scholarly journals Conserved Sequence Analysis of Influenza A Virus HA Segment and Its Application in Rapid Typing

Diagnostics ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1328
Author(s):  
Qianyu Lin ◽  
Xiang Ji ◽  
Feng Wu ◽  
Lan Ma
Keyword(s):  
Sequence Analysis ◽  
Influenza A Virus ◽  
Mutation Rate ◽  
Influenza A ◽  
High Specificity ◽  
High Mutation Rate ◽  
Conserved Sequences ◽  
Conserved Sequence ◽  
Searching Method

The high mutation rate of the influenza A virus hemagglutinin segment poses great challenges to its long-term effective testing and subtyping. Our conserved sequence searching method achieves high-specificity conserved sequences on H1–H9 subtypes. In addition, PCR experiments show that primers based on conserved sequences can be used in influenza A virus HA subtyping. Conserved sequence-based primers are expected to be long-term, effective subtyping tools for influenza A virus HA.

scholarly journals Large scale multiple sequence alignment of intraspecies samples: conserved sequence analysis of influenza A virus HA segment and its application in rapid typing

2020 ◽  
Author(s):  
Qianyu Lin ◽  
Xiang Ji ◽  
Feng Wu ◽  
Lan Ma
Keyword(s):  
Influenza A Virus ◽  
Influenza A ◽  
Large Scale ◽  
High Specificity ◽  
Multiple Sequence ◽  
Conserved Sequences ◽  
Conserved Sequence ◽  
Searching Method ◽  
Subtype H1

Background The high mutation rate of influenza A virus hemagglutinin segment brings great challenges to its long-term effective testing and subtyping. Method We analyzed the conserved sequences of hemagglutinin subtype H1-H9 by breadth first, and designed primers for HA subtyping based on conserved sequences. Results Our conserved sequence searching method get high specificity conserved sequences on H1-H9 subtypes respectively. And PCR experiments show that primers based on conserved sequences can be used in influenza A virus HA subtyping. Conclusions Conserved sequences based primers are expected to be the long-term effective influenza A virus HA subtyping tools.

scholarly journals The mutation rates and mutational bias of influenza A virus

2017 ◽  
Author(s):  
Matthew D. Pauly ◽  
Megan Procario ◽  
Adam S. Lauring
Keyword(s):  
Influenza Virus ◽  
Influenza A Virus ◽  
Mutation Rate ◽  
Influenza A ◽  
Rapid Evolution ◽  
Viral Fitness ◽  
High Mutation Rate ◽  
Mutation Rates ◽  
Mutational Bias ◽  
Neutral Mutations

AbstractInfluenza virus has a high mutation rate, and this low replicative fidelity contributes to its capacity for rapid evolution. Clonal sequencing and fluctuation tests have suggested that the mutation rate of influenza A virus is 7.1 × 10−6− 4.5 × 10−5substitutions per nucleotide per cell infection cycle and 2.7 × 10−6− 3.0 × 10−5substitutions per nucleotide per strand copied (s/n/r). However, sequencing assays are biased toward mutations with minimal impacts on viral fitness and fluctuation tests typically investigate only a subset of the twelve mutational classes. We developed a fluctuation test based on reversion to fluorescence in a set of virally encoded mutant green fluorescent proteins. This method allowed us to measure the rates of selectively neutral mutations representative of all 12 mutational classes in the context of an unstructured RNA. We measured an overall mutation rate of 1.8 × 10−4s/n/r for PR8 (H1N1) and 2.5 × 10−4s/n/r for Hong Kong 2014 (H3N2). The replication mode was linear. The mutation rates of these divergent strains are significantly higher than previous estimates and suggest that each replicated genome will have an average of 2-3 mutations. The viral mutational spectrum is heavily biased toward A to G and U to C transitions, resulting in a transition to transversion bias of 2.7 and 3.6 for the two strains. These mutation rates were relatively constant over a range of physiological temperatures. Our high-resolution analysis of influenza virus mutation rates will enable more refined models of its molecular evolution.SignificanceThe rapid evolution of influenza virus is a major problem in public health. A key factor driving this rapid evolution is the virus’ very high mutation rate. We developed a new method for measuring the rates of all 12 mutational classes in influenza virus, which eliminates some of the biases of existing assays. We find that the influenza virus mutation rate is much higher than previously reported and is consistent across two distinct strains and a range of temperatures. Our data suggest that influenza viruses replicate at their maximally tolerable mutation rates, highlighting both the virus’ evolutionary potential and its significant constraints.

scholarly journals Thin-section Computed Tomography Detects Long-term Pulmonary Sequelae 3 Years after Novel Influenza A Virus-associated Pneumonia

2015 ◽  
Vol 128 (7) ◽  
pp. 902-908 ◽  
Author(s):  
Zhi-Heng Xing ◽  
Xin Sun ◽  
Long Xu ◽  
Qi Wu ◽  
Li Li ◽  
...  
Keyword(s):  
Computed Tomography ◽  
Influenza A Virus ◽  
Thin Section ◽  
Influenza A ◽  
Novel Influenza A

scholarly journals Long-term variation in influenza A virus prevalence and subtype diversity in migratory mallards in northern Europe

2014 ◽  
Vol 281 (1781) ◽  
pp. 20140098 ◽  
Author(s):  
Neus Latorre-Margalef ◽  
Conny Tolf ◽  
Vladimir Grosbois ◽  
Alexis Avril ◽  
Daniel Bengtsson ◽  
...  
Keyword(s):  
Influenza A Virus ◽  
Influenza A ◽  
Herd Immunity ◽  
Stopover Site ◽  
Virus Prevalence ◽  
Early Autumn ◽  
Temporal Occurrence ◽  
Wildlife Populations ◽  
Pronounced Peak

Data on long-term circulation of pathogens in wildlife populations are seldom collected, and hence understanding of spatial–temporal variation in prevalence and genotypes is limited. Here, we analysed a long-term surveillance series on influenza A virus (IAV) in mallards collected at an important migratory stopover site from 2002 to 2010, and characterized seasonal dynamics in virus prevalence and subtype diversity. Prevalence dynamics were influenced by year, but retained a common pattern for all years whereby prevalence was low in spring and summer, but increased in early autumn with a first peak in August, and a second more pronounced peak during October–November. A total of 74 haemagglutinin (HA)/neuraminidase (NA) combinations were isolated, including all NA and most HA (H1–H12) subtypes. The most common subtype combinations were H4N6, H1N1, H2N3, H5N2, H6N2 and H11N9, and showed a clear linkage between specific HA and NA subtypes. Furthermore, there was a temporal structuring of subtypes within seasons based on HA phylogenetic relatedness. Dissimilar HA subtypes tended to have different temporal occurrence within seasons, where the subtypes that dominated in early autumn were rare in late autumn, and vice versa. This suggests that build-up of herd immunity affected IAV dynamics in this system.

scholarly journals Small Interfering RNA Targeting M2 Gene Induces Effective and Long Term Inhibition of Influenza A Virus Replication

PLoS ONE ◽  
2009 ◽  
Vol 4 (5) ◽  
pp. e5671 ◽  
Author(s):  
Hong-Yan Sui ◽  
Guang-Yu Zhao ◽  
Jian-Dong Huang ◽  
Dong-Yan Jin ◽  
Kwok-Yung Yuen ◽  
...  
Keyword(s):  
Influenza A Virus ◽  
Virus Replication ◽  
Small Interfering Rna ◽  
Influenza A ◽  
Rna Targeting ◽  
Interfering Rna

scholarly journals Long-Term Neuroinflammation Induced by Influenza A Virus Infection and the Impact on Hippocampal Neuron Morphology and Function

2018 ◽  
Vol 38 (12) ◽  
pp. 3060-3080 ◽  
Author(s):  
Shirin Hosseini ◽  
Esther Wilk ◽  
Kristin Michaelsen-Preusse ◽  
Ingo Gerhauser ◽  
Wolfgang Baumgärtner ◽  
...  
Keyword(s):  
Virus Infection ◽  
Influenza A Virus ◽  
Influenza A ◽  
Hippocampal Neuron ◽  
Neuron Morphology ◽  
Influenza A Virus Infection ◽  
And Function ◽  
The Impact

Sequence analysis of reassortants within H3N2 subtype influenza A virus circulated in Hong Kong, 2014–2017

2020 ◽  
Vol 33 ◽  
pp. 101510
Author(s):  
Liang Chen ◽  
Jiasheng Xiong ◽  
Li Peng ◽  
Pengfei Yang ◽  
Hao Yu ◽  
...  
Keyword(s):  
Hong Kong ◽  
Sequence Analysis ◽  
Influenza A Virus ◽  
Influenza A ◽  
H3n2 Subtype

Structure and sequence analysis of influenza A virus nucleoprotein

2009 ◽  
Vol 52 (5) ◽  
pp. 439-449 ◽  
Author(s):  
Andy Ka-Leung Ng ◽  
Jia-Huai Wang ◽  
Pang-Chui Shaw
Keyword(s):  
Sequence Analysis ◽  
Influenza A Virus ◽  
Influenza A

Characterization of a unique protein produced by influenza a virus recovered from a long-term persistent infection

Virology ◽  
1988 ◽  
Vol 166 (2) ◽  
pp. 620-623 ◽  
Author(s):  
William T. Lucas ◽  
Patricia Whitaker-Dowling ◽  
Christopher R. Kaifer ◽  
Julius S. Youngner
Keyword(s):  
Influenza A Virus ◽  
Persistent Infection ◽  
Influenza A ◽  
Unique Protein
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