Conserved secondary structures predicted within the 5′ packaging signal region of influenza A virus PB2 segment

Meta Gene ◽  
2018 ◽  
Vol 15 ◽  
pp. 75-79 ◽  
Author(s):  
Yuki Kobayashi ◽  
Oliver G. Pybus ◽  
Takuya Itou ◽  
Yoshiyuki Suzuki
Keyword(s):  
Influenza A Virus ◽  
Influenza A ◽  
Secondary Structures ◽  
Packaging Signal ◽  
Signal Region

scholarly journals vRNA-vRNA interactions in influenza A virus HA vRNA packaging

2020 ◽  
Author(s):  
Sho Miyamoto ◽  
Yukiko Muramoto ◽  
Keiko Shindo ◽  
Yoko Fujita ◽  
Takeshi Morikawa ◽  
...  
Keyword(s):  
Influenza A Virus ◽  
Influenza A ◽  
Influenza Viruses ◽  
Packaging Signal ◽  
Genome Packaging ◽  
Coding Regions ◽  
Signal Region ◽  
Rna Interaction ◽  
Negative Sense

AbstractThe genome of the influenza A virus is composed of eight single-stranded negative-sense RNA segments (vRNAs). The eight different vRNAs are selectively packaged into progeny virions. This process likely involves specific interactions among vRNAs via segment-specific packaging signals located in the 3’ and 5’ terminal coding regions of vRNAs. To identify vRNA(s) that interact with hemagglutinin (HA) vRNA during genome packaging, we generated a mutant virus, HA 5m2, which possessed five silent mutations in the 5’ packaging signal region of HA vRNA. The HA 5m2 virus had a specific defect in HA vRNA incorporation, which reduced the viral replication efficiency. After serial passaging in cells, the virus acquired additional mutations in the 5’ terminal packaging signal regions of both HA and PB2 vRNAs. These mutations contributed to recovery of viral growth and packaging efficiency of HA vRNA. A direct RNA-RNA interaction between the 5’ ends of HA and PB2 vRNAs was confirmed in vitro. Our results indicate that direct interactions of HA vRNA with PB2 vRNA via their packaging signal regions are important for selective genome packaging and enhance our knowledge on the emergence of pandemic influenza viruses through genetic reassortment.

scholarly journals Identification and targeting of a pan-genotypic influenza A virus RNA structure that mediates packaging and disease.

2021 ◽  
Author(s):  
Rachel J. Hagey ◽  
Menashe Elazar ◽  
Siqi Tian ◽  
Edward A. Pham ◽  
Wipapat Kladwang ◽  
...  
Keyword(s):  
Influenza A Virus ◽  
Rna Structure ◽  
Influenza A ◽  
Locked Nucleic Acid ◽  
Antiviral Resistance ◽  
Packaging Signal ◽  
Oseltamivir Carboxylate ◽  
Virus Rna ◽  
Different Strains

Currently approved anti-influenza drugs target viral proteins, are subtype limited, and are challenged by rising antiviral resistance. To overcome these limitations, we sought to identify a conserved essential RNA secondary structure within the genomic RNA predicted to have greater constraints on mutation in response to therapeutics targeting this structure. Here, we identified and genetically validated an RNA stemloop structure we termed PSL2, which serves as a packaging signal for genome segment PB2 and is highly conserved across influenza A virus (IAV) isolates. RNA structural modeling rationalized known packaging-defective mutations and allowed for predictive mutagenesis tests. Disrupting and compensating mutations of PSL2's structure give striking attenuation and restoration, respectively, of in vitro virus packaging and mortality in mice. Antisense Locked Nucleic Acid oligonucleotides (LNAs) designed against PSL2 dramatically inhibit IAV in vitro against viruses of different strains and subtypes, possess a high barrier to the development of antiviral resistance, and are equally effective against oseltamivir carboxylate-resistant virus. A single dose of LNA administered 3 days after, or 14 days before, a lethal IAV inoculum provides 100% survival. Moreover, such treatment led to the development of strong immunity to rechallenge with a ten-fold lethal inoculum. Together, these results have exciting implications for the development of a versatile novel class of antiviral therapeutics capable of prophylaxis, post-exposure treatment, and 'just-in-time' universal vaccination against all IAV strains, including drug-resistant pandemics.

scholarly journals Mutations designed to modify the NS gene mRNA secondary structure affect influenza A pathogenicity in vivo

2021 ◽  
Vol 8 (1) ◽  
pp. 1-9
Author(s):  
I. L. Baranovskaya ◽  
M. V. Sergeeva ◽  
A. S. Taraskin ◽  
A. A. Lozhkov ◽  
A. V. Vasin
Keyword(s):  
Secondary Structure ◽  
Viral Replication ◽  
Influenza A Virus ◽  
Messenger Rna ◽  
Influenza A ◽  
Early Stage ◽  
Secondary Structures ◽  
Mrna Secondary Structure ◽  
Splice Sites ◽  
Ns Gene

The influenza A virus genome consists of eight segments of negative-sense RNA that encode up to 18 proteins. During the process of viral replication, positive-sense (+)RNA (cRNA) or messenger RNA (mRNA) is synthesized. Today, there is only a partial understanding of the function of several secondary structures within vRNA and cRNA promoters, and splice sites in the M and NS genes. The most precise secondary structure of (+)RNA has been determined for the NS segment of influenza A virus.  The influenza A virus NS gene features two regions with a conserved mRNA secondary structure located near splice sites. Here, we compared 4 variants of the A/Puerto Rico/8/1934 strain featuring different combinations of secondary structures at the NS segment (+)RNA regions 82-148 and 497-564. We found that RNA structures did not affect viral replication in cell culture. However, one of the viruses demonstrated lower NS1 and NEP expression levels during early stage cell infection as well as reduced pathogenicity in mice compared to other variants. In particular, this virus is characterized by an RNA hairpin in the 82-148 region and a stable hairpin in the 497-564 region.

scholarly journals Identification of the 5′-Terminal Packaging Signal of the H1N1 Influenza A Virus Neuraminidase Segment at Single-Nucleotide Resolution

2021 ◽  
Vol 12 ◽  
Author(s):  
Erika Seshimo ◽  
Fumitaka Momose ◽  
Yuko Morikawa
Keyword(s):  
Influenza A Virus ◽  
Influenza A ◽  
Synonymous Codon ◽  
Gene Segment ◽  
H1n1 Influenza ◽  
Terminal Region ◽  
Selective Assembly ◽  
Wild Type ◽  
Packaging Signal ◽  
Nucleotide Resolution

The genome of the influenza A virus is an eight-segmented negative-strand RNA (vRNA). Progeny vRNAs replicated in the nucleus selectively assemble into a single set of eight different segments, probably in the cytoplasm, and are packaged into progeny virions at the cell membrane. In these processes, a region of approximately 100 nucleotides at both ends of each segment is thought to function as a selective assembly/packaging signal; however, the details of the mechanism, such as the required sequences, are still unknown. In this study, we focused on the 5′-terminus of the sixth neuraminidase gene segment vRNA (Seg.6) to identify the essential sequence for selective packaging. The 5′-terminal region of the A/Puerto Rico/8/34 strain Seg.6 was divided into seven regions of 15 nucleotides each from A to G, and mutations were introduced into each region by complementary base substitutions or synonymous codon substitutions. Mutant viruses were generated and compared for infectious titers, and the relative ratios of the eight segments packaged into virions were measured. We also ascertained whether mutant vRNA was eliminated by competitive packaging with wild-type vRNA. Mutations in the A–C regions reduced infectious titers and eliminated mutant vRNAs by competition with wild-type vRNA. Even under non-competitive conditions, the packaging efficiency of the A or B region mutant Seg.6 was reduced. Next, we designed an artificial vRNA with a 50-nucleotide duplication at the 5′-terminal region. Using this, a virus library was created by randomly replacing each region, which became an untranslated region (UTR), with complementary bases. After selecting proliferative viruses from the library, nine wild-type nucleotides in the A and B regions were identified as essential bases, and we found that these bases were highly conserved in Seg.6 vRNAs encoding the N1 subtype neuraminidase. From these results, we conclude that the identified bases function as the 5′-terminal packaging signal for the N1 subtype Seg.6 vRNA.

scholarly journals Packaging signal of influenza A virus

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Xiuli Li ◽  
Min Gu ◽  
Qinmei Zheng ◽  
Ruyi Gao ◽  
Xiufan Liu
Keyword(s):  
Influenza A Virus ◽  
Influenza A ◽  
Packaging Signal ◽  
Genome Packaging ◽  
Genetic Reassortment ◽  
A Genome ◽  
Virus Genotypes ◽  
Virus Packaging ◽  
Negative Sense ◽  
Packaging Signals

AbstractInfluenza A virus (IAV) contains a genome with eight single-stranded, negative-sense RNA segments that encode 17 proteins. During its assembly, all eight separate viral RNA (vRNA) segments are incorporated into virions in a selective manner. Evidence suggested that the highly selective genome packaging mechanism relies on RNA-RNA or protein-RNA interactions. The specific structures of each vRNA that contribute to mediating the packaging of the vRNA into virions have been described and identified as packaging signals. Abundant research indicated that sequences required for genome incorporation are not series and are varied among virus genotypes. The packaging signals play important roles in determining the virus replication, genome incorporation and genetic reassortment of influenza A virus. In this review, we discuss recent studies on influenza A virus packaging signals to provide an overview of their characteristics and functions.

scholarly journals Computational and molecular analysis of conserved influenza A virus RNA secondary structures involved in infectious virion production

RNA Biology ◽  
2016 ◽  
Vol 13 (9) ◽  
pp. 883-894 ◽  
Author(s):  
Yuki Kobayashi ◽  
Bernadeta Dadonaite ◽  
Neeltje van Doremalen ◽  
Yoshiyuki Suzuki ◽  
Wendy S. Barclay ◽  
...  
Keyword(s):  
Influenza A Virus ◽  
Molecular Analysis ◽  
Influenza A ◽  
Secondary Structures ◽  
Rna Secondary Structures ◽  
Infectious Virion ◽  
Virion Production ◽  
Virus Rna

scholarly journals Heterologous Packaging Signals on Segment 4, but Not Segment 6 or Segment 8, Limit Influenza A Virus Reassortment

2017 ◽  
Vol 91 (11) ◽  
Author(s):  
Maria C. White ◽  
John Steel ◽  
Anice C. Lowen
Keyword(s):  
Public Health ◽  
Influenza A Virus ◽  
Influenza A ◽  
Influenza A Viruses ◽  
Packaging Signal ◽  
Significant Preference ◽  
Virus Reassortment ◽  
Segment 8 ◽  
The Impact ◽  
Packaging Signals

ABSTRACT Influenza A virus (IAV) RNA packaging signals serve to direct the incorporation of IAV gene segments into virus particles, and this process is thought to be mediated by segment-segment interactions. These packaging signals are segment and strain specific, and as such, they have the potential to impact reassortment outcomes between different IAV strains. Our study aimed to quantify the impact of packaging signal mismatch on IAV reassortment using the human seasonal influenza A/Panama/2007/99 (H3N2) and pandemic influenza A/Netherlands/602/2009 (H1N1) viruses. Focusing on the three most divergent segments, we constructed pairs of viruses that encoded identical proteins but differed in the packaging signal regions on a single segment. We then evaluated the frequency with which segments carrying homologous versus heterologous packaging signals were incorporated into reassortant progeny viruses. We found that, when segment 4 (HA) of coinfecting parental viruses was modified, there was a significant preference for the segment containing matched packaging signals relative to the background of the virus. This preference was apparent even when the homologous HA constituted a minority of the HA segment population available in the cell for packaging. Conversely, when segment 6 (NA) or segment 8 (NS) carried modified packaging signals, there was no significant preference for homologous packaging signals. These data suggest that movement of NA and NS segments between the human H3N2 and H1N1 lineages is unlikely to be restricted by packaging signal mismatch, while movement of the HA segment would be more constrained. Our results indicate that the importance of packaging signals in IAV reassortment is segment dependent. IMPORTANCE Influenza A viruses (IAVs) can exchange genes through reassortment. This process contributes to both the highly diverse population of IAVs found in nature and the formation of novel epidemic and pandemic IAV strains. Our study sought to determine the extent to which IAV packaging signal divergence impacts reassortment between seasonal IAVs. Our knowledge in this area is lacking, and insight into the factors that influence IAV reassortment will inform and strengthen ongoing public health efforts to anticipate the emergence of new viruses. We found that the packaging signals on the HA segment, but not the NA or NS segments, restricted IAV reassortment. Thus, the packaging signals of the HA segment could be an important factor in determining the likelihood that two IAV strains of public health interest will undergo reassortment.

Antiviral effect of polyphenol-enriched extract of Rumex Acetosa L. against Influenza A virus

Planta Medica ◽  
2012 ◽  
Vol 78 (11) ◽  
Author(s):  
A Derksen ◽  
W Hafezi ◽  
A Hensel ◽  
J Kühn
Keyword(s):  
Influenza A Virus ◽  
Influenza A ◽  
Antiviral Effect ◽  
Rumex Acetosa
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