Global and Local Persistence of Influenza A(H5N1) Virus

Li, Xianbin; Zhang, Zhong; AiLian, Yu; Ho, Simon Y. W.; Carr, Michael J.; Zheng, Wengang; Zhang, Yanzhou; Zhu, Chao‐Dong; Lei, Fumin; Shi, Weifeng

doi:10.3201/eid2008.130910

Cited by 42 publications

(52 citation statements)

References 38 publications

(63 reference statements)

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“…Mean rate (also named as μ) was used to compare the evolutionary rate [8,9] and Kappa (also named as κ) denotes the transition/transversion ratio. Both of them are important evolutionary parameters in several bioinformatics and evolutionary programs [10,11]. The estimate of tMRCA is often used to date the origin and transmission of a viral pathogen [7,12,13].…”

Section: Resultsmentioning

confidence: 99%

Non-coding regions of the Ebola virus genome contain indispensable phylogenetic and evolutionary information

Jiang

Zhang

Zhuang

et al. 2015

Sci. China Life Sci.

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We compared the numbers of nucleotide substitutions occurring in the non-coding regions and coding regions of Ebola virus genomes and found that non-coding regions contain indispensable phylogenetic and evolutionary information. The omission of genetic data from non-coding regions can lead to unreliable phylogenies and inaccurate estimates of evolutionary parameters. EBOV, Ebola Materials and methodsFull-length EBOV genomes identified from the 2014 West African outbreak (n=81; 78 from Sierra Leone and three from Guinea) and previously identified EBOV genomes (n=26) were downloaded from GenBank and aligned using ClustalOmega [2] (Table S1 in Supporting Information).The alignment was 18,960 bp in length.To gain insight into whether the nucleotide substitutions in the non-coding regions bear phylogenetic and evolutionary information, we compiled three different datasets, the full-length genome sequences of EBOV, concatenated coding regions, and the glycoprotein (GP) sequences. The GP protein of EBOV is responsible for receptor binding and fusion of the viral and cellular membranes. Recently, it has been reported to be able to mediate the level of certain microRNAs [3], which could be served as potential targets for Ebola drugs. Phylogenic analyses were performed using a Bayesian evolutionary analysis by sampling trees (Beast) approach [4], and 24 different combinations of molecular clock models (n=3) and coalescent models (n=8) were applied (Table S2 in Supporting Information). Fifty million steps were run and the first five million steps were removed as burn-in. Results obtained from different model combinations were compared using Bayes factor estimator of the marginal likelihood [5]. Maximum clade credibility trees were generated using TreeAnnotator v1.8 with a burn-in

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Section: Resultsmentioning

confidence: 99%

Non-coding regions of the Ebola virus genome contain indispensable phylogenetic and evolutionary information

Jiang

Zhang

Zhuang

et al. 2015

Sci. China Life Sci.

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“…Furthermore, Asia and North Africa's low temperature in winter with cold and dry weather (especially January and February) increase poultry outbreaks and H5N1 transmission, this lead increase of human infection. [15][16][17][18][19]. Increasing the incidence of human cases in Egypt in second decade and unique increase incidence since November 2014 [20][21][22], can be regarded to mixture of some factors, including lower public health awareness of risks in Egypt and seasonal factors like cold weather and possible longer survival of the viruses in the environment [23].…”

Section: Discussionmentioning

confidence: 99%

Epidemiological parameter changes of global Avian Influenza H5N1 over two decades, from 1997 to 2017

Haji

Babakir‐Mina

Gubari

2017

KJAR

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(n=143) respectively. Case fatality rates were 50.7%. In conclusion most cases were in second decade than first decade of (H5N1) outbreak, but death were more in first decade, Also most cases were in low temperature seasons and in very young children but death were more in adults. In first decade, morbidity were more in Asia countries like China, Vietnam, and Indonesia but in second decade, mortality were more in North Africa (Egypt). However, cases were more in Egypt than Indonesia but deaths were more in Indonesia. H5N1 virus must be currently studied and its controlling is highly requested.

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“…The emergence of Highly Pathogenic Avian Influenza (HPAI) H5N1 from the Asian continent has led to the adaptation, evolution and hence the re-emergence of a re-assortant causal virus in Africa, 1 first detected in Nigeria in 2006 2,3 and subsequently reported in other 11 African countries. 4 The rapid spread of HPAI H5N1 infection has led to the decimation of poultry population with negative attendant consequences on the sales of poultry and poultry products and economics of production.…”

Section: Introductionmentioning

confidence: 99%

Highly Pathogenic Avian Influenza H5N1 Persistence in Africa: Household Poultry Perspective & Public Health Implications

Gabriel

2017

JDVAR

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Abbreviations: HHP, house hold poultry; HPAI, highly pathogenic avian influenza; OIE, world organisation for animal health IntroductionThe emergence of Highly Pathogenic Avian Influenza (HPAI) H5N1 from the Asian continent has led to the adaptation, evolution and hence the re-emergence of a re-assortant causal virus in Africa, 1 first detected in Nigeria in 2006 2,3 and subsequently reported in other 11 African countries. 4 The rapid spread of HPAI H5N1 infection has led to the decimation of poultry population with negative attendant consequences on the sales of poultry and poultry products and economics of production.5-7 Due to its zoonotic potential and ability for re-assortment HPAI H5N1 remains a major threat to human health in Africa; so far, Egypt has the highest number of confirmed human cases and reported case fatality across the globe. 8,9 Analyses and comparative assessments of data of HPAI H5N1 outbreaks in poultry from [2006][2007][2008][2009][2010][2011][2012][2013][2014][2015][2016] (Table 1). 10,11 Household poultryThe predisposing factors to the perpetuation and persistence of HPAI H5N1 in Africa are inexhaustible; but among the important factors strongly believed to facilitate H5N1 persistence and spread is household poultry (HHP), otherwise referred to as backyard or traditional poultry; this constitute about 80% of poultry stocks made up largely of indigenous breeds and various species mixed in the same flock and reared especially by semi intensive or extensive husbandry methods. 12-14HHP has become a common practice in most countries of Africa, especially Nigeria and Egypt, because it involves the rearing of multispecies of poultry (duck, turkey, pigeon, quail and chicken) and other livestock (pig, cane rat, rabbit, goat etc.), in close proximity with human habitations; and characterised by poor biosecurity measures; which has been proven to be an indispensable tool for the mitigation of the spread of infections.15-18 A recent study conducted shows that epidemiological dynamics of HPAI has changed, with the origins of majority of the outbreaks pointing towards household/backyard poultry and associated with human cases of H5N1 infections, 19,20 this was further corroborated by OIE, 21 that HPAI H5N1 outbreaks in Nigeria between 2014-2016 has a significant number of the outbreaks in HHP. Public health implicationsDue to the poultry husbandry method practiced in Africa and the nearness of its operations to residential houses, as at the end of 2015, Egypt had the highest number of confirmed human cases (346) across the globe with 116 deaths recorded, second to Indonesia, (Table 2). 9It is worrisome to observe that since the first HPAI H5N1 outbreak in Egypt in 2006, the cases, death and case fatality rate in poultry and humans continue to increase unabated. 22-24 ConclusionThis is a reflection and a pointer towards the endemic state of HPAI H5N1 in Africa, and all these portend a bleak and elusive hope of controlling and eradicating the deadly viral sub-type in the continent of Africa. Therefor...

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Global and Local Persistence of Influenza A(H5N1) Virus

Cited by 42 publications

References 38 publications

Non-coding regions of the Ebola virus genome contain indispensable phylogenetic and evolutionary information

Non-coding regions of the Ebola virus genome contain indispensable phylogenetic and evolutionary information

Epidemiological parameter changes of global Avian Influenza H5N1 over two decades, from 1997 to 2017

Highly Pathogenic Avian Influenza H5N1 Persistence in Africa: Household Poultry Perspective & Public Health Implications

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