scholarly journals Full Genomic Sequences of H5N1 Highly Pathogenic Avian Influenza Virus in Human Autopsy Specimens Reveal Genetic Variability and Adaptive Changes for Growth in MDCK Cell Cultures

2021 ◽  
Vol 2021 ◽  
pp. 1-13
Author(s):  
Kantima Sangsiriwut ◽  
Pirom Noisumdaeng ◽  
Mongkol Uiprasertkul ◽  
Jarunee Prasertsopon ◽  
Sunchai Payungporn ◽  
...  
Keyword(s):  
Amino Acid ◽  
Avian Influenza ◽  
Highly Pathogenic Avian Influenza ◽  
Mdck Cells ◽  
Amino Acid Residues ◽  
Highly Pathogenic ◽  
Viral Genomes ◽  
Pathogenic Avian Influenza ◽  
Autopsy Specimens ◽  
Virus Isolates

The entire H5N1 highly pathogenic avian influenza viral genomes were identified in the frozen autopsy specimens: the trachea, lung, colon, and intestinal feces from a patient who died of the disease in 2006. Phylogenetic analysis of the viral genomes showed that these viruses belonged to clade 1 and were the reassortants generated from the reassortment of the viruses within the same clade. The sequencing data from the autopsy specimens revealed at least 8 quasispecies of the H5N1 viruses across all 4 specimen types. These sequences were compared to those derived from the virus isolates grown in Madin Darby canine kidney (MDCK) cells. The virus isolates from the trachea, lung, and fecal specimens showed 27 nucleotide substitutions, leading to the changes of 18 amino acid residues. However, there was no change in the amino acid residues that determined the viral virulence. The changes were more commonly observed in the lung, particularly in the HA and NA genes. Our study suggested that the adaptation changes for the viral fitness to survive in a new host species (MDCK cells) might involve many genes, for example, the amino acid substitution 177G or 177W adjacent to the receptor-binding residues in the HA1 globular head and the substitution M315I in PB2. However, a mutation changes near the receptor binding domain may play an important role in determining the cell tropism and is needed to be further explored.

scholarly journals Molecular analysis of highly pathogenic avian influenza virus of subtype H5N1 isolated from wild birds and mammals in northern Germany

2007 ◽  
Vol 88 (2) ◽  
pp. 554-558 ◽  
Author(s):  
Siegfried Weber ◽  
Timm Harder ◽  
Elke Starick ◽  
Martin Beer ◽  
Ortrud Werner ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Amino Acid ◽  
Avian Influenza ◽  
Avian Influenza Virus ◽  
Wild Bird ◽  
Highly Pathogenic Avian Influenza ◽  
Highly Pathogenic ◽  
Pathogenic Avian Influenza ◽  
H5n1 Isolate ◽  
Pathogenic Avian Influenza Virus

Analysis of the full-length sequences of all eight segments of the German wild-bird H5N1 highly pathogenic avian influenza virus index isolate, A/Cygnus cygnus/Germany/R65/2006, and an H5N1 isolate from a cat (A/cat/Germany/R606/2006) obtained during an outbreak in February 2006 revealed a very high similarity between these two sequences. One amino acid substitution in the PA gene, encoding a protein involved in virus RNA replication, and one amino acid substitution in the haemagglutinin (HA) protein were observed. Phylogenetic analyses of the HA and neuraminidase nucleotide sequences showed that avian influenza H5N1 isolates from the Astrakhan region located in southern Russia were the closest relatives. Reassortment events could be excluded in comparison with other ‘Qinghai-like’ H5N1 viruses. In addition, an H5N1 isolate originating from a single outbreak in poultry in Germany was found to be related closely to the H5N1 viruses circulating at that time in the wild-bird population.

scholarly journals The Emergence of H7N7 Highly Pathogenic Avian Influenza Virus from Low Pathogenicity Avian Influenza Virus Using an in ovo Embryo Culture Model

Viruses ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 920
Author(s):  
Amanda Seekings ◽  
Wendy Howard ◽  
Alejandro Nuñéz ◽  
Marek Slomka ◽  
Ashley Banyard ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Amino Acid ◽  
Avian Influenza ◽  
Avian Influenza Virus ◽  
Cleavage Site ◽  
Highly Pathogenic Avian Influenza ◽  
Basic Amino Acid ◽  
Highly Pathogenic ◽  
Pathogenic Avian Influenza ◽  
Pathogenic Avian Influenza Virus

Outbreaks of highly pathogenic avian influenza virus (HPAIV) often result in the infection of millions of poultry, causing up to 100% mortality. HPAIV has been shown to emerge from low pathogenicity avian influenza virus (LPAIV) in field outbreaks. Direct evidence for the emergence of H7N7 HPAIV from a LPAIV precursor with a rare di-basic cleavage site (DBCS) was identified in the UK in 2008. The DBCS contained an additional basic amino acid compared to commonly circulating LPAIVs that harbor a single-basic amino acid at the cleavage site (SBCS). Using reverse genetics, outbreak HPAIVs were rescued with a DBCS (H7N7DB), as seen in the LPAIV precursor or an SBCS representative of common H7 LPAIVs (H7N7SB). Passage of H7N7DB in chicken embryo tissues showed spontaneous evolution to a HPAIV. In contrast, deep sequencing of extracts from embryo tissues in which H7N7SB was serially passaged showed retention of the LPAIV genotype. Thus, in chicken embryos, an H7N7 virus containing a DBCS appears naturally unstable, enabling rapid evolution to HPAIV. Evaluation in embryo tissue presents a useful approach to study AIV evolution and allows a laboratory-based dissection of molecular mechanisms behind the emergence of HPAIV.

scholarly journals Genetic analysis of nucleotide sequences of neuraminidase gene of highly pathogenic avian influenza A/H5N8 virus isolates recovered in the Russian Federation in 2020

2021 ◽  
pp. 301-307
Author(s):  
P. B. Akshalova ◽  
N. G. Zinyakov ◽  
A. V. Andriyasov ◽  
P. D. Zhestkov ◽  
Z. B. Nikonova ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Influenza Virus ◽  
Avian Influenza ◽  
Russian Federation ◽  
Highly Pathogenic Avian Influenza ◽  
Nucleotide Sequences ◽  
Highly Pathogenic ◽  
Pathogenic Avian Influenza ◽  
The Russian Federation ◽  
Virus Isolates

Avian influenza is a highly dangerous viral disease that causes huge economic damage to poultry farming. Currently, highly virulent influenza virus with N8 neur- aminidase subtype is quite often detected in populations of domestic and wild birds in various countries of the world. The article provides data on complete nucleotide sequences of the neuraminidase gene of highly pathogenic avian influenza virus isolates recovered in the second half of 2020 from pathological material received from four regions of the Russian Federation. The conducted research showed that the subtype of the isolated virus was N8. According to the phylogenetic analysis, isolates of N8 virus belong to group 8C.4. During the phylogenetic analysis of the neuraminidase, we also took into account data on hemagglutinin classification, according to which H5N8 virus isolates belong to a widespread clade 2.3.4.4. Viruses of the clade were first registered in 2010 in China and they have been circulating up to now. The paper also provides data of a comparative analysis of nucleotide sequences of the studied isolates and the isolates from the international GenBank and GISAID databases, recovered in other countries from 2007 to 2020. During the analysis of the amino acid sequence of the studied isolates, no substitutions were found in the positions that affect resistance to neuraminidase inhibitors. The complete nucleotide sequences of the neuraminidase gene of the avian influenza virus subtype N8 (isolates A/domestic goose/OMSK/1521-1/2020, A/duck/Chelyabinsk/1207-1/2020, A/duck/Saratov/1578-2/2020, A/goose/Tatarstan/1730-2/2020) are published in the international GenBank and GISAID databases. Based on the analysis of the nucleotide sequences of the studied isolates, the article shows gradual evolution of the N8 subtype virus.

scholarly journals Genetic diversification of H5N1 highly pathogenic avian influenza A virus during replication in wild ducks

2011 ◽  
Vol 92 (9) ◽  
pp. 2105-2110 ◽  
Author(s):  
Yohei Watanabe ◽  
Madiha S. Ibrahim ◽  
Hany F. Ellakany ◽  
Hatem S. Abd El-Hamid ◽  
Kazuyoshi Ikuta
Keyword(s):  
Amino Acid ◽  
Avian Influenza ◽  
Influenza A Virus ◽  
Influenza A ◽  
Highly Pathogenic Avian Influenza ◽  
Amino Acid Substitutions ◽  
Highly Pathogenic ◽  
Pathogenic Avian Influenza ◽  
Novel Variants ◽  
Avian Influenza A Virus

Highly pathogenic avian influenza A virus subtype H5N1 can potentially generate novel variants during replication of infected hosts. To determine which H5N1 variants predominate in wild birds, we determined the sequences of RT-PCR amplified viral genes from several organs of infected chickens and ducks from Egypt, where H5N1 outbreaks in birds are endemic. Comparison of the sequences in viruses from trachea, lung, brain and liver revealed diversification with different amino acid substitutions in different ducks, but no diversification in chickens. These specific amino acid substitutions were rare among viruses currently circulating in Egypt. In addition, the H5N1 variants showed distinct growth kinetics in duck, canine and human cells. Our findings suggested that ducks can generate H5N1 variants with novel amino acid substitutions that might serve as aetiological agents for new influenza virus outbreaks and epidemics.

scholarly journals Phylodynamic assessment of control measures for highly pathogenic avian influenza epidemics in France

2021 ◽  
Author(s):  
Debapriyo Chakraborty ◽  
Claire Guinat ◽  
Nicola Felix Müller ◽  
Francois-Xavier Briand ◽  
Mathieu Andraud ◽  
...  
Keyword(s):  
Avian Influenza ◽  
Large Scale ◽  
Highly Pathogenic Avian Influenza ◽  
Control Measures ◽  
Highly Pathogenic ◽  
Viral Genomes ◽  
Viral Spread ◽  
Pathogenic Avian Influenza ◽  
Pathogenic Avian Influenza Virus ◽  
Phylodynamic Analysis

Phylodynamic methods have successfully been used to describe viral spread history but their applications for assessing specific control measures are rare. In 2016-17, France experienced a devastating epidemic of a highly pathogenic avian influenza virus (H5N8 clade 2.3.4.4b). Using 196 viral genomes, we conducted a phylodynamic analysis combined with generalised linear model and showed that the large-scale preventive culling of ducks significantly reduced the viral spread between départements (French administrative division). We also found that the virus likely spread more frequently between départements that shared borders, but the spread was not linked to duck transport between départements. Duck transport within départements increased the within-département transmission intensity, although the association was weak. Together, these results indicated that the virus spread in short-distances, either between adjacent départements or within départements. Results also suggested that the restrictions on duck transport within départements might not have stopped the viral spread completely. Overall, by testing specific hypothesis related to different control measures, we demonstrated that phylodynamics methods are capable of investigating the impacts of control measures on viral spread.

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