scholarly journals Phylogenomic analysis of Uganda influenza type-A viruses to assess their relatedness to the vaccine strains and other Africa viruses: a molecular epidemiology study.

2021 ◽  
Author(s):  
Grace Nabakooza ◽  
David Collins Owuor ◽  
Zaydah R. de Laurent ◽  
Nicholas Owor ◽  
John Timothy Kayiwa ◽  
...  
Keyword(s):  
Amino Acid ◽  
Matrix Protein ◽  
Genetic Relatedness ◽  
Type A ◽  
Influenza Viruses ◽  
Antigenic Drift ◽  
H3n2 Virus ◽  
Influenza Surveillance ◽  
Phylogenomic Analysis ◽  
Influenza Type

Background: Genetic characterisation of circulating influenza viruses is essential for vaccine selection and mitigation of viral transmission. The current scantiness of viral genomic data and underutilisation of advanced molecular analysis methods on influenza viruses circulating in Africa has limited their extensive study and representation in the global influenza ecology. We aimed to sequence influenza type-A viruses (IAVs) that previously circulated in Uganda and characterised their genetic relatedness to the vaccine viruses and publicly available Africa IAVs. Methods: This was an observational study nested to the Uganda national influenza surveillance programme. We used Next-generation sequencing to locally generate genomes from 116 A(H1N1)pdm09 and 118 A(H3N2) viruses collected between 2010 and 2018 from 7 districts across Uganda. A total of 206 hemagglutinin (HA), 207 neuraminidase (NA), and 213 matrix protein (MP) sequences were genetically compared to the WHO-recommended vaccines and other viruses isolated from Africa since 1994. Viral temporal and spatial divergence and circulating genetic clades were characterised using phylogenetic methods. Findings: We successfully generated gene sequences for 91.9% (215/234) viruses. Uganda A(H1N1)pdm09 and A(H3N2) virus HA, NA, and MP proteins had 96.36-99.09%, 96.49-99.39%, and 97.48-99.95% amino acid similarity, respectively, to vaccines recommended from 2010 through 2020. The local viruses incorporated amino acid substitutions (AAS) in their antigenic, receptor binding, and glycosylation sites each year causing them to antigenically drift away from vaccines. For seasons when vaccine formulations differed, Uganda IAV antigenic sites had 1-2 extra AAS relative to the Southern than Northern hemisphere vaccine viruses. All Uganda IAVs carried the adamantine-resistance marker S31N but not the neuraminidase inhibitor (NAI) resistance markers H274Y and H275Y. However, some A(H1N1)pdm09 viruses had permissive substitutions V234I, N369K, and V241I typical of NAI-resistant viruses. The 2017-2018 A(H1N1)pdm09 viruses belonged to global genetic clade 6B.1, while the A(H3N2) viruses isolated in 2017 belonged to clades 3C.2a and 3C.3a. Uganda IAVs obtained before 2016 clustered distinctly from other Africa viruses while later viruses mixed with other Africa, especially Kenya and Congo, and global viruses. Several unique viral lineages (bootstrap >90) persisted in Uganda and other countries for 1-3 years. Interpretation: The study reveals Uganda as part of the global influenza ecology with continuous importation, antigenic drift, and extensive local transmission of IAVs, presenting a potential risk of future outbreaks. For a country with limited health resources and where social distancing is not sustainable, viral prevention by vaccination should be prioritized. The notable viral diversity in Africa is a warning to countries to broaden and incorporate genome analysis in routine surveillance to monitor circulating and detect new viruses. This knowledge can inform virus selection for vaccine production and assist in developing cost-effective virus control strategies.

scholarly journals Analysis of influenza A virus reinfection in children in Japan during 1983–91

1995 ◽  
Vol 115 (3) ◽  
pp. 591-601 ◽  
Author(s):  
S. Nakajima ◽  
F. Nishikawa ◽  
K. Nakamura ◽  
K. Nakajima
Keyword(s):  
Amino Acid ◽  
Influenza A Virus ◽  
Influenza A ◽  
Haemagglutination Inhibition ◽  
Influenza Viruses ◽  
Antigenic Drift ◽  
H3n2 Virus ◽  
Influenza B ◽  
Influenza A H1n1 ◽  
Influenza H3n2

SummaryThe epidemiology of influenza A in Japan was studied during 1979–91 and viruses isolated from reinfections during 1983–91 were analysed, Of 2963 influenza viruses isolated during this period, 922 and 1006 were influenza A(H1N1) and A(H3N2) viruses respectively; the others were influenza B viruses. Influenza A(H1N1) and A(H3N2) caused 5 and 6 epidemics respectively, most accompanied by antigenic drift. Seventeen reinfections with H1N1 and 17 with H3N2 were detected during our study. The primary and reinfection strains isolated from 7 H1N1 and 10 H3N2 cases were studied by haemagglutination-inhibition, and amino acid and nucleotide sequences of the HA1 region of the haemagglutinin. Most of the primary and reinfection strains were antigenically and genetically similar to the epidemic viruses circulating at that time. However, in 4 out of 10 cases of reinfection with influenza H3N2 virus, reinfection strains were genetically different from the epidemic viruses.

scholarly journals Two amino acid residues in the matrix protein M1 contribute to the virulence difference of H5N1 avian influenza viruses in mice

Virology ◽  
2009 ◽  
Vol 384 (1) ◽  
pp. 28-32 ◽  
Author(s):  
Shufang Fan ◽  
Guohua Deng ◽  
Jiasheng Song ◽  
Guobin Tian ◽  
Yongbing Suo ◽  
...  
Keyword(s):  
Amino Acid ◽  
Avian Influenza ◽  
Matrix Protein ◽  
Influenza Viruses ◽  
Amino Acid Residues ◽  
Avian Influenza Viruses ◽  
H5n1 Avian Influenza ◽  
The Matrix ◽  
Matrix Protein M1

scholarly journals Molecular Characterization of Seasonal Influenza A and B from Hospitalized Patients in Thailand in 2018–2019

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 977
Author(s):  
Kobporn Boonnak ◽  
Chayasin Mansanguan ◽  
Dennis Schuerch ◽  
Usa Boonyuen ◽  
Hatairat Lerdsamran ◽  
...  
Keyword(s):  
Amino Acid ◽  
Influenza A ◽  
Seasonal Influenza ◽  
Influenza Viruses ◽  
Surface Proteins ◽  
Antigenic Drift ◽  
Influenza B ◽  
Receptor Binding Site ◽  
Antigenic Sites ◽  
Ha Protein

Influenza viruses continue to be a major public health threat due to the possible emergence of more virulent influenza virus strains resulting from dynamic changes in virus adaptability, consequent of functional mutations and antigenic drift in surface proteins, especially hemagglutinin (HA) and neuraminidase (NA). In this study, we describe the genetic and evolutionary characteristics of H1N1, H3N2, and influenza B strains detected in severe cases of seasonal influenza in Thailand from 2018 to 2019. We genetically characterized seven A/H1N1 isolates, seven A/H3N2 isolates, and six influenza B isolates. Five of the seven A/H1N1 viruses were found to belong to clade 6B.1 and were antigenically similar to A/Switzerland/3330/2017 (H1N1), whereas two isolates belonged to clade 6B.1A1 and clustered with A/Brisbane/02/2018 (H1N1). Interestingly, we observed additional mutations at antigenic sites (S91R, S181T, T202I) as well as a unique mutation at a receptor binding site (S200P). Three-dimensional (3D) protein structure analysis of hemagglutinin protein reveals that this unique mutation may lead to the altered binding of the HA protein to a sialic acid receptor. A/H3N2 isolates were found to belong to clade 3C.2a2 and 3C.2a1b, clustering with A/Switzerland/8060/2017 (H3N2) and A/South Australia/34/2019 (H3N2), respectively. Amino acid sequence analysis revealed 10 mutations at antigenic sites including T144A/I, T151K, Q213R, S214P, T176K, D69N, Q277R, N137K, N187K, and E78K/G. All influenza B isolates in this study belong to the Victoria lineage. Five out of six isolates belong to clade 1A3-DEL, which relate closely to B/Washington/02/2009, with one isolate lacking the three amino acid deletion on the HA segment at position K162, N163, and D164. In comparison to the B/Colorado/06/2017, which is the representative of influenza B Victoria lineage vaccine strain, these substitutions include G129D, G133R, K136E, and V180R for HA protein. Importantly, the susceptibility to oseltamivir of influenza B isolates, but not A/H1N1 and A/H3N2 isolates, were reduced as assessed by the phenotypic assay. This study demonstrates the importance of monitoring genetic variation in influenza viruses regarding how acquired mutations could be associated with an improved adaptability for efficient transmission.

scholarly journals In vivo anti-influenza virus activity of a zinc finger peptide.

1997 ◽  
Vol 41 (3) ◽  
pp. 687-692 ◽  
Author(s):  
A K Judd ◽  
A Sanchez ◽  
D J Bucher ◽  
J H Huffman ◽  
K Bailey ◽  
...  
Keyword(s):  
Amino Acids ◽  
Influenza Virus ◽  
Amino Acid ◽  
Virus Infection ◽  
Zinc Finger ◽  
Matrix Protein ◽  
H3n2 Virus ◽  
Arterial Oxygen ◽  
Treatment Schedule ◽  
Zinc Finger Peptide

Matrix protein (M1) is a major structural protein of influenza virus, and it inhibits its own polymerase. A 19-amino-acid peptide, corresponding to a zinc finger region of the M1 sequence of influenza virus strain A/PR/8/34 (H1N1), centered around amino acids 148 to 166, was synthesized. This peptide, designated peptide 6, represents a zinc finger which includes a 7-amino-acid loop or finger and a 4-amino-acid tail at the carboxyl terminus, in addition to the 8 amino acids involved in the coordination of Zn. Three experiments were run to evaluate the activity of peptide 6 on infections induced in mice by influenza A/PR/8/34 and A/Victoria/3/75 (H3N2) viruses. Intranasal (i.n.) treatment of the H1N1 virus infection with 30 or 60 mg/kg of body weight/day, three times daily for 5 days, beginning 4 h pre-or 8 h post-virus exposure, was effective in preventing death, reducing the arterial oxygen decline, and inhibiting lung consolidation. Virus titers in the lungs determined on day 5 were reduced by up to 1.5 log10 in treated groups, but considerable variation in the titers of the recovered virus was seen. The H3N2 virus infection was treated i.n. with 30, 60, or 120 mg of peptide 6/kg/day by using the above-mentioned delayed initiation treatment schedule, and similar protection was seen, although lung virus titers were not reduced in the day-5 assay. Peptide 6 was well tolerated at doses up to 60 mg/kg/day. This zinc finger peptide may provide a new class of antivirals effective against influenza virus.

scholarly journals Genotype patterns of contemporary reassorted H3N2 virus in US swine

2013 ◽  
Vol 94 (6) ◽  
pp. 1236-1241 ◽  
Author(s):  
Pravina Kitikoon ◽  
Martha I. Nelson ◽  
Mary Lea Killian ◽  
Tavis K. Anderson ◽  
Leo Koster ◽  
...  
Keyword(s):  
North American ◽  
Swine Influenza ◽  
Cross Reactivity ◽  
Influenza Viruses ◽  
Antigenic Drift ◽  
H3n2 Virus ◽  
Specific Subset ◽  
The Usa ◽  
Genome Scale ◽  
Viral Isolates

To understand the evolution of swine-origin H3N2v influenza viruses that have infected 320 humans in the USA since August 2011, we performed a phylogenetic analysis at a whole genome scale of North American swine influenza viruses (n  =  200). All viral isolates evolved from the prototypical North American H3 cluster 4 (c4), with evidence for further diversification into subclusters. At least ten distinct reassorted H3N2/pandemic H1N1 (rH3N2p) genotypes were identified in swine. Genotype 1 (G1) was most frequently detected in swine and all human H3N2v viruses clustered within a single G1 clade. These data suggest that the genetic requirements for transmission to humans may be restricted to a specific subset of swine viruses. Mutations at putative antigenic sites as well as reduced serological cross-reactivity among the H3 subclusters suggest antigenic drift of these contemporary viruses.

scholarly journals Antibody to influenza virus matrix protein detects a common antigen on the surface of cells infected with type A influenza viruses.

1977 ◽  
Vol 146 (3) ◽  
pp. 690-697 ◽  
Author(s):  
W E Biddison ◽  
P C Doherty ◽  
R G Webster
Keyword(s):  
Influenza Virus ◽  
Matrix Protein ◽  
Type A ◽  
Cross Reactivity ◽  
T Cell Response ◽  
Influenza Viruses ◽  
Cytotoxic T Cell ◽  
Target Cells ◽  
Common Antigen ◽  
Infected Cells

Antisera to the type-specific internal influenza virus matrix (M) protein of a type A influenza virus were produced in goats. In the presence of complement, anti-M serum was cytotoxic for target cells which were infected with a variety of serologically distinct type A influenza viruses, but did not react with type B influenza virus-infected cells. Absorption experiments indicated that anti-M serum detected a common antigen(s) on the surface of type A-infected cells. This serological cross-reactivity parallels the cross-reactivity observed for the cytotoxic T-cell response to type A viruses.

scholarly journals Serological studies of influenza viruses in pigs in Great Britain 1991–2

1995 ◽  
Vol 114 (3) ◽  
pp. 511-520 ◽  
Author(s):  
I. H. Brown ◽  
P. A. Harris ◽  
D. J. Alexander
Keyword(s):  
Great Britain ◽  
Influenza A ◽  
H1n1 Virus ◽  
Haemagglutination Inhibition ◽  
Influenza Viruses ◽  
Antigenic Drift ◽  
H3n2 Virus ◽  
Influenza B Virus ◽  
Influenza B ◽  
Influenza A Viruses

SUMMARYSamples from a sow serum bank representative of the pig population of Great Britain collected during 1991–2, were examined for antibodies to influenza A, B and C viruses, using viruses which had been isolated from a variety of hosts. For influenza A viruses there was evidence of the continued circulation of ‘classical swine’ H1N1 virus (26%) seroprevalence), and human H3N2 viruses (39%) which are antigenically most closely-related to A/Port Chalmers/1/73 virus. In addition antibodies were detected to A/swine/England/201635/92 (8%), a strain of H3N2 virus which appears to have arisen by antigenic drift from conventional H3N2 swine strains. Specific antibodies (2%) were detected to an H1N1 virus (A/swine/England/195852/92) related most closely to avian H1N1 strains. In tests with human H1N1 and H3N2 viruses, excluding isolates from pigs, the highest seroprevalence was detected to the prevailing strains from the human population. Serological tests with avian H4 and H10, human H2, equine 1 and 2 influenza A viruses were all negative. Seven pigs seropositive by haemagglutination-inhibition, virus neutralization and immunoblotting assays for antibody to influenza B virus, were randomly distributed geographically suggesting that influenza B viruses may be transmitted to pigs but fail to spread. The seroprevalence to influenza C viruses was 9·9% indicating that these viruses are widespread in pigs. These results provide further evidence that the pig can be infected by a number of influenza viruses, some of which may have significance in the epidemiology of human influenza.

scholarly journals Evaluation of the immune status of birds and domestic and companion animals for the influenza A virus in Eastern Saudi Arabia

2020 ◽  
Vol 13 (9) ◽  
pp. 1966-1969
Author(s):  
Abdelmohsen Abduallah Alnaeem ◽  
Abdulkareem Al-Shabeb ◽  
Maged Gomaa Hemida
Keyword(s):  
Saudi Arabia ◽  
Influenza A ◽  
Large Scale ◽  
Immune Status ◽  
Companion Animals ◽  
Type A ◽  
Influenza Viruses ◽  
Enzyme Linked Immunosorbent Assay ◽  
Serum Samples ◽  
Influenza Type

Background and Aim: Influenza type A virus infections are still one of the major concerns for the health of humans and various species of domestic and companion animals. Wild birds play an essential role in the transmission cycle of the virus. Regularly monitoring the spread of the virus is a significant step in its mitigation. Highly pathogenic avian influenza viruses, including H5N1 and H5N8, have been reported in birds in the Arabian Peninsula, including Saudi Arabia, in recent decades. This study aimed to evaluate the immune status of birds, domestic and companion animals for Influenza type A virus in Eastern Province of Saudi Arabia. Materials and Methods: We collected 195 serum samples from dromedary camels, sheep, goats, native breed chickens, doves, dogs, and cats. We tested these sera for the presence of specific antibodies against influenza type A virus using a commercially available enzyme-linked immunosorbent assay. Results: Our results show that 4% of the tested samples had antibodies in sera, including some doves, chickens, and dogs. These data suggest exposure and seroconversion of these animals or birds to the influenza type A virus. Conclusion: The presence of antibodies against influenza type A virus in sera of some animals and birds without a previous vaccination history against the virus indicates a natural exposure history regarding this virus and seroconversion. Further large-scale molecular and epidemiological studies are needed to obtain a better understanding of the dynamics of influenza type A virus among various species of animals and birds.

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