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Ye H, Zhang J, Sang Y, Shan N, Qiu W, Zhong W, Li J, Yuan Z. Divergent Reassortment and Transmission Dynamics of Highly Pathogenic Avian Influenza A(H5N8) Virus in Birds of China During 2021. Front Microbiol 2022; 13:913551. [PMID: 35847056 PMCID: PMC9279683 DOI: 10.3389/fmicb.2022.913551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Highly pathogenic influenza A(H5N8) viruses had caused several outbreaks among wild bird and poultry populations across the globe, and strikingly, caused human infection, posing serious public health concerns. In this study, we conducted influenza surveillance in China during 2021 to monitor the evolution of influenza viruses in poultry. A total of 35 influenza viruses were obtained in chickens, ducks, and geese, of which 30 H5N8 viruses, 3 H5N1 viruses, and 2 H5N6 viruses. Phylogenetic analysis suggested all of H5N1, H5N6, and H5N8 isolates were derived from clade 2.3.4.4b H5N8 viruses during 2020/21 season, and notably, the internal genes of H5N1 and H5N6 viruses shared different genetic heterogeneity with H5N8 viruses and had been reassorted with wild bird-origin H5N1 viruses from Europe. By contrast, almost all H5N8 viruses exhibited only one phylogenic cluster with wild bird-origin H5N8 viruses in China and Korea, indicating that H5N8 viruses in China were more stable. Besides, we found that Korea is the main output geographic location in the spread of these H5N8 viruses to northern and eastern China, and especially, the co-circulation of H5N8 viruses occurred within China, with central China acted as a seeding population during the H5N8 epidemic. The statistical support was strong for viral migration from wild birds to chickens and ducks, indicating that 2.3.4.4b poultry-origin H5N8 viruses during 2020–2021 were originated from wild birds. Our findings provide novel insights into evolution and transmission dynamics of H5 subtype influenza viruses among poultry after novel H5N8 viruses invaded China for nearly one year.
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Affiliation(s)
- Hejia Ye
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangzhou South China Biological Medicine, Co., Ltd, Guangzhou, China
| | - Jiahao Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- National Avian Influenza Para-Reference Laboratory, Guangzhou, China
- Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Guangzhou, China
| | - Yunfen Sang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- National Avian Influenza Para-Reference Laboratory, Guangzhou, China
- Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Guangzhou, China
| | - Nan Shan
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of the People’s Republic of China, Nanjing, China
| | - Weihong Qiu
- Guangzhou South China Biological Medicine, Co., Ltd, Guangzhou, China
| | - Wenting Zhong
- Guangzhou South China Biological Medicine, Co., Ltd, Guangzhou, China
| | - Junbao Li
- Guangzhou South China Biological Medicine, Co., Ltd, Guangzhou, China
| | - Zhaoxia Yuan
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- Guangdong Province Key Laboratory of Waterfowl Healthy Breeding, Guangzhou, China
- *Correspondence: Zhaoxia Yuan,
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2
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Krishnan RG, Cenci S, Bourouiba L. Mitigating bias in estimating epidemic severity due to heterogeneity of epidemic onset and data aggregation. Ann Epidemiol 2022; 65:1-14. [PMID: 34419601 PMCID: PMC8375253 DOI: 10.1016/j.annepidem.2021.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 06/11/2021] [Accepted: 07/18/2021] [Indexed: 11/16/2022]
Abstract
Outbreaks of infectious diseases, such as influenza, are a major societal burden. Mitigation policies during an outbreak or pandemic are guided by the analysis of data of ongoing or preceding epidemics. The reproduction number, R0, defined as the expected number of secondary infections arising from a single individual in a population of susceptibles is critical to epidemiology. For typical compartmental models such as the Susceptible-Infected-Recovered (SIR) R0 represents the severity of an epidemic. It is an estimate of the early-stage growth rate of an epidemic and is an important threshold parameter used to gain insights into the spread or decay of an outbreak. Models typically use incidence counts as indicators of cases within a single large population; however, epidemic data are the result of a hierarchical aggregation, where incidence counts from spatially separated monitoring sites (or sub-regions) are pooled and used to infer R0. Is this aggregation approach valid when the epidemic has different dynamics across the regions monitored? We characterize bias in the estimation of R0 from a merged data set when the epidemics of the sub-regions, used in the merger, exhibit delays in onset. We propose a method to mitigate this bias, and study its efficacy on synthetic data as well as real-world influenza and COVID-19 data.
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Affiliation(s)
- R G Krishnan
- Massachusetts Institute of Technology, Cambridge, MA
| | - S Cenci
- Massachusetts Institute of Technology, Cambridge, MA; Imperial College London, UK
| | - L Bourouiba
- Massachusetts Institute of Technology, Cambridge, MA; Health Sciences & Technology Program, Harvard Medical School, Boston, MA.
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3
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Zhang J, Li X, Wang X, Ye H, Li B, Chen Y, Chen J, Zhang T, Qiu Z, Li H, Jia W, Liao M, Qi W. Genomic evolution, transmission dynamics, and pathogenicity of avian influenza A (H5N8) viruses emerging in China, 2020. Virus Evol 2021; 7:veab046. [PMID: 34141450 PMCID: PMC8206605 DOI: 10.1093/ve/veab046] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Multiple recent outbreaks of highly pathogenic H5N8 viruses originating in aquatic birds frequently occurred in most European countries, Russia, South Korea, and Japan during the winter of 2020–21, and one zoonotic event of poultry workers infected with novel H5N8 viruses were reported in Russia. Strikingly, these novel H5N8 viruses had emerged and been co-circulating in wild birds and poultry in multiple provinces of China during 2020–21. In China, the population of aquatic birds has risen significantly in the past twenty years, and China is regarded as the largest reservoir for influenza viruses carried in aquatic birds across the globe. Hence, the co-circulation of these novel H5N8 viruses poses an alarming threat to not only poultry industry but also human health. In this study, we sequenced full-length genomes of these H5N8 viruses circulating in China. Phylogenetic analysis demonstrated that poultry-origin H5N8 viruses in China fell within wild birds-origin clade 2.3.4.4b H5N8 viruses from Europe during 2020–21, and notably, were genetically closely related to human-infecting H5N8 viruses in Russia. Moreover, they possessed several molecular markers associated with mammalian adaption. Bayesian coalescent analysis showed that these H5N8 viruses might have introduced into China during June–September 2020, suggesting that these H5N8 viruses might have introduced via wild bird migration or poultry trade. Besides, we also found that the effective population size of clade 2.3.4.4b H5N8 viruses dramatically increased during the winter season of 2020/21, as is consistent with previous increase of genetic diversity during the winter seasons of 2013/14 and 2016/17, which indicated that the wild bird migration accelerates the genetic diversity of these H5N8 viruses during the winter season of 2020/21. Notably, these novel H5N8 viruses were lethal to chickens and mice, highly transmissible to ducks, and were antigenically distinct from 2.3.4.4h H5 viruses circulating in China, posing considerable threats to public health. Our findings offer novel insights into the evolution and risk assessment of H5N8 viruses during the winter season of 2020–21.
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Affiliation(s)
- Jiahao Zhang
- National Avian Influenza Para-Reference Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Wushan Rd, Tianhe District, Guangzhou 510642, Guangdong, China.,Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China
| | - Xudong Li
- National Avian Influenza Para-Reference Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Wushan Rd, Tianhe District, Guangzhou 510642, Guangdong, China.,Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China
| | - Xiaomin Wang
- National Avian Influenza Para-Reference Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Wushan Rd, Tianhe District, Guangzhou 510642, Guangdong, China.,Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China
| | - Hejia Ye
- Guangzhou South China Biological Medicine, Co., Ltd, Wushan Rd, Tianhe District, Guangzhou 510642, Guangdong, China
| | - Bo Li
- National Avian Influenza Para-Reference Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Wushan Rd, Tianhe District, Guangzhou 510642, Guangdong, China.,Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China
| | - Yiqun Chen
- National Avian Influenza Para-Reference Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Wushan Rd, Tianhe District, Guangzhou 510642, Guangdong, China.,Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China
| | - Junhong Chen
- National Avian Influenza Para-Reference Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Wushan Rd, Tianhe District, Guangzhou 510642, Guangdong, China.,Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China
| | - Tao Zhang
- National Avian Influenza Para-Reference Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Wushan Rd, Tianhe District, Guangzhou 510642, Guangdong, China.,Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China
| | - Ziwen Qiu
- National Avian Influenza Para-Reference Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Wushan Rd, Tianhe District, Guangzhou 510642, Guangdong, China.,Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China
| | - Huanan Li
- National Avian Influenza Para-Reference Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Wushan Rd, Tianhe District, Guangzhou 510642, Guangdong, China.,Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China
| | - Weixin Jia
- National Avian Influenza Para-Reference Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Wushan Rd, Tianhe District, Guangzhou 510642, Guangdong, China.,Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China.,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou 510642, China.,Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Wushan Rd, Tianhe District, Guangzhou 510642, Guangdong, China
| | - Ming Liao
- National Avian Influenza Para-Reference Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Wushan Rd, Tianhe District, Guangzhou 510642, Guangdong, China.,Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China.,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou 510642, China.,Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Wushan Rd, Tianhe District, Guangzhou 510642, Guangdong, China
| | - Wenbao Qi
- National Avian Influenza Para-Reference Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Wushan Rd, Tianhe District, Guangzhou 510642, Guangdong, China.,Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China.,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou 510642, China.,Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Wushan Rd, Tianhe District, Guangzhou 510642, Guangdong, China
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4
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Yin S, de Knegt HJ, de Jong MCM, Si Y, Prins HHT, Huang ZYX, de Boer WF. Effects of migration network configuration and migration synchrony on infection prevalence in geese. J Theor Biol 2020; 502:110315. [PMID: 32387368 DOI: 10.1016/j.jtbi.2020.110315] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 04/29/2020] [Accepted: 04/30/2020] [Indexed: 11/15/2022]
Abstract
Migration can influence dynamics of pathogen-host interactions. However, it is not clearly known how migration pattern, in terms of the configuration of the migration network and the synchrony of migration, affects infection prevalence. We therefore applied a discrete-time SIR model, integrating environmental transmission and migration, to various migration networks, including networks with serial, parallel, or both serial and parallel stopover sites, and with various levels of migration synchrony. We applied the model to the infection of avian influenza virus in a migratory geese population. In a network with only serial stopover sites, increasing the number of stopover sites reduced infection prevalence, because with every new stopover site, the amount of virus in the environment was lower than that in the previous stopover site, thereby reducing the exposure of the migratory population. In a network with parallel stopover sites, both increasing the number and earlier appearance of the stopover sites led to an earlier peak of infection prevalence in the migratory population, because the migratory population is exposed to larger total amount of virus in the environment, speeding-up the infection accumulation. Furthermore, higher migration synchrony reduced the average number of cumulative infection, because the majority of the population can fly to a new stopover site where the amount of virus is still relatively low and has not been increased due to virus shedding of infected birds. Our simulations indicate that a migration pattern with multiple serial stopover sites and with highly synchronized migration reduces the infection prevalence.
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Affiliation(s)
- Shenglai Yin
- Wildlife Ecology and Conservation Group, Wageningen University, 6708PB Wageningen, The Netherlands.
| | - Henrik J de Knegt
- Wildlife Ecology and Conservation Group, Wageningen University, 6708PB Wageningen, The Netherlands.
| | - Mart C M de Jong
- Quantitative Veterinary Epidemiology Group, Wageningen University, 6708PB Wageningen, The Netherlands.
| | - Yali Si
- Institute for China Sustainable Urbanization, Tsinghua University, 100091 Beijing, China; Institute of Environmental Sciences, Leiden University, 2300RA Leiden, Netherlands.
| | - Herbert H T Prins
- Wildlife Ecology and Conservation Group, Wageningen University, 6708PB Wageningen, The Netherlands.
| | - Zheng Y X Huang
- College of Life Science, Nanjing Normal University, 210046 Nanjing, China.
| | - Willem F de Boer
- Wildlife Ecology and Conservation Group, Wageningen University, 6708PB Wageningen, The Netherlands.
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5
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Canavan BC. Opening Pandora's Box at the roof of the world: Landscape, climate and avian influenza (H5N1). Acta Trop 2019; 196:93-101. [PMID: 31063711 DOI: 10.1016/j.actatropica.2019.04.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 04/14/2019] [Accepted: 04/18/2019] [Indexed: 11/27/2022]
Abstract
The purpose of this case study is to examine how environmental disruption and agricultural practices act synergistically to create a perfect storm for the spread of avian influenza. Actors in this case study include the vast permafrost landscape of the Qinghai-Tibet Plateau; a wild goose that migrates over the Himalayas; the highest altitude railway in the world that traverses the plateau into Tibet; and an avian virus (H5N1). Commencing in 2001, tens of thousands of railway workers travelled to remote regions of the plateau to work on the railway. In order to feed and shelter these workers, the Chinese government established captive-bred goose farms as a source of high protein food. Beginning in 2005 and continuing in subsequent years, Qinghai Lake was the scene for the unprecedented appearance of avian influenza among migratory geese. This was a key moment in the global spread of H5N1 to poultry on three continents. Remote sensing technology suggested an ecological pathway for the transfer of avian viruses among chickens, captive-bred geese, and wild geese. Within a region experiencing rapid climate change, Qinghai Lake is warming even faster than the global average. This may relate to the persistent outbreaks of avian flu strains from Qinghai during the past twelve years. Globally, exponential increases in bird flu outbreaks are not merely a matter of chance mutations in flu viruses but also a result of antecedent social and environmental factors. The Qinghai case study provides real-world examples that bring these factors into sharp focus.
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Affiliation(s)
- Barbara C Canavan
- Independent Scholar, Global Health and The Environment, 320 SE 62nd Ave., Portland, Oregon, United States.
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6
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Xu Y, Gong P, Wielstra B, Si Y. Southward autumn migration of waterfowl facilitates cross-continental transmission of the highly pathogenic avian influenza H5N1 virus. Sci Rep 2016; 6:30262. [PMID: 27507581 PMCID: PMC4978953 DOI: 10.1038/srep30262] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 07/04/2016] [Indexed: 01/21/2023] Open
Abstract
The highly pathogenic avian influenza subtype H5N1 (HPAI H5N1) is a worldwide zoonotic infectious disease, threatening humans, poultry and wild birds. The role of wild birds in the spread of HPAI H5N1 has previously been investigated by comparing disease spread patterns with bird migration routes. However, the different roles that the southward autumn and northward spring migration might play in virus transmission have hardly been explored. Using direction analysis, we analyze HPAI H5N1 transmission directions and angular concentration of currently circulating viral clades, and compare these with waterfowl seasonal migration directions along major waterfowl flyways. Out of 22 HPAI H5N1 transmission directions, 18 had both a southward direction and a relatively high concentration. Differences between disease transmission and waterfowl migration directions were significantly smaller for autumn than for spring migration. The four northward transmission directions were found along Asian flyways, where the initial epicenter of the virus was located. We suggest waterfowl first picked up the virus from East Asia, then brought it to the north via spring migration, and then spread it to other parts of world mainly by autumn migration. We emphasize waterfowl autumn migration plays a relatively important role in HPAI H5N1 transmission compared to spring migration.
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Affiliation(s)
- Yanjie Xu
- Ministry of Education Key Laboratory for Earth System Modeling, and Center for Earth System Science, Tsinghua University, Beijing, China
| | - Peng Gong
- Ministry of Education Key Laboratory for Earth System Modeling, and Center for Earth System Science, Tsinghua University, Beijing, China.,Joint Center for Global Change Studies, Beijing 100875, China
| | - Ben Wielstra
- Department of Animal and Plant Sciences, University of Sheffield, S10 2TN Sheffield, UK.,Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
| | - Yali Si
- Ministry of Education Key Laboratory for Earth System Modeling, and Center for Earth System Science, Tsinghua University, Beijing, China.,Resource Ecology Group, Wageningen University, Droevendaalsesteeg 3a, 6708 PB Wageningen, The Netherlands
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7
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Impact of Spring Bird Migration on the Range Expansion of Ixodes scapularis Tick Population. Bull Math Biol 2015; 78:138-68. [PMID: 26688012 DOI: 10.1007/s11538-015-0133-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 11/27/2015] [Indexed: 01/23/2023]
Abstract
Many observational studies suggest that seasonal migratory birds play an important role in spreading Ixodes scapularis, a vector of Lyme disease, along their migratory flyways, and they are believed to be responsible for geographic range expansion of I. scapularis in Canada. However, the interplay between the dynamics of I. scapularis on land and migratory birds in the air is not well understood. In this study, we develop a periodic delay meta-population model which takes into consideration the local landscape for tick reproduction within patches and the times needed for ticks to be transported by birds between patches. Assuming that the tick population is endemic in the source region, we find that bird migration may boost an already established tick population at the subsequent region and thus increase the risk to humans, or bird migration may help ticks to establish in a region where the local landscape is not appropriate for ticks to survive in the absence of bird migration, imposing risks to public health. This theoretical study reveals that bird migration plays an important role in the geographic range expansion of I. scapularis, and therefore our findings may suggest some strategies for Lyme disease prevention and control.
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8
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De Marco MA, Delogu M, Sivay M, Sharshov K, Yurlov A, Cotti C, Shestopalov A. Virological evaluation of avian influenza virus persistence in natural and anthropic ecosystems of Western Siberia (Novosibirsk Region, summer 2012). PLoS One 2014; 9:e100859. [PMID: 24972026 PMCID: PMC4074073 DOI: 10.1371/journal.pone.0100859] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 05/30/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Wild aquatic birds, reservoir of low-pathogenicity (LP) avian influenza viruses (AIVs), congregate in huge numbers in Western Siberia wetlands, where major intra- and inter-continental bird flyways overlap. In 2005 and 2006, highly pathogenic (HP) AIV H5N1 epizootics affected wild and domestic birds in the Novosibirsk Region. In 2012, we evaluated AIV persistence in Siberian natural and anthropic ecosystems. METHODOLOGY/PRINCIPAL FINDINGS In Novosibirsk Region, 166 wild birds ecologically linked to aquatic environments and 152 domestic waterfowl were examined for AIV isolation in embryonating chicken eggs. Biological samples were obtained by integrating the conventional cloacal swab collection with the harvesting of samples from birds' plumage. Haemagglutinating allantoic fluids were further characterized by serological and molecular methods. In August-September 2012, 17 AIVs, including three H3N8, eight H4N6, two H4N?, one H2N?, one H?N2, and two unsubtyped LPAIVs, were isolated from 15 wild ducks. Whereas comparable proportions of wild Anseriformes (n.118) tested virus isolation (VI)-positive from cloaca and feathers (5.9% vs 8.5%) were detected, the overall prevalence of virus isolation, obtained from both sampling methods, was 2.4 times higher than that calculated on results from cloacal swab examination only (14.4% vs 5.9%). Unlike previously described in this area, the H4N6 antigenic subtype was found to be the prevalent one in 2012. Both cloacal and feather samples collected from domestic waterfowl tested VI-negative. CONCLUSION/SIGNIFICANCE We found lack of evidence for the H5N1 HPAIV circulation, explainable by the poor environmental fitness of HPAIVs in natural ecosystems. Our LPAIV isolation data emphasise the importance of Siberia wetlands in influenza A virus ecology, providing evidence of changes in circulation dynamics of HN antigenic subtypes harboured in wild bird reservoirs. Further studies of isolates, based on bioinformatic approaches to virus molecular evolution and phylogenesis, will be needed to better elucidate mechanisms involved in AIV perpetuation in this area.
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Affiliation(s)
- Maria A. De Marco
- Laboratorio di Genetica, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano Emilia (BO), Italy
- * E-mail:
| | - Mauro Delogu
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano Emilia (BO), Italy
| | - Mariya Sivay
- Research Center of Clinical and Experimental Medicine, Siberian Division of the Russian Academy of Medical Sciences, Novosibirsk, Russia
| | - Kirill Sharshov
- Research Center of Clinical and Experimental Medicine, Siberian Division of the Russian Academy of Medical Sciences, Novosibirsk, Russia
| | - Alexander Yurlov
- Institute of Systematics and Ecology of Animals of the Siberian Branch of the Russian Academy of Sciences (RAS), Novosibirsk, Russia
| | - Claudia Cotti
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano Emilia (BO), Italy
| | - Alexander Shestopalov
- Research Center of Clinical and Experimental Medicine, Siberian Division of the Russian Academy of Medical Sciences, Novosibirsk, Russia
- Research Division, Novosibirsk State University, Novosibirsk, Russia
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9
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Pandit PS, Bunn DA, Pande SA, Aly SS. Modeling highly pathogenic avian influenza transmission in wild birds and poultry in West Bengal, India. Sci Rep 2014; 3:2175. [PMID: 23846233 PMCID: PMC3807259 DOI: 10.1038/srep02175] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 06/24/2013] [Indexed: 11/10/2022] Open
Abstract
Wild birds are suspected to have played a role in highly pathogenic avian influenza (HPAI) H5N1 outbreaks in West Bengal. Cluster analysis showed that H5N1 was introduced in West Bengal at least 3 times between 2008 and 2010. We simulated the introduction of H5N1 by wild birds and their contact with poultry through a stochastic continuous-time mathematical model. Results showed that reducing contact between wild birds and domestic poultry, and increasing the culling rate of infected domestic poultry communities will reduce the probability of outbreaks. Poultry communities that shared habitat with wild birds or those indistricts with previous outbreaks were more likely to suffer an outbreak. These results indicate that wild birds can introduce HPAI to domestic poultry and that limiting their contact at shared habitats together with swift culling of infected domestic poultry can greatly reduce the likelihood of HPAI outbreaks.
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Affiliation(s)
- Pranav S Pandit
- School of Veterinary Medicine, University of California, Davis, California, USA
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10
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Arab A, Courter JR. Spatio-temporal Trend Analysis of Spring Arrival Data for Migratory Birds. COMMUN STAT-SIMUL C 2014. [DOI: 10.1080/03610918.2013.809100] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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11
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M. Heffernan J, Lou Y, Wu J. Range expansion of Ixodes scapularis ticks and of Borrelia burgdorferi by migratory birds. ACTA ACUST UNITED AC 2014. [DOI: 10.3934/dcdsb.2014.19.3147] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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12
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Virological investigation of avian influenza virus on postglacial species of phasianidae and tetraonidae in the italian alps. ISRN VETERINARY SCIENCE 2013; 2013:601732. [PMID: 24167732 PMCID: PMC3791578 DOI: 10.1155/2013/601732] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 08/14/2013] [Indexed: 11/17/2022]
Abstract
Land-based birds, belonging to Galliformes order are considered to be potential intermediaries in the emergence of new strains of influenza A viruses (AIVs), but the viral circulation in these birds remains largely unknown. To gain insights into the circulation of AIV in the wild Galliformes populations in Italian Alps, we conducted a virological survey on rock partridge (Alectoris graeca saxatilis) belonging to Phasianidae family and on tetraonids including rock ptarmigan (Lagopus mutus helveticus) and black grouse (Tetrao tetrix tetrix). In 2003 and 2004, during the hunting seasons, 79 wild Galliformes, categorised into age and sex classes, were hunted in the Sondrio Province (Central Alps). Cloacal swabs were collected from 11 rock partridges and from 68 tetraonids including 23 alpine rock ptarmigans and 45 black grouses. We tested cloacal swabs by a high sensitive reverse transcription- (RT-) PCR detecting the matrix gene of AIV. No AIV was detected in the investigated samples, thus, suggesting the lack of AIV circulation in these relict populations in the study period. In terms of threatened species conservation, during wildlife management activities, it is very important to exclude the introduction of AIV-carrier birds in shared territories, a fact representing a health risk for these populations.
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13
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Delogu M, Piredda I, Pintore A, Cabras P, Cotti C, Ghetti G, Raffini E, De Marco MA. Avian influenza and animal health risk: conservation of endemic threatened wild birds in Sardinia Island. Avian Dis 2013; 56:1034-9. [PMID: 23402132 DOI: 10.1637/10174-041012-resnote.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Sardinia is a Mediterranean island with a long geological history, leading to a separation process from continental Europe during the Miocene. As a consequence, in this insular habitat some wild bird species developed endemic forms, some of which are currently threatened. The aim of this study is to evaluate the possible animal health risk associated with a potential avian influenza virus (AIV) circulation in Sardinian wild bird populations. Overall, 147 cloacal swabs were sampled in the Sardinia region from June 2009 to September 2011. Samples were obtained from 12 taxonomic orders, including 16 families and 40 species of birds. Based on the endangered host status or on the ecology of the host-virus interaction, samples were categorized into three groups of species: 1) endemic, endangered, or both (17 species); 2) potential reservoir (21 species); and 3) potential spillover (two species). Cloacal swabs were tested by reverse transcription (RT)-PCR for influenza A virus matrix gene amplification. Forty-one serum samples were tested by nucleoprotein-enzyme-linked immunosorbent assay (NP-ELISA) for antibodies against influenza A virus nucleoprotein and by hemagglutination inhibition assay for detection of seropositivity against H5 and H7 AIV subtypes. No cloacal swabs tested RT-PCR positive for AIV, whereas two weak seropositive results were detected by NP-ELISA in a mallard (Anas platyrhynchos) and in a yellow-legged gull (Larus michahellis). The low or absent AIV circulation detected in Sardinia's wild birds during the study suggests a naïve status in these avian populations. These data provide new information on AIV circulation in Sardinia's wild birds that could be applied to implement conservation strategies for threatened species.
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Affiliation(s)
- Mauro Delogu
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra 50, 40064 Ozzano Emilia (BO), Italy.
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Lebarbenchon C, Sreevatsan S, Lefèvre T, Yang M, Ramakrishnan MA, Brown JD, Stallknecht DE. Reassortant influenza A viruses in wild duck populations: effects on viral shedding and persistence in water. Proc Biol Sci 2012; 279:3967-75. [PMID: 22859590 DOI: 10.1098/rspb.2012.1271] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Wild ducks of the genus Anas represent the natural hosts for a large genetic diversity of influenza A viruses. In these hosts, co-infections with different virus genotypes are frequent and result in high rates of genetic reassortment. Recent genomic data have provided information regarding the pattern and frequency of these reassortant viruses in duck populations; however, potential consequences on viral shedding and maintenance in the environment have not been investigated. On the basis of full-genome sequencing, we identified five virus genotypes, in a wild duck population in northwestern Minnesota (USA), that naturally arose from genetic reassortments. We investigated the effects of influenza A virus genotype on the viral shedding pattern in Mallards (Anas platyrhynchos) and the duration of infectivity in water, under different temperature regimens. Overall, we found that variation in the viral genome composition of these isolates had limited effects on duration, extent and pattern of viral shedding, as well as on the reduction of infectivity in water over time. These results support that, in wild ducks, functionally equivalent gene segments could be maintained in virus populations with no fitness costs when genetic reassortments occur.
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Affiliation(s)
- Camille Lebarbenchon
- Department of Population Health, College of Veterinary Medicine, Southeastern Cooperative Wildlife Disease Study, University of Georgia, Athens, GA 30602, USA.
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15
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Wang XS, Wu J. Seasonal migration dynamics: periodicity, transition delay and finite-dimensional reduction. Proc Math Phys Eng Sci 2012. [DOI: 10.1098/rspa.2011.0236] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We study a model of bird migration between the summer breeding ground and the winter refuge site. The model involves time lags for the transition time between the patches, and the model parameters are periodic in time as the biological activities related to the migration and reproduction are seasonal. It has been shown in previous studies that the model system exhibits threshold dynamics: either all solutions converge to the trivial solution, or the system has a positive and globally attractive periodic solution. Two issues remain and will be addressed in this paper: how to express the threshold condition in terms of model parameters explicitly (rather than the abstract spectral radius of a certain monodromy operator) and how to describe the temporal pattern of the positive periodic solution. We make an interesting and surprising observation that the delay differential system is completely characterized by a finite-dimensional ordinary differential system and then a finite-dimensional map in the sense that the bird population at the initial time of spring migration determines the future status of the system. As a consequence, we derive the threshold condition, explicitly in terms of the model parameters, for the extinction and persistence of the considered bird species.
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Affiliation(s)
- Xiang-Sheng Wang
- Mprime Centre for Disease Modelling, York Institute for Health Research, York University, Toronto, Canada M3J 1P3
| | - Jianhong Wu
- Laboratory for Industrial and Applied Mathematics, Department of Mathematics and Statistics, York University, Toronto, Canada M3J 1P3
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16
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Effects of infection-induced migration delays on the epidemiology of avian influenza in wild mallard populations. PLoS One 2011; 6:e26118. [PMID: 22028812 PMCID: PMC3196538 DOI: 10.1371/journal.pone.0026118] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Accepted: 09/19/2011] [Indexed: 11/23/2022] Open
Abstract
Wild waterfowl populations form a natural reservoir of Avian Influenza (AI) virus, and fears exist that these birds may contribute to an AI pandemic by spreading the virus along their migratory flyways. Observational studies suggest that individuals infected with AI virus may delay departure from migratory staging sites. Here, we explore the epidemiological dynamics of avian influenza virus in a migrating mallard (Anas platyrhynchos) population with a specific view to understanding the role of infection-induced migration delays on the spread of virus strains of differing transmissibility. We develop a host-pathogen model that combines the transmission dynamics of influenza with the migration, reproduction and mortality of the host bird species. Our modeling predicts that delayed migration of individuals influences both the timing and size of outbreaks of AI virus. We find that (1) delayed migration leads to a lower total number of cases of infection each year than in the absence of migration delay, (2) when the transmission rate of a strain is high, the outbreak starts at the staging sites at which birds arrive in the early part of the fall migration, (3) when the transmission rate is low, infection predominantly occurs later in the season, which is further delayed when there is a migration delay. As such, the rise of more virulent AI strains in waterfowl could lead to a higher prevalence of infection later in the year, which could change the exposure risk for farmed poultry. A sensitivity analysis shows the importance of generation time and loss of immunity for the effect of migration delays. Thus, we demonstrate, in contrast to many current transmission risk models solely using empirical information on bird movements to assess the potential for transmission, that a consideration of infection-induced delays is critical to understanding the dynamics of AI infection along the entire flyway.
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17
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Shamoun-Baranes J, van Loon EE, Purves RS, Speckmann B, Weiskopf D, Camphuysen CJ. Analysis and visualization of animal movement. Biol Lett 2011; 8:6-9. [PMID: 21865243 DOI: 10.1098/rsbl.2011.0764] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The interdisciplinary workshop 'Analysis and Visualization of Moving Objects' was held at the Lorentz Centre in Leiden, The Netherlands, from 27 June to 1 July 2011. It brought together international specialists from ecology, computer science and geographical information science actively involved in the exploration, visualization and analysis of moving objects, such as marine reptiles, mammals, birds, storms, ships, cars and pedestrians. The aim was to share expertise, methodologies, data and common questions between different fields, and to work towards making significant advances in movement research. A data challenge based on GPS tracking of lesser black-backed gulls (Larus fuscus) was used to stimulate initial discussions, cross-fertilization between research groups and to serve as an initial focus for activities during the workshop.
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Affiliation(s)
- Judy Shamoun-Baranes
- Computational Geo-Ecology, IBED, University of Amsterdam, Amsterdam, The Netherlands.
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18
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Lebarbenchon C, Stallknecht DE. Host shifts and molecular evolution of H7 avian influenza virus hemagglutinin. Virol J 2011; 8:328. [PMID: 21711553 PMCID: PMC3141685 DOI: 10.1186/1743-422x-8-328] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Accepted: 06/28/2011] [Indexed: 11/22/2022] Open
Abstract
Evolutionary consequences of host shifts represent a challenge to identify the mechanisms involved in the emergence of influenza A (IA) viruses. In this study we focused on the evolutionary history of H7 IA virus in wild and domestic birds, with a particular emphasis on host shifts consequences on the molecular evolution of the hemagglutinin (HA) gene. Based on a dataset of 414 HA nucleotide sequences, we performed an extensive phylogeographic analysis in order to identify the overall genetic structure of H7 IA viruses. We then identified host shift events and investigated viral population dynamics in wild and domestic birds, independently. Finally, we estimated changes in nucleotide substitution rates and tested for positive selection in the HA gene. A strong association between the geographic origin and the genetic structure was observed, with four main clades including viruses isolated in North America, South America, Australia and Eurasia-Africa. We identified ten potential events of virus introduction from wild to domestic birds, but little evidence for spillover of viruses from poultry to wild waterbirds. Several sites involved in host specificity (addition of a glycosylation site in the receptor binding domain) and virulence (insertion of amino acids in the cleavage site) were found to be positively selected in HA nucleotide sequences, in genetically unrelated lineages, suggesting parallel evolution for the HA gene of IA viruses in domestic birds. These results highlight that evolutionary consequences of bird host shifts would need to be further studied to understand the ecological and molecular mechanisms involved in the emergence of domestic bird-adapted viruses.
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Affiliation(s)
- Camille Lebarbenchon
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, The University of Georgia, Athens, Georgia 30602, USA.
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Bourouiba L, Teslya A, Wu J. Highly pathogenic avian influenza outbreak mitigated by seasonal low pathogenic strains: insights from dynamic modeling. J Theor Biol 2010; 271:181-201. [PMID: 21146544 DOI: 10.1016/j.jtbi.2010.11.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Revised: 10/28/2010] [Accepted: 11/08/2010] [Indexed: 10/18/2022]
Abstract
The spread of highly pathogenic avian influenza (HPAI) H5N1 remains a threat for both wild and domestic bird populations, while low pathogenic avian influenza (LPAI) strains have been reported to induce partial immunity to HPAI in poultry and some wild birds inoculated with both HPAI and LPAI strains. Here, based on the reported data and experiments, we develop a two-strain avian influenza model to examine the extent to which this partial immunity observed at the individual level can affect the outcome of the outbreaks among migratory birds in the wild at the population level during different seasons. We find a distinct mitigating effect of LPAI on the death toll induced by HPAI strain, and this effect is particularly important for populations previously exposed to and recovered from LPAI. We further investigate the effect of the dominant mode of transmission of an HPAI strain on the outcome of the epidemic. Four combinations of contact based direct transmission and indirect fecal-to-oral (or environmental) routes are examined. For a given infection peak of HPAI, indirect fecal-to-oral transmission of HPAI can lead to a higher death toll than that associated with direct transmission. The mitigating effect of LPAI can, in turn, be dependent on the route of infection of HPAI.
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Affiliation(s)
- L Bourouiba
- Department of Mathematics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139-4307, USA
| | - A Teslya
- Department of Mathematics, Ryerson University, 350 Victoria St., Toronto, Canada ON M5B 2K3
| | - J Wu
- Department of Mathematics and Statistics, York University, 4700 Keele Street, Toronto, Canada ON M3J 1P3; Centre for Disease Modelling, York University, 4700 Keele Street, Toronto, Canada ON M3J 1P3
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