scholarly journals Bayesian phylodynamics of avian influenza virus H9N2 in Asia with time-dependent predictors of migration

2018 ◽  
Author(s):  
Jing Yang ◽  
Nicola F. Müller ◽  
Remco Bouckaert ◽  
Bing Xu ◽  
Alexei J. Drummond
Keyword(s):  
Time Series ◽  
Avian Influenza ◽  
Wild Bird ◽  
Time Dependent ◽  
Poultry Production ◽  
Geographic Proximity ◽  
Effective Population ◽  
Migration Rates ◽  
Bird Populations ◽  
Population Sizes

AbstractModel-based phylodynamic approaches recently employed generalized linear models (GLMs) to uncover potential predictors of viral spread. Very recently some of these models have allowed both the predictors and their coefficients to be time-dependent. However, these studies mainly focused on predictors that are assumed to be constant through time. Here we inferred the phylodynamics of H9N2 viruses isolated in 12 Asian countries and regions under both discrete trait analysis (DTA) and structured coalescent (MASCOT) approaches. Using MASCOT we applied a new time-dependent GLM to uncover the underlying factors behind H9N2 spread. We curated a rich set of time-series predictors including annual international live poultry trade and national poultry production figures. This time-dependent phylodynamic prediction model was compared to commonly employed time-independent alternatives. Additionally the time-dependent MASCOT model allowed for the estimation of viral effective sub-population sizes and their changes through time and these effective population dynamics within each country were predicted by a GLM. International annual poultry trade is a strongly supported predictor of virus migration rates. There was also strong support for geographic proximity as a predictor of migration rate in all GLMs investigated. In time-dependent MASCOT models, national poultry production was also identified as a predictor of virus genetic diversity through time and this signal was obvious in mainland China and Bangladesh. Our application of a recently introduced time-dependent GLM predictors integrated rich time-series data in Bayesian phylodynamic prediction. We demonstrated the contribution of poultry trade and geographic proximity (potentially unheralded wild bird movements) to avian influenza spread in Asia. To gain a better understanding of the drivers of H9N2 spread, we suggest increased surveillance of the H9N2 virus in countries that are currently under-sampled as well as in wild bird populations in the most affected countries.Author summaryWhat drives the geographic dispersal and genetic diversity of H9N2 avian influenza virus in Asia? We used two model-based approaches, DTA and MASCOT, to reconstruct the phylogeographic dynamics of the virus. Further, multiple potential predictors were used to inform the virus spread and population dynamics by GLMs. Here, we maximised the power of time-series predictors in Bayesian phylodynamic prediction. For the first time, we were able to quantify the contribution of both time-series and constant predictors to both migration rates and effective population sizes in a structured population. We identified a positive association of international poultry trade and national poultry production time-series with virus migration rates and effective population sizes respectively. We also identify geographic proximity as a strongly supported driver to virus migration rates and this points to the potential role of wild bird populations in virus dispersal across countries. Our study is a practical exemplar of the use of temporal information in predictors to model heterogeneous spatial diffusion and population dynamic processes and provides direction to H9N2 control efforts in Asia.

scholarly journals Avian influenza surveillance in wild birds using sentinel ducks

2020 ◽  
Vol 29 (1) ◽  
pp. 3-8
Author(s):  
Bayarmagnai Davganyam ◽  
Nyamsuren Otgontogtokh ◽  
Baljidmaa Batmunkh ◽  
Davaasuren Nergui ◽  
Ariunaa Tserendorj ◽  
...  
Keyword(s):  
Avian Influenza ◽  
Wild Bird ◽  
Sentinel Surveillance ◽  
Wild Birds ◽  
Influenza Surveillance ◽  
Serum Samples ◽  
Bird Populations ◽  
Bird Habitat ◽  
Insulated Isothermal Pcr ◽  
H5n1 Hpai

We conducted active surveillance for avian influenza virus using sentinel ducks in central region of Mongolia (Khunt lake Saikhan soum, Bulgan province) that major wild bird habitat and outbreak site of H5N1 HPAI in wild birds in Mongolia from 2005 to 2011. Total of 39/104 (37,5%) samples were positive by insulated isothermal PCR (iiPCR) and 42/104 (40,38%) swab samples were positive by real time PCR (qPCR). In addition, AIV antibody detected in 35/104 (33,65%) serum samples tested by AIV NP ELISA kit. These results indicated that sentinel surveillance using domestic birds could be an effective method for avian pathogens including influenza in Mongolia. Enhanced sentinel surveillance in wild bird populations in Mongolia is therefore crucial for the understanding of global AIV transmission and epidemiology. Шувууны томуугийн тандах судалгаанд туршуул шувуу (Sentinel bird) байршуулах арга ашигласан дүнгээс Бид шувууны томуугийн тандах судалгаанд туршуул шувуу байршуулах арга зүйг ашиглах боломжийг судлах зорилгоор урьдчилсан туршилтыг 2019 оны 7-10 сард Булган аймгийн Сайхан сумын Хунт нууранд хийж гүйцэтгэв. Хунт нуур нь олон тооны нүүдлийн усны шувууд зусах болон дайрч өнгөрдөг ач холбогдолтой цэг бөгөөд 2005-2011 онд өндөр хоруу чанартай шувууны томуугийн (HPAI) A/H5N1 дэд хэвшлийн вирус илэрч байсан. Шувуунаас авсан арчдасны зарим дээжийг insulated isothermal PCR (iiPCR)-р шинжлэхэд 39/104 (37,5%), дээж эерэг, бүх дээжийг PCR (qPCR)-р шинжлэхэд 42/104 (40,38%) нь дээж эерэг дүн үзүүлсэн. Харин ийлдсэнд шувууны томуугийн эсрэг бием илрүүлэх ELISA-ийн шинжилгээгээр  35/104 (33,65%) дээжинд  эсрэг бием илэрсэн. Иймд энэ арга зүйг Монгол орны нөхцөлд тохируулан сайжруулж шувууны томуугийн үүсгэгчийг илрүүлэхэд ашиглах нь уг өвчний эпидемиологийн байдлыг танин мэдэхэд чухал ач холбогдолтой  юм. Түлхүүр үг: нугас, вирус, дархлаа, эпидемиологи, тархалт, ПГУ (Полимеразан  гинжин урвал)

scholarly journals Novel real-time PCR-based patho- and phylotyping of potentially zoonotic avian influenza A subtype H5 viruses at risk of incursion into Europe in 2017

2017 ◽  
Vol 22 (1) ◽  
Author(s):  
Mahmoud M Naguib ◽  
Annika Graaf ◽  
Andrea Fortin ◽  
Christine Luttermann ◽  
Ulrich Wernery ◽  
...  
Keyword(s):  
Avian Influenza ◽  
Real Time ◽  
Influenza A ◽  
Wild Bird ◽  
Reaction Times ◽  
Highly Pathogenic ◽  
Bird Populations ◽  
Western Africa ◽  
Speed Up ◽  
Development And Validation

Since November 2016, Europe witnesses another wave of incursion of highly pathogenic avian influenza (HPAI) A(H5) viruses of the Asian origin goose/Guangdong (gs/GD) lineage. Infections with H5 viruses of clade 2.3.4.4b affect wild bird and poultry populations. H5 viruses of clades 2.2, 2.3.1.2c and 2.3.4.4a were detected previously in Europe in 2006, 2010 and 2014. Clades 2.2.1.2 and 2.3.2.1.c are endemic in Egypt and Western Africa, respectively and have caused human fatalities. Evidence exists of their co-circulation in the Middle East. Subtype H5 viruses of low pathogenicity (LPAI) are endemic in migratory wild bird populations. They potentially mutate into highly pathogenic phenotypes following transmission into poultry holdings. However, to date only the gs/GD H5 lineage had an impact on human health. Rapid and specific diagnosis marks the cornerstone for control and eradication of HPAI virus incursions. We present the development and validation of five real-time RT-PCR assays (RT-qPCR) that allow sequencing-independent pathotype and clade-specific distinction of major gs/GD HPAI H5 virus clades and of Eurasian LPAI viruses currently circulating. Together with an influenza A virus-generic RT-qPCR, the assays significantly speed up time-to-diagnosis and reduce reaction times in a OneHealth approach of curbing the spread of gs/GD HPAI viruses.

scholarly journals Risk assessment of Avian Influenza and Newcastle disease viruses exposure from peridomestic wild birds in a conservation breeding site in the United Arab Emirates

2021 ◽  
Author(s):  
Julien Hirschinger ◽  
Timothée Vergne ◽  
Tifenn Corre ◽  
Yves Hingrat ◽  
Jean-Luc Guerin ◽  
...  
Keyword(s):  
Avian Influenza ◽  
United Arab Emirates ◽  
Newcastle Disease ◽  
Wild Bird ◽  
Breeding Site ◽  
Wild Birds ◽  
Prevalence Survey ◽  
Breeding Sites ◽  
Bird Populations ◽  
Conservation Breeding

Worldwide, wild birds are frequently suspected to be involved in the occurrence of outbreaks in captive-bred birds although proofs are lacking and most of the dedicated studies are insufficiently conclusive to confirm or characterize the roles of wild birds in such outbreaks. The aim of this study was to assess and compare, for the most prevalent peridomestic wild birds, the different exposure routes for Avian Influenza and Newcastle disease viruses in conservation breeding sites of Houbara bustards in the United Arab Emirates. To do so, we considered all of the potential pathways by which captive bustards could be exposed to Avian Influenza and Newcastle disease viruses by wild birds, and ran a comparative study of the likelihood of exposure via each of the pathways considered. We merged data from an ecological study dedicated to local wild bird communities with an analysis of the contacts between wild birds and captive bustards and with a prevalence survey of AIV and NDV in wild bird populations. We also extracted data from an extensive review of the scientific literature and by the elicitation of expert opinion. Overall, this analysis highlighted that captive bustards had a high risk of being exposed to pathogens by wild birds. This risk was higher for Newcastle disease virus than Avian influenza virus, and House sparrows represented the riskiest species for the transmission of both viruses through indirect exposure from consumption of water contaminated from the faeces of an infectious bird that got inside the aviary. Thus, this analysis reveals that wild peridomestic birds may play a role in the transmission of avian pathogens to captive bred birds. These results also reaffirm the need to implement sanitary measures to limit contacts between wild and captive birds and highlight priority targets for a thoughtful and efficient sanitary management strategy.

scholarly journals Distinguishing gene flow between malaria parasite populations

2021 ◽  
Author(s):  
Tyler Steven Brown ◽  
Aimee R. Taylor ◽  
Olufunmilayo Arogbokun ◽  
Caroline O. Buckee ◽  
Hsiao-Han Chang
Keyword(s):  
Gene Flow ◽  
Malaria Parasite ◽  
Sequence Data ◽  
Simulated Data ◽  
Whole Genome Sequence ◽  
Effective Population ◽  
Migration Rates ◽  
Population Sizes ◽  
And Migration ◽  
Parasite Populations

Measuring gene flow between malaria parasite populations in different geographic locations can provide strategic information for malaria control interventions. Multiple important questions pertaining to the design of such studies remain unanswered, limiting efforts to operationalize genomic surveillance tools for routine public health use. This report evaluates numerically the ability to distinguish different levels of gene flow between malaria populations, using different amounts of real and simulated data, where data are simulated using parameters that approximate different epidemiological conditions. Specifically, using Plasmodium falciparum  whole genome sequence data and sequence data simulated for a metapopulation with different migration rates and effective population sizes, we compare two estimators of gene flow, explore the number of genetic markers and number of individuals required to reliably rank highly connected locations, and describe how these thresholds change given different effective population sizes and migration rates. Our results have implications for the design and implementation of malaria genomic surveillance efforts.

scholarly journals Maximum-Likelihood Estimation of Migration Rates and Effective Population Numbers in Two Populations Using a Coalescent Approach

Genetics ◽  
1999 ◽  
Vol 152 (2) ◽  
pp. 763-773 ◽  
Author(s):  
Peter Beerli ◽  
Joseph Felsenstein
Keyword(s):  
Maximum Likelihood ◽  
Mutation Rate ◽  
Likelihood Estimation ◽  
Effective Population ◽  
Migration Rates ◽  
Coalescent Approach ◽  
Population Sizes ◽  
Two Populations ◽  
Better Than ◽  
Population Numbers

Abstract A new method for the estimation of migration rates and effective population sizes is described. It uses a maximum-likelihood framework based on coalescence theory. The parameters are estimated by Metropolis-Hastings importance sampling. In a two-population model this method estimates four parameters: the effective population size and the immigration rate for each population relative to the mutation rate. Summarizing over loci can be done by assuming either that the mutation rate is the same for all loci or that the mutation rates are gamma distributed among loci but the same for all sites of a locus. The estimates are as good as or better than those from an optimized FST-based measure. The program is available on the World Wide Web at http://evolution.genetics.washington.edu/lamarc.html/.

scholarly journals Results of scientific expedition to natural biotopes of the Republic of Tyva in 2019 with the purpose of infectious disease monitoring in wild bird populations

2020 ◽  
pp. 83-88
Author(s):  
M. S. Volkov ◽  
V. N. Irza ◽  
A. V. Varkentin ◽  
S. V. Rogolyov ◽  
A. V. Andriyasov
Keyword(s):  
Avian Influenza ◽  
Wild Bird ◽  
Migratory Birds ◽  
Virus Genome ◽  
Wild Birds ◽  
Laboratory Diagnostics ◽  
Active Monitoring ◽  
Bird Populations ◽  
Two Samples ◽  
The Republic

The results of the scientific expedition to Tere Khol and Uvs Nuur Lakes in the Republic of Tyva with the purpose of active monitoring of highly dangerous diseases in wild migratory waterfowl and epidemic analysis of these biotope water areas are presented in the paper. The Uvs Nuur Lake is a kind of an indicator for avian influenza introduction to the Russian Federation, because this is the resting and nesting area for many migratory wild birds during the period of mass migrations from Central and South-East Asian countries. In the process of active monitoring the complete autopsy of bird carcasses with description of organs and systems and sampling for laboratory diagnostics were performed. Droppings (pooled samples), parts of internal organs from dead and shot birds, blood (if possible) served as biological and pathological material for testing. While sampling, species were identified using an ornithological guide. The autopsy of dead waterfowl and birds shot for diagnostic purposes demonstrated a high worm burden of nematodes and cestodes. Two samples from European herring gulls were positive for avian influenza type A virus genome and subtype H13N6 was identified in one of them. Avian paramyxovirus serotype 1 (APMV-1), the agent of Newcastle disease, was found in one sample from gulls. The lakes of the Republic of Tyva are the most significant sites for sampling of biological material from wild birds, as the primary detection of highly pathogenic avian influenza virus in this territory is a serious signal of potential further virus spread and a precursor to a probable epizooty. Notwithstanding the absence of AIV very virulent isolate detections in wild bird populations the middle term prognosis for 2020 can be designated as cautious, as the avian influenza epidemic situation is deteriorating globally, especially in the European countries, and the threat of the virus introduction to the Russian territory with migratory birds still exists.

scholarly journals Inferring time-dependent migration and coalescence patterns from genetic sequence and predictor data in structured populations

2019 ◽  
Vol 5 (2) ◽  
Author(s):  
Nicola F Müller ◽  
Gytis Dudas ◽  
Tanja Stadler
Keyword(s):  
Population Dynamics ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Structured Populations ◽  
Model Parameters ◽  
Effective Population ◽  
Genetic Sequence ◽  
Migration Rates ◽  
Population Sizes ◽  
Structured Coalescent

Abstract Population dynamics can be inferred from genetic sequence data by using phylodynamic methods. These methods typically quantify the dynamics in unstructured populations or assume migration rates and effective population sizes to be constant through time in structured populations. When considering rates to vary through time in structured populations, the number of parameters to infer increases rapidly and the available data might not be sufficient to inform these. Additionally, it is often of interest to know what predicts these parameters rather than knowing the parameters themselves. Here, we introduce a method to  infer the predictors for time-varying migration rates and effective population sizes by using a generalized linear model (GLM) approach under the marginal approximation of the structured coalescent. Using simulations, we show that our approach is able to reliably infer the model parameters and its predictors from phylogenetic trees. Furthermore, when simulating trees under the structured coalescent, we show that our new approach outperforms the discrete trait GLM model. We then apply our framework to a previously described Ebola virus dataset, where we infer the parameters and its predictors from genome sequences while accounting for phylogenetic uncertainty. We infer weekly cases to be the strongest predictor for effective population size and geographic distance the strongest predictor for migration. This approach is implemented as part of the BEAST2 package MASCOT, which allows us to jointly infer population dynamics, i.e. the parameters and predictors, within structured populations, the phylogenetic tree, and evolutionary parameters.

scholarly journals Multiple gene segments are associated with enhanced virulence of clade 2.3.4.4 H5N8 highly pathogenic avian influenza virus in mallards

2021 ◽  
Author(s):  
Christina M. Leyson ◽  
Sungsu Youk ◽  
Helena L. Ferreira ◽  
David L. Suarez ◽  
Mary Pantin-Jackwood
Keyword(s):  
Avian Influenza ◽  
High Mortality ◽  
Wild Bird ◽  
Highly Pathogenic Avian Influenza ◽  
Morbidity And Mortality ◽  
Highly Pathogenic ◽  
Bird Populations ◽  
Pathogenic Avian Influenza ◽  
Single Segment ◽  
H5n8 Virus

Highly pathogenic avian influenza (HPAI) viruses from the H5Nx Goose/Guangdong/96 lineage continue to cause outbreaks in domestic and wild bird populations. Two distinct genetic groups of H5N8 HPAI viruses, HA clades 2.3.4.4A and 2.3.4.4B, caused intercontinental outbreaks in 2014-2015 and 2016-2017 respectively. Experimental infections using viruses from these outbreaks demonstrated a marked difference in virulence in mallards, with the H5N8 virus from 2014 causing mild clinical disease and the 2016 H5N8 virus causing high mortality. To assess which gene segments are associated with enhanced virulence of H5N8 HPAI viruses in mallards, we generated reassortant viruses with 2014 and 2016 viruses. For single-segment reassortants in the genetic backbone of the 2016 virus, pathogenesis experiments in mallards revealed that morbidity and mortality were reduced for all eight single-segment reassortants compared to the parental 2016 virus, with significant reductions in mortality observed with the PB2, NP, and M reassortants. No differences in morbidity and mortality were observed with reassortants that either have the polymerase complex segments or the HA and NA segments of the 2016 virus in the genetic backbone of the 2014 virus. In vitro assays showed that the NP and PA segments of the 2014 virus lowered polymerase activity when combined with the polymerase complex segments of the 2016 virus. Furthermore, the M segment of the 2016 H5N8 virus was linked to filamentous virion morphology. Phylogenetic analyses demonstrated that gene segments related to the more virulent 2016 H5N8 virus have persisted in the contemporary H5Nx HPAI gene pool until 2020. Importance Outbreaks of H5Nx highly pathogenic avian influenza (HPAI) viruses from the Goose/Guangdong/96 lineage continue to occur in many countries and have resulted in substantial impact on wild birds and poultry. Epidemiological evidence has shown that wild waterfowl play a major role in the spread of these viruses. While HPAI virus infection in gallinaceous species causes high mortality, a wide range of disease outcomes have been observed in waterfowl species. In this study, we examined which gene segments contribute to severe disease in mallards infected with H5N8 HPAI viruses. No virus gene was solely responsible for attenuating the high virulence of a 2016 H5N8 virus, but the PB2, NP, and M segments significantly reduced mortality. The findings herein advance our knowledge on the pathobiology of avian influenza viruses in waterfowl and has potential implications in the ecology and epidemiology of H5Nx HPAI in wild bird populations.

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