Gateways: International Journal of Community Research and Engagement, 8(1): 23–42. September 2015.
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Lessons from Ebola: Improving infectious disease surveillance to inform outbreak management. Woolhouse, M. E. J.; Rambaut, A.; and Kellam, P. Science translational medicine, 7(307): 307rv5. September 2015.
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Induction of Antimicrobial Resistance in Escherichia coli and Non-Typhoidal Salmonella Strains after Adaptation to Disinfectant Commonly Used on Farms in Vietnam. Nhung, N. T.; Thuy, C. T.; Trung, N. V.; Campbell, J.; Baker, S.; Thwaites, G.; Hoa, N. T.; and Carrique-Mas, J. Antibiotics (Basel, Switzerland), 4(4): 480–494. October 2015.
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In vitro activity of colistin in antimicrobial combination against carbapenem-resistant Acinetobacter baumannii isolated from patients with ventilator-associated pneumonia in Vietnam. Le Minh, V.; Thi Khanh Nhu, N.; Vinh Phat, V.; Thompson, C.; Huong Lan, N. P.; Thieu Nga, T. V.; Thanh Tam, P. T.; Tuyen, H. T.; Hoang Nhu, T. D.; Van Hao, N.; Thi Loan, H.; Minh Yen, L.; Parry, C. M.; Trung Nghia, H. D.; Campbell, J. I.; Hien, T. T.; Thwaites, L.; Thwaites, G.; Van Vinh Chau, N.; and Baker, S. Journal of medical microbiology, 64(10): 1162–1169. October 2015.
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How important are rats as vectors of leptospirosis in the Mekong Delta of Vietnam?. Loan, H. K.; Van Cuong, N.; Takhampunya, R.; Kiet, B. T.; Campbell, J.; Them, L. N.; Bryant, J. E.; Tippayachai, B.; Van Hoang, N.; Morand, S.; Hien, V. B.; and Carrique-Mas, J. J. Vector borne and zoonotic diseases (Larchmont, N.Y.), 15(1): 56–64. January 2015.
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High levels of contamination and antimicrobial-resistant non-typhoidal Salmonella serovars on pig and poultry farms in the Mekong Delta of Vietnam. Tu, L. T. P.; Hoang, N. V. M.; Cuong, N. V.; Campbell, J.; Bryant, J. E.; Hoa, N. T.; Kiet, B. T.; Thompson, C.; Duy, D. T.; Phat, V. V.; Hien, V. B.; Thwaites, G.; Baker, S.; and Carrique-Mas, J. J. Epidemiology and infection, 143(14): 3074–3086. October 2015.
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High levels of antimicrobial resistance among escherichia coli isolates from livestock farms and synanthropic rats and shrews in the Mekong Delta of Vietnam. Nhung, N. T.; Cuong, N. V.; Campbell, J.; Hoa, N. T.; Bryant, J. E.; Truc, V. N. T.; Kiet, B. T.; Jombart, T.; Trung, N. V.; Hien, V. B.; Thwaites, G.; Baker, S.; and Carrique-Mas, J. Applied and environmental microbiology, 81(3): 812–820. February 2015.
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Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis. Weinert, L. A.; Chaudhuri, R. R.; Wang, J.; Peters, S. E.; Corander, J.; Jombart, T.; Baig, A.; Howell, K. J.; Vehkala, M.; Valimaki, N.; Harris, D.; Chieu, T. T. B.; Van Vinh Chau, N.; Campbell, J.; Schultsz, C.; Parkhill, J.; Bentley, S. D.; Langford, P. R.; Rycroft, A. N.; Wren, B. W.; Farrar, J.; Baker, S.; Hoa, N. T.; Holden, M. T. G.; Tucker, A. W.; and Maskell, D. J. Nature communications, 6: 6740. March 2015.
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Diversity of Bartonella spp. in Bats, Southern Vietnam. Anh, P. H.; Van Cuong, N.; Son, N. T.; Tue, N. T.; Kosoy, M.; Woolhouse, M. E. J.; Baker, S.; Bryant, J. E.; Thwaites, G.; Carrique-Mas, J. J.; and Rabaa, M. A. Emerging infectious diseases, 21(7): 1266–1267. July 2015.
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Diagnosing Rhodococcus equi infections in a setting where tuberculosis is highly endemic: a double challenge. Le, T.; Cash-Goldwasser, S.; Tho, P. V.; Lan, N. P. H.; Campbell, J. I.; van Doorn, H. R.; Lam, N. T.; Trung, N. V.; Trinh, D. T.; Van Kinh, N.; and Wertheim, H. F. L. Journal of clinical microbiology, 53(4): 1431–1433. April 2015.
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Bartonella species and trombiculid mites of rats from the Mekong Delta of Vietnam. Loan, H. K.; Cuong, N. V.; Takhampunya, R.; Klangthong, K.; Osikowicz, L.; Kiet, B. T.; Campbell, J.; Bryant, J.; Promstaporn, S.; Kosoy, M.; Hoang, N. V.; Morand, S.; Chaval, Y.; Hien, V. B.; and Carrique-Mas, J. Vector borne and zoonotic diseases (Larchmont, N.Y.), 15(1): 40–47. January 2015.
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A prospective multi-center observational study of children hospitalized with diarrhea in Ho Chi Minh City, Vietnam. Thompson, C. N.; Phan, M. V. T.; Hoang, N. V. M.; Minh, P. V.; Vinh, N. T.; Thuy, C. T.; Nga, T. T. T.; Rabaa, M. A.; Duy, P. T.; Dung, T. T. N.; Phat, V. V.; Nga, T. V. T.; Tu, L. T. P.; Tuyen, H. T.; Yoshihara, K.; Jenkins, C.; Duong, V. T.; Phuc, H. L.; Tuyet, P. T. N.; Ngoc, N. M.; Vinh, H.; Chinh, N. T.; Thuong, T. C.; Tuan, H. M.; Hien, T. T.; Campbell, J. I.; Chau, N. V. V.; Thwaites, G.; and Baker, S. The American journal of tropical medicine and hygiene, 92(5): 1045–1052. May 2015.
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2014 (14)

Viral aetiology of central nervous system infections in adults admitted to a tertiary referral hospital in southern Vietnam over 12 years. Tan, L. V.; Thai, L. H.; Phu, N. H.; Nghia, H. D. T.; Chuong, L. V.; Sinh, D. X.; Phong, N. D.; Mai, N. T. H.; Man, D. N. H.; Hien, V. M.; Vinh, N. T.; Day, J.; Chau, N. V. V.; Hien, T. T.; Farrar, J.; de Jong, M. D.; Thwaites, G.; van Doorn, H. R.; and Chau, T. T. H. PLoS neglected tropical diseases, 8(8): e3127. August 2014.
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The prevalence and genetic diversity of group A rotaviruses on pig farms in the Mekong Delta region of Vietnam. Pham, H. A.; Carrique-Mas, J. J.; Nguyen, V. C.; Ngo, T. H.; Nguyet, L. A.; Do, T. D.; Vo, B. H.; Phan, V. T. M.; Rabaa, M. A.; Farrar, J.; Baker, S.; and Bryant, J. E. Veterinary microbiology, 170(3-4): 258–265. June 2014.
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Serological and virological surveillance for porcine reproductive and respiratory syndrome virus, porcine circovirus type 2, and influenza A viruses among smallholder swine farms of the Mekong Delta, Vietnam. Cuong, N. V.; Carrique-Mas, J.; Thu, H. T. V.; Hien, N. D.; Hoa, N. T.; Nguyet, L. A.; Anh, P. H.; and Bryant, J. E. JOURNAL OF SWINE HEALTH AND PRODUCTION, 22(5): 224–231. 2014.
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Raw pig blood consumption and potential risk for Streptococcus suis infection, Vietnam. Huong, V. T. L.; Hoa, N. T.; Horby, P.; Bryant, J. E.; Van Kinh, N.; Toan, T. K.; and Wertheim, H. F. L. Emerging infectious diseases, 20(11): 1895–1898. November 2014.
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Prevalence, genetic diversity and recombination of species G enteroviruses infecting pigs in Vietnam. Van Dung, N.; Anh, P. H.; Van Cuong, N.; Hoa, N. T.; Carrique-Mas, J.; Hien, V. B.; Campbell, J.; Baker, S.; Farrar, J.; Woolhouse, M. E.; Bryant, J. E.; and Simmonds, P. The Journal of general virology, 95(Pt 3): 549–556. March 2014.
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Open source clinical science for emerging infections. Dunning, J. W.; Merson, L.; Rohde, G. G. U.; Gao, Z.; Semple, M. G.; Tran, D.; Gordon, A.; Olliaro, P. L.; Khoo, S. H.; Bruzzone, R.; Horby, P.; Cobb, J. P.; Longuere, K.; Kellam, P.; Nichol, A.; Brett, S.; Everett, D.; Walsh, T. S.; Hien, T.; Yu, H.; Zambon, M.; Ruiz-Palacios, G.; Lang, T.; Akhvlediani, T.; Hayden, F. G.; Marshall, J.; Webb, S.; Angus, D. C.; Shindo, N.; van der Werf, S.; Openshaw, P. J. M.; Farrar, J.; Carson, G.; and Baillie, J. K. The Lancet. Infectious diseases, 14(1): 8–9. January 2014.
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Novel porcine-like human G26P[19] rotavirus identified in hospitalized paediatric diarrhoea patients in Ho Chi Minh City, Vietnam. My, P. V. T.; Rabaa, M. A.; Donato, C.; Cowley, D.; Phat, V. V.; Dung, T. T. N.; Anh, P. H.; Vinh, H.; Bryant, J. E.; Kellam, P.; Thwaites, G.; Woolhouse, M. E. J.; Kirkwood, C. D.; and Baker, S. The Journal of general virology, 95(Pt 12): 2727–2733. December 2014.
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Limited geographic distribution of the novel cyclovirus CyCV-VN. Le, V. T.; de Jong, M. D.; Nguyen, V. K.; Nguyen, V. T.; Taylor, W.; Wertheim, H. F. L.; van der Ende, A.; van der Hoek, L.; Canuti, M.; Crusat, M.; Sona, S.; Nguyen, H. U.; Giri, A.; Nguyen, T. T. C. B.; Ho, D. T. N.; Farrar, J.; Bryant, J. E.; Tran, T. H.; Nguyen, V. V. C.; and van Doorn, H. R. Scientific reports, 4: 3967. February 2014.
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High rates of infection with novel enterovirus variants in wild populations of mandrills and other old world monkey species. Van Nguyen, D.; Harvala, H.; Ngole, E. M.; Delaporte, E.; Woolhouse, M. E. J.; Peeters, M.; and Simmonds, P. Journal of virology, 88(11): 5967–5976. June 2014.
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Epidemiology, clinical manifestations, and outcomes of Streptococcus suis infection in humans. Huong, V. T. L.; Ha, N.; Huy, N. T.; Horby, P.; Nghia, H. D. T.; Thiem, V. D.; Zhu, X.; Hoa, N. T.; Hien, T. T.; Zamora, J.; Schultsz, C.; Wertheim, H. F. L.; and Hirayama, K. Emerging infectious diseases, 20(7): 1105–1114. July 2014.
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Emergence of carbapenem-resistant Acinetobacter baumannii as the major cause of ventilator-associated pneumonia in intensive care unit patients at an infectious disease hospital in southern Vietnam. Nhu, N. T. K.; Lan, N. P. H.; Campbell, J. I.; Parry, C. M.; Thompson, C.; Tuyen, H. T.; Hoang, N. V. M.; Tam, P. T. T.; Le, V. M.; Nga, T. V. T.; Nhu, T. D. H.; Van Minh, P.; Nga, N. T. T.; Thuy, C. T.; Dung, L. T.; Yen, N. T. T.; Van Hao, N.; Loan, H. T.; Yen, L. M.; Nghia, H. D. T.; Hien, T. T.; Thwaites, L.; Thwaites, G.; Chau, N. V. V.; and Baker, S. Journal of medical microbiology, 63(Pt 10): 1386–1394. October 2014.
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Deep sequencing of norovirus genomes defines evolutionary patterns in an urban tropical setting. Cotten, M.; Petrova, V.; Phan, M. V. T.; Rabaa, M. A.; Watson, S. J.; Ong, S. H.; Kellam, P.; and Baker, S. Journal of virology, 88(19): 11056–11069. October 2014.
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An epidemiological investigation of Campylobacter in pig and poultry farms in the Mekong delta of Vietnam. Carrique-Mas, J. J.; Bryant, J. E.; Cuong, N. V.; Hoang, N. V. M.; Campbell, J.; Hoang, N. V.; Dung, T. T. N.; Duy, D. T.; Hoa, N. T.; Thompson, C.; Hien, V. V.; Phat, V. V.; Farrar, J.; and Baker, S. Epidemiology and infection, 142(7): 1425–1436. July 2014.
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2013 (30)

Understanding and managing zoonotic risk in the new livestock industries. Liverani, M.; Waage, J.; Barnett, T.; Pfeiffer, D. U.; Rushton, J.; Rudge, J. W.; Loevinsohn, M. E.; Scoones, I.; Smith, R. D.; Cooper, B. S.; White, L. J.; Goh, S.; Horby, P.; Wren, B.; Gundogdu, O.; Woods, A.; and Coker, R. J. Environmental health perspectives, 121(8): 873–877. August 2013.
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Transmission and evolution of the Middle East respiratory syndrome coronavirus in Saudi Arabia: a descriptive genomic study. Cotten, M.; Watson, S. J.; Kellam, P.; Al-Rabeeah, A. A.; Makhdoom, H. Q.; Assiri, A.; Al-Tawfiq, J. A.; Alhakeem, R. F.; Madani, H.; AlRabiah, F. A.; Al Hajjar, S.; Al-nassir, W. N.; Albarrak, A.; Flemban, H.; Balkhy, H. H.; Alsubaie, S.; Palser, A. L.; Gall, A.; Bashford-Rogers, R.; Rambaut, A.; Zumla, A. I.; and Memish, Z. A. Lancet (London, England), 382(9909): 1993–2002. December 2013.
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Tracking the establishment of local endemic populations of an emergent enteric pathogen. Holt, K. E.; Thieu Nga, T. V.; Thanh, D. P.; Vinh, H.; Kim, D. W.; Vu Tra, M. P.; Campbell, J. I.; Hoang, N. V. M.; Vinh, N. T.; Minh, P. V.; Thuy, C. T.; Nga, T. T. T.; Thompson, C.; Dung, T. T. N.; Nhu, N. T. K.; Vinh, P. V.; Tuyet, P. T. N.; Phuc, H. L.; Lien, N. T. N.; Phu, B. D.; Ai, N. T. T.; Tien, N. M.; Dong, N.; Parry, C. M.; Hien, T. T.; Farrar, J. J.; Parkhill, J.; Dougan, G.; Thomson, N. R.; and Baker, S. Proceedings of the National Academy of Sciences of the United States of America, 110(43): 17522–17527. October 2013.
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The validation and utility of a quantitative one-step multiplex RT real-time PCR targeting rotavirus A and norovirus. Dung, T. T. N.; Phat, V. V.; Nga, T. V. T.; My, P. V. T.; Duy, P. T.; Campbell, J. I.; Thuy, C. T.; Hoang, N. V. M.; Van Minh, P.; Le Phuc, H.; Tuyet, P. T. N.; Vinh, H.; Kien, D. T. H.; Huy, H. L. A.; Vinh, N. T.; Nga, T. T. T.; Hau, N. T. T.; Chinh, N. T.; Thuong, T. C.; Tuan, H. M.; Simmons, C.; Farrar, J. J.; and Baker, S. Journal of virological methods, 187(1): 138–143. January 2013.
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The policy of free healthcare for children under the age of 6 years in Vietnam: assessment of the uptake for children hospitalised with acute diarrhoea in Ho Chi Minh City. Shieh, M.; Thompson, C.; Phan, V. T. M.; Van, T. T. L.; Tediosi, F.; Merson, L.; Farrar, J. J.; Ha, M. T.; Ho, L. V.; Pham, T. N. T.; and Baker, S. Tropical medicine & international health : TM & IH, 18(12): 1444–1451. December 2013.
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The dynamics of GII.4 Norovirus in Ho Chi Minh City, Vietnam. Tra My, P. V.; Lam, H. M.; Thompson, C. N.; Phuc, H. L.; Tuyet, P. T. N.; Vinh, H.; Hoang, N. V. M.; Minh, P.; Vinh, N. T.; Thuy, C. T.; Nga, T. T. T.; Hau, N. T. T.; Chinh, N. T.; Thuong, T. C.; Tuan, H. M.; Campbell, J. I.; Clements, A. C. A.; Farrar, J.; Boni, M. F.; and Baker, S. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 18: 335–343. August 2013.
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The characterization of ESBL genes in Escherichia coli and Klebsiella pneumoniae causing nosocomial infections in Vietnam. Trang, N. H. T.; Nga, T. V. T.; Campbell, J. I.; Hiep, N. T.; Farrar, J.; Baker, S.; and Duy, P. T. Journal of infection in developing countries, 7(12): 922–928. December 2013.
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Subclinical avian influenza A(H5N1) virus infection in human, Vietnam. Le, M. Q.; Horby, P.; Fox, A.; Nguyen, H. T.; Le Nguyen, H. K.; Hoang, P. M. V.; Nguyen, K. C.; de Jong, M. D.; Jeeninga, R. E.; Rogier van Doorn, H.; Farrar, J.; and Wertheim, H. F. L. Emerging infectious diseases, 19(10): 1674–1677. October 2013.
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Streptococcus suis and porcine reproductive and respiratory syndrome, Vietnam. Hoa, N. T.; Chieu, T. T. B.; Do Dung, S.; Long, N. T.; Hieu, T. Q.; Luc, N. T.; Nhuong, P. T.; Huong, V. T. L.; Trinh, D. T.; Wertheim, H. F. L.; Van Kinh, N.; Campbell, J. I.; Farrar, J.; Chau, N. V. V.; Baker, S.; and Bryant, J. E. Emerging infectious diseases, 19(2): 331–333. February 2013.
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Microbiology. Sources of antimicrobial resistance. Woolhouse, M. E. J.; and Ward, M. J. Science (New York, N.Y.), 341(6153): 1460–1461. September 2013.
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Prospects for emerging infections in East and southeast Asia 10 years after severe acute respiratory syndrome. Horby, P. W.; Pfeiffer, D.; and Oshitani, H. Emerging infectious diseases, 19(6): 853–860. June 2013.
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Modeling the association of space, time, and host species with variation of the HA, NA, and NS genes of H5N1 highly pathogenic avian influenza viruses isolated from birds in Romania in 2005-2007. Alkhamis, M.; Perez, A.; Batey, N.; Howard, W.; Baillie, G.; Watson, S.; Franz, S.; Focosi-Snyman, R.; Onita, I.; Cioranu, R.; Turcitu, M.; Kellam, P.; Brown, I. H.; and Breed, A. C. Avian diseases, 57(3): 612–621. September 2013.
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Migration and persistence of human influenza A viruses, Vietnam, 2001-2008. Le, M. Q.; Lam, H. M.; Cuong, V. D.; Lam, T. T.; Halpin, R. A.; Wentworth, D. E.; Hien, N. T.; Thanh, L. T.; Phuong, H. V. M.; Horby, P.; and Boni, M. F. Emerging infectious diseases, 19(11): 1756–1765. November 2013.
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Identification of a new cyclovirus in cerebrospinal fluid of patients with acute central nervous system infections. Tan, L. V.; van Doorn, H. R.; Nghia, H. D. T.; Chau, T. T. H.; Tu, L. T. P.; de Vries, M.; Canuti, M.; Deijs, M.; Jebbink, M. F.; Baker, S.; Bryant, J. E.; Tham, N. T.; BKrong, N. T. T. C.; Boni, M. F.; Loi, T. Q.; Phuong, L. T.; Verhoeven, J. T. P.; Crusat, M.; Jeeninga, R. E.; Schultsz, C.; Chau, N. V. V.; Hien, T. T.; van der Hoek, L.; Farrar, J.; and de Jong, M. D. mBio, 4(3): e00231–00213. June 2013.
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Hospital outbreak of Middle East respiratory syndrome coronavirus. Assiri, A.; McGeer, A.; Perl, T. M.; Price, C. S.; Al Rabeeah, A. A.; Cummings, D. A. T.; Alabdullatif, Z. N.; Assad, M.; Almulhim, A.; Makhdoom, H.; Madani, H.; Alhakeem, R.; Al-Tawfiq, J. A.; Cotten, M.; Watson, S. J.; Kellam, P.; Zumla, A. I.; and Memish, Z. A. The New England journal of medicine, 369(5): 407–416. August 2013.
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H7N9 is a virus worth worrying about. Horby, P. Nature, 496(7446): 399. April 2013.
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Full-genome deep sequencing and phylogenetic analysis of novel human betacoronavirus. Cotten, M.; Lam, T. T.; Watson, S. J.; Palser, A. L.; Petrova, V.; Grant, P.; Pybus, O. G.; Rambaut, A.; Guan, Y.; Pillay, D.; Kellam, P.; and Nastouli, E. Emerging infectious diseases, 19(5): 736–742B. May 2013.
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Epidemiological features and risk factors of Salmonella gastroenteritis in children resident in Ho Chi Minh City, Vietnam. Thompson, C. N.; Phan, V. T. M.; Le, T. P. T.; Pham, T. N. T.; Hoang, L. P.; Ha, V.; Nguyen, V. M. H.; Pham, V. M.; Nguyen, T. V.; Cao, T. T.; Tran, T. T. N.; Nguyen, T. T. H.; Dao, M. T.; Campbell, J. I.; Nguyen, T. C.; Tang, C. T.; Ha, M. T.; Farrar, J.; and Baker, S. Epidemiology and infection, 141(8): 1604–1613. August 2013.
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Endemic norovirus infections in children, Ho Chi Minh City, Vietnam, 2009-2010. My, P. V. T.; Thompson, C.; Phuc, H. L.; Tuyet, P. T. N.; Vinh, H.; Hoang, N. V. M.; Minh, P. V.; Vinh, N. T.; Thuy, C. T.; Nga, T. T. T.; Hau, N. T. T.; Campbell, J.; Chinh, N. T.; Thuong, T. C.; Tuan, H. M.; Farrar, J.; and Baker, S. Emerging infectious diseases, 19(6): 977–980. June 2013.
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Emergence of multiple clade 2.3.2.1 influenza A (H5N1) virus subgroups in Vietnam and detection of novel reassortants. Creanga, A.; Thi Nguyen, D.; Gerloff, N.; Thi Do, H.; Balish, A.; Dang Nguyen, H.; Jang, Y.; Thi Dam, V.; Thor, S.; Jones, J.; Simpson, N.; Shu, B.; Emery, S.; Berman, L.; Nguyen, H. T.; Bryant, J. E.; Lindstrom, S.; Klimov, A.; Donis, R. O.; Davis, C. T.; and Nguyen, T. Virology, 444(1-2): 12–20. September 2013.
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Ecological and taxonomic variation among human RNA viruses. Woolhouse, M. E. J.; and Adair, K. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology, 58(2): 344–345. October 2013.
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Detection of HPAI H5N1 viruses in ducks sampled from live bird markets in Vietnam. Phan, M. Q.; Henry, W.; Bui, C. B.; DO, D. H.; Hoang, N. V.; Thu, N. T.; Nguyen, T. T.; LE, T. D.; Diep, T. Q.; Inui, K.; Weaver, J.; and Carrique-Mas, J. Epidemiology and infection, 141(3): 601–611. March 2013.
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Dengue virus in sub-tropical northern and central Viet Nam: population immunity and climate shape patterns of viral invasion and maintenance. Rabaa, M. A.; Simmons, C. P.; Fox, A.; Le, M. Q.; Nguyen, T. T. T.; Le, H. Y.; Gibbons, R. V.; Nguyen, X. T.; Holmes, E. C.; and Aaskov, J. G. PLoS neglected tropical diseases, 7(12): e2581. 2013.
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Avian influenza A(H7N9): information-sharing through government web sites in the Western Pacific Region. Harada, N.; Alexander, N.; and Olowokure, B. Western Pacific surveillance and response journal : WPSAR, 4(2): 44–46. June 2013.
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Avian influenza A(H7N9) and the closure of live bird markets. Murhekar, M.; Arima, Y.; Horby, P.; Vandemaele, K. A. H.; Vong, S.; Zijian, F.; Lee, C.; and Li, A. Western Pacific surveillance and response journal : WPSAR, 4(2): 4–7. June 2013.
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An updated systematic review of the role of host genetics in susceptibility to influenza. Horby, P.; Nguyen, N. Y.; Dunstan, S. J.; and Baillie, J. K. Influenza and other respiratory viruses, 7 Suppl 2: 37–41. September 2013.
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Autologous antibody capture to enrich immunogenic viruses for viral discovery. Oude Munnink, B. B.; Jazaeri Farsani, S. M.; Deijs, M.; Jonkers, J.; Verhoeven, J. T. P.; Ieven, M.; Goossens, H.; de Jong, M. D.; Berkhout, B.; Loens, K.; Kellam, P.; Bakker, M.; Canuti, M.; Cotten, M.; and van der Hoek, L. PloS one, 8(11): e78454. 2013.
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Antibiotic use and resistance in emerging economies: a situation analysis for Viet Nam. Nguyen, K. V.; Thi Do, N. T.; Chandna, A.; Nguyen, T. V.; Pham, C. V.; Doan, P. M.; Nguyen, A. Q.; Thi Nguyen, C. K.; Larsson, M.; Escalante, S.; Olowokure, B.; Laxminarayan, R.; Gelband, H.; Horby, P.; Thi Ngo, H. B.; Hoang, M. T.; Farrar, J.; Hien, T. T.; and Wertheim, H. F. L. BMC public health, 13: 1158. December 2013.
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A successful antimicrobial regime for Chromobacterium violaceum induced bacteremia. Campbell, J. I.; Lan, N. P. H.; Qui, P. T.; Dung, L. T.; Farrar, J. J.; and Baker, S. BMC infectious diseases, 13: 4. January 2013.
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A Review of Foodborne Bacterial and Parasitic Zoonoses in Vietnam. Carrique-Mas, J. J; and Bryant, J E Ecohealth, 10(4): 465–489. 2013.
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2012 (10)

The spectrum of central nervous system infections in an adult referral hospital in Hanoi, Vietnam. Taylor, W. R.; Nguyen, K.; Nguyen, D.; Nguyen, H.; Horby, P.; Nguyen, H. L.; Lien, T.; Tran, G.; Tran, N.; Nguyen, H. M.; Nguyen, T.; Nguyen, H. H.; Nguyen, T.; Tran, G.; Farrar, J.; de Jong, M.; Schultsz, C.; Tran, H.; Nguyen, D.; Vu, B.; Le, H.; Dao, T.; Nguyen, T.; and Wertheim, H. PloS one, 7(8): e42099. 2012.
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The epidemiology of interpandemic and pandemic influenza in Vietnam, 2007-2010: the Ha Nam household cohort study I. Horby, P.; Mai, L. Q.; Fox, A.; Thai, P. Q.; Thi Thu Yen, N.; Thanh, L. T.; Le Khanh Hang, N.; Duong, T. N.; Thoang, D. D.; Farrar, J.; Wolbers, M.; and Hien, N. T. American journal of epidemiology, 175(10): 1062–1074. May 2012.
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The co-selection of fluoroquinolone resistance genes in the gut flora of Vietnamese children. Vien, L. T. M.; Minh, N. N. Q.; Thuong, T. C.; Khuong, H. D.; Nga, T. V. T.; Thompson, C.; Campbell, J. I.; de Jong, M.; Farrar, J. J.; Schultsz, C.; van Doorn, H. R.; and Baker, S. PloS one, 7(8): e42919. 2012.
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H5N1 surveillance: Shift expertise to where it matters. Farrar, J. Nature, 483(7391): 534–535. March 2012.
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Prediction and prevention of the next pandemic zoonosis. Morse, S. S.; Mazet, J. A. K.; Woolhouse, M.; Parrish, C. R.; Carroll, D.; Karesh, W. B.; Zambrana-Torrelio, C.; Lipkin, W. I.; and Daszak, P. Lancet (London, England), 380(9857): 1956–1965. December 2012.
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No evidence for intra-segment recombination of 2009 H1N1 influenza virus in swine. Boni, M. F.; Smith, G. J. D.; Holmes, E. C.; and Vijaykrishna, D. Gene, 494(2): 242–245. February 2012.
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Influenza infection rates, measurement errors and the interpretation of paired serology. Cauchemez, S.; Horby, P.; Fox, A.; Mai, L. Q.; Thanh, L. T.; Thai, P. Q.; Hoa, L. N. M.; Hien, N. T.; and Ferguson, N. M. PLoS pathogens, 8(12): e1003061. 2012.
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Comparison of the Roche RealTime ready Influenza A/H1N1 Detection Set with CDC A/H1N1pdm09 RT-PCR on samples from three hospitals in Ho Chi Minh City, Vietnam. Tham, N. t.; Hang, V. t. T.; Khanh, T. H.; Viet, D. C.; Hien, T. T.; Farrar, J.; Chau, N. v. V.; and van Doorn, H. R. Diagnostic microbiology and infectious disease, 74(2): 131–136. October 2012.
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Clinical validation of a point-of-care multiplexed in vitro immunoassay using monoclonal antibodies (the MSD influenza test) in four hospitals in Vietnam. van Doorn, H. R.; Kinh, N. v.; Tuan, H. M.; Tuan, T. A.; Minh, N. N. Q.; Bryant, J. E.; Hang, V. t. T.; Uyen, L. t. T.; Thinh, L. Q.; Anh, T. t. N.; Lan, N. P. H.; Trung, N. V.; Taylor, W.; Merson, L.; Wertheim, H. F. L.; Farrar, J.; Wolbers, M.; Chau, N. v. V.; and de Jong, M. D. Journal of clinical microbiology, 50(5): 1621–1625. May 2012.
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Aetiologies of central nervous system infection in Viet Nam: a prospective provincial hospital-based descriptive surveillance study. Ho Dang Trung, N.; Le Thi Phuong, T.; Wolbers, M.; Nguyen Van Minh, H.; Nguyen Thanh, V.; Van, M. P.; Thieu, N. T. V.; Van, T. L.; Song, D. T.; Thi, P. L.; Thi Phuong, T. N.; Van, C. B.; Tang, V.; Ngoc Anh, T. H.; Nguyen, D.; Trung, T. P.; Thi Nam, L. N.; Kiem, H. T.; Thi Thanh, T. N.; Campbell, J.; Caws, M.; Day, J.; de Jong, M. D.; Van Vinh, C. N.; Van Doorn, H. R.; Tinh, H. T.; Farrar, J.; and Schultsz, C. PloS one, 7(5): e37825. 2012.
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