scholarly journals Next-Gen sequencing of novel pandemic swine flu [A(H1N1)pdm09] virus in India revealed novel mutations across the genome

2019 ◽  
Author(s):  
Paban Kumar Dash ◽  
Chitra Pattabiraman ◽  
Kundan Tandel ◽  
Shashi Sharma ◽  
Jyoti S Kumar ◽  
...  
Keyword(s):  
Influenza A ◽  
Viral Evolution ◽  
Influenza Viruses ◽  
Swine Flu ◽  
Outbreak Response ◽  
Novel Mutations ◽  
Phylogeographic Analysis ◽  
Influenza A H1n1 ◽  
Culture Isolate ◽  
Pandemic Flu

AbstractThe Influenza A H1N1 virus of 2009 was the first pandemic flu virus of the 21st century. Identifying the emergence of mutations in rapidly mutating Influenza viruses that allow increased transmission or confer resistance are invaluable to global outbreak response. Here we recovered 5 complete Influenza A genomes from 4 oropharygeal swabs and one cell culture isolate from a severe Indian outbreak of flu in early 2015. Multiple amino acids substitutions including those known to confer resistance to Oseltamivir and increased pathogenecity in mice were found in the Neuraminidase gene. Additional mutations both reported and novel were found throughout the genome compared to the vaccine strain (California/04/2009). All eight segments of the complete genomes were found to be genetically related to the 2009 pandemic strain, A(H1N1)pdm09 and belonging to the emerging genogroup 6B. This group was found to be of south East Asian origin by time scale phylogentic analysis. A phylogeographic analysis revealed 39 significant migration events among globally circulating viruses. This study is the first extensive complete genome and phylogeographic analysis of 2015 Indian A(H1N1) pdm09 viruses. We report several novel mutations in the 2015 Indian strains which need to be evaluated for effect on viral replication, transmission and resistance to therapy. The identification of mutant A(H1N1)pdm09 from India warrants continuous monitoring of viral evolution for implementation of suitable medical countermeasures.

scholarly journals Detection methods for influenza A H1N1 virus with special reference to biosensors: a review

2020 ◽  
Vol 40 (2) ◽  
Author(s):  
Ravina ◽  
Anita Dalal ◽  
Hari Mohan ◽  
Minakshi Prasad ◽  
C.S. Pundir
Keyword(s):  
Influenza A ◽  
Influenza Viruses ◽  
Detection Methods ◽  
Swine Flu ◽  
Dna Biosensors ◽  
Human Respiratory Tract ◽  
Influenza A H1n1 ◽  
Fast Multiplication ◽  
Specific Receptors ◽  
Antigen Antibody

Abstract H1N1 (Swine flu) is caused by influenza A virus, which is a member of Orthomyxoviridae family. Transmission of H1N1 occurs from human to human through air or sometimes from pigs to humans. The influenza virus has different RNA segments, which can reassert to make new virus strain with the possibility to create an outbreak in unimmunized people. Gene reassortment is a process through which new strains are emerging in pigs, as it has specific receptors for both human influenza and avian influenza viruses. H1N1 binds specifically with an α-2,6 glycosidic bond, which is present in human respiratory tract cells as well as in pigs. Considering the fact of fast multiplication of viruses inside the living cells, rapid detection methods need an hour. Currently, WHO recommended methods for the detection of swine flu include real-time PCR in specific testing centres that take 3–4 h. More recently, a number of methods such as Antigen–Antibody or RT-LAMP and DNA biosensors have also been developed that are rapid and more sensitive. This review describes the various challenges in the diagnosis of H1N1, and merits and demerits of conventional vis-à-vis latest methods with special emphasis on biosensors.

Fra usikkerhed om sygdom til usikkerhed om bivirkninger. En aktør-netværksteoretisk analyse af usikkerheder om influenza A (H1N1)

2013 ◽  
Vol 24 (2) ◽  
pp. 35-56
Author(s):  
Nina Blom Andersen ◽  
Pernille Almlund
Keyword(s):  
Influenza A ◽  
Medical Science ◽  
Swine Flu ◽  
Public Authorities ◽  
Actor Network ◽  
The Public ◽  
Health Authorities ◽  
Danish Health ◽  
Influenza A H1n1 ◽  
Pandemic Flu

I artiklen præsenteres en analyse af nogle af de kontroverser eller usikkerheder, der opstod i forbindelse med den pandemiske svineinfluenza, der spredte sig globalt i 2009. Med udgangspunkt i en aktør-netværksteoretisk analyse viser denne artikel, hvordan identifikationen af virus sætter gang i en lang række strategier for håndtering rundt omkring i verden, og hvordan der genereres en stigende kompleksitet i usikkerhederne, fra virus identificeres i Mexico og 9 måneder frem. Den situerede analyse viser også, hvordan der blev skabt kontroverser og relationer, der var særlige for Danmark. Analysen peger på, at kontroverserne var overskuelige i spørgsmålet om virus’ farlighed og i spørgsmålet om, hvordan man kan håndtere at smitten breder sig. Usikkerheden omkring den virus, der viste sig at være mild og ikke så dødelig, som først antaget, var overskuelige. Den vaccine, der indledningsvis blev anset for at være en måde at håndtere truslen om influenzaen på, blev til gengæld med tiden til en større usikkerhed og skabte mere komplekse kontroverser end influenzaen selv. Artiklen peger derfor bl.a. på, at myndigheders og lægevidenskabens håndtering af influenzaen er et eksempel på en hændelse, der udvikler sig til en socio-teknisk kontrovers. ENGELSK ABSTRACT: Nina Blom Andersen and Pernille Almlund: From Insecurity about Illness to Insecurity about Side-Effects: An Actor-Network Based Analysis of Insecurities Surrounding Influenza A (H1N1) This article analyses some of the controversies that emerged in relation to the swine flu epidemic that spread across the globe in 2009. Applying an actor- network analysis, we demonstrate how identification of the virus initiated several strategies for dealing with it globally. We also show how a growing complexity of controversies can be identified by the time the virus is detected in Mexico. However the analysis also reveals that the production of some of these controversies is specific in a Danish context. The analysis shows that it was possible for the Danish health authorities to deal with the controversies related to the threat of the virus and the controversies concerning minimizing the contagion. In other words, the uncertainty about the virus – milder and less mortal than initially predicted – was manageable. However, the vaccine, initially regarded as a strategy to treat the threat of the virus, turned out to be an even worse threat than the virus itself. It turned out to initiate more complex controversies than the flu itself. Our article suggests that the public authorities’ and the medical science community’s management of the flu are an example of how an incident turns into a socio-technical controversy. Key words: ANT, pandemic flu A (H1N1), uncertainties, risk.

Phylogenetic analysis of pandemic influenza A/H1N1 virus

Biologia ◽  
2012 ◽  
Vol 67 (1) ◽  
Author(s):  
Ramaiah Arunachalam ◽  
Kanniah Paulkumar ◽  
Gurusamy Annadurai
Keyword(s):  
Influenza A ◽  
Phylogenetic Trees ◽  
Extensive Study ◽  
Influenza Viruses ◽  
Swine Flu ◽  
Influenza A H1n1 ◽  
Group A ◽  
Group B ◽  
Human Viruses ◽  
Relationship Of

AbstractThe principle of the present study was to determine the evolution of pandemic novel influenza A/H1N1 2009 virus (NIV) by phylogenetic, comparative and statistical analyses. The phylogenetic trees of eight genomic segments illustrate that, so far, the sequences of the NIVs (outbreak group A) are relatively homogeneous and derived by the event of multiple genetic reassortment of Eurasian and North American swine, avian and human viruses (group B). It implies that some of the influenza viruses in group B had higher potential to evolve and getting the ability to transmit from human-to-human after animal-to-human cross-species transmission. The second analysis shows that NIV had attempted a little evolutionary change among humans and before introduction into human it had long evolutionary history. Statistical analysis shows that viruses from both outbreak and nearest group have homologous genes in their genomes which might be reflecting the phylogenetic relationship of strains, and also the presence of unique mutations between groups A-B may associate with increased virulence of NIVs. Both phylogenetic and cluster analyses confirm that the gene exchange takes place between viruses originated from different species and it could be generated NIV with unpredictable pandemic potential. Hence, we conclude that an extensive study should be made to recognize, which reassortment groups are closely related to NIVs, and to determine the sites in the genes of NIV under greatest or least selection pressure, which will ultimately be important in the effective design of vaccine and drugs for ‘swine flu’.

scholarly journals A clinico-epidemiological profile of patients with influenza A H1N1 attending a tertiary care hospital in southern Rajasthan region of India

2019 ◽  
Vol 7 (5) ◽  
pp. 1877
Author(s):  
Yogesh Kumar Singhal ◽  
Nitin Kothari
Keyword(s):  
Rural Areas ◽  
Influenza A ◽  
Clinical Symptoms ◽  
Tertiary Care ◽  
Influenza Viruses ◽  
Swine Flu ◽  
Care Hospital ◽  
Epidemiological Factors ◽  
Influenza A H1n1 ◽  
Epidemiological Profile

Background: Influenza, commonly referred to as the flu, is an infectious disease caused by RNA viruses of the family Orthomyxoviridae (the influenza viruses). Swine flu cases resurfaced in month of January 2015 in Southern region of India which are continuation of pandemic 2009. Aim of this study is to summaries the clinical and epidemiological factors associated with swine flu as well as to estimate the burden of Influenza A H1N1 (Swine Flu) cases.Methods: A complete data of all the patients visiting swine flu OPDs, swine flu wards and ICU were maintained for year 2015. Each patient visiting either the swine flu OPD or the swine flu ward, who was suspected clinically to be H1N1 positive were tested for real time PCR.Results: Out of 1247 samples tested for rt-PCR 491 (39.37%) cases were identified as positive for H1N1. Maximum swine positivity was seen in the age group of 16-30 year i.e. 147 (29.94%). Overall swine positivity was significantly (<0.001) higher in females than male and extremely statistically significant (p<0.0001) higher in rural areas than urban. Cough was the most common clinical symptoms affecting 469(95.52%) patients followed by fever (92.26%) and breathlessness 402(81.87%).Conclusions: Our study will help epidemiologist and clinician to identify epidemiological factors and clinical picture of swine flu.

scholarly journals Lessons from History: Methodological Problems arising from Comparing the Influenza A (H1N1) Pandemic 2009-10 to Seasonal Influenza 2010-2019 at the United States

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
James A Koziol ◽  
Jan E Schnitzer
Keyword(s):  
United States ◽  
Influenza A ◽  
H1n1 Influenza ◽  
The United States ◽  
Cross Reactivity ◽  
Influenza Viruses ◽  
Vaccination Programs ◽  
Influenza A H1n1 ◽  
Pandemic Flu ◽  
Novel H1n1 Influenza

Pandemics of human influenza are when influenza viruses that have little or no immunity become capable of transmitting from one person to another. A novel H1N1 influenza virus was discovered in children in the southwest United States in April 2009. Retroactively, it was shown that these cases were the result of an ongoing epidemic in Mexico. A number of national vaccination programs were established in response to the pandemic. Surprisingly early clinical trials data from humans have shown that one dose of nonadjuvanted pandemic flu A (H1N1) 2009 monovalent, inactivated vaccine (pMIV), has resulted in a significant seroprotective response. This is despite previous studies showing no cross-reactivity between pandemic and seasonal H1N1 viruses.

scholarly journals Influenza: An Emerging and Re-emerging Public Health Threat in Nepal

2018 ◽  
Vol 3 (2) ◽  
pp. 1-2
Author(s):  
Bishnu Prasad Upadhyay
Keyword(s):  
Influenza Virus ◽  
Influenza A ◽  
Winter Season ◽  
Emerging Infectious Diseases ◽  
Influenza Viruses ◽  
Influenza B ◽  
Influenza A Viruses ◽  
Influenza A H1n1 ◽  
New Variant ◽  
Seasonal Epidemics

Influenza virus type A and B are responsible for seasonal epidemics as well as pandemics in human. Influenza A viruses are further divided into two major groups namely, low pathogenic seasonal influenza (A/H1N1, A/H1N1 pdm09, A/H3N2) and highly pathogenic influenza virus (H5N1, H5N6, H7N9) on the basis of two surface antigens: hemagglutinin (HA) and neuraminidase (NA). Mutations, including substitutions, deletions, and insertions, are one of the most important mechanisms for producing new variant of influenza viruses. During the last 30 years; more than 50 viral threat has been evolved in South-East Asian countriesof them influenza is one of the major emerging and re-emerging infectious diseases of global concern. Similar to tropical and sub-tropical countries of Southeast Asia; circulation of A/H1N1 pdm09, A/H3N2 and influenza B has been circulating throughout the year with the peak during July-November in Nepal. However; the rate of infection transmission reach peak during the post-rain and winter season of Nepal.

Modeling and simulation of the spread of H1N1 flu with periodic vaccination

2015 ◽  
Vol 09 (01) ◽  
pp. 1650003 ◽  
Author(s):  
Islam A. Moneim
Keyword(s):  
Influenza A ◽  
Vaccination Strategy ◽  
Vaccination Rate ◽  
Influenza Viruses ◽  
Sirs Epidemic Model ◽  
Sirs Model ◽  
Influenza A H1n1 ◽  
Large Populations ◽  
Stability Results ◽  
Influenza H1n1

Influenza H1N1 has been found to exhibit oscillatory levels of incidence in large populations. Clear peaks for influenza H1N1 are observed in several countries including Vietnam each year [M. F. Boni, B. H. Manh, P. Q. Thai, J. Farrar, T. Hien, N. T. Hien, N. Van Kinh and P. Horby, Modelling the progression of pandemic influenza A (H1N1) in Vietnam and the opportunities for reassortment with other influenza viruses, BMC Med. 7 (2009) 43, Doi: 10.1186/1741-7015-7-43]. So it is important to study seasonal forces and factors which can affect the transmission of this disease. This paper studies an SIRS epidemic model with seasonal vaccination rate. This SIRS model has a unique disease-free solution (DFS). The value R0, the basic reproduction number is obtained when the vaccination is a periodic function. Stability results for the DFS are obtained when R0 < 1. The disease persists in the population and remains endemic if R0 > 1. Also when R0 > 1 existence of a nonzero periodic solution is proved. These results obtained for our model when the vaccination strategy is a non-constant time-dependent function.

scholarly journals MOLECULAR AND GENETIC CHARACTERISTICS OF SURFACE AND NONSTRUCTURE PROTEINS OF PANDEMIC INFLUENZA VIRUSES A(H1N1)PDM09 IN 2015-2016 EPIDEMIC SEASON

2016 ◽  
Vol 72 (2) ◽  
pp. 44-48
Author(s):  
O. Smutko ◽  
L. Radchenko ◽  
A. Mironenko
Keyword(s):  
Amino Acid ◽  
Pandemic Influenza ◽  
Influenza A ◽  
Phylogenetic Trees ◽  
Influenza Viruses ◽  
Amino Acid Substitutions ◽  
Ns1 Protein ◽  
Genetic Characteristics ◽  
Epidemic Season ◽  
Influenza A H1n1

The aim of the present study was identifying of molecular and genetic changes in hemaglutinin (HA), neuraminidase (NA) and non-structure protein (NS1) genes of pandemic influenza A(H1N1)pdm09 strains, that circulated in Ukraine during 2015-2016 epidemic season. Samples (nasopharyngeal swabs from patients) were analyzed using real-time polymerase chain reaction (RTPCR). Phylogenetic trees were constructed using MEGA 7 software. 3D structures were constructed in Chimera 1.11.2rc software. Viruses were collected in 2015-2016 season fell into genetic group 6B and in two emerging subgroups, 6B.1 and 6B.2 by gene of HA and NA. Subgroups 6B.1 and 6B.2 are defined by the following amino acid substitutions. In the NS1 protein were identified new amino acid substitutions D2E, N48S, and E125D in 2015-2016 epidemic season. Specific changes were observed in HA protein antigenic sites, but viruses saved similarity to vaccine strain. NS1 protein acquired substitution associated with increased virulence of the influenza virus.

scholarly journals Cluster analysis of the origins of the new influenza A(H1N1) virus

2009 ◽  
Vol 14 (21) ◽  
Author(s):  
A Solovyov ◽  
G Palacios ◽  
T Briese ◽  
W I Lipkin ◽  
R Rabadan
Keyword(s):  
Cluster Analysis ◽  
Influenza A ◽  
H1n1 Virus ◽  
Swine Influenza ◽  
The United States ◽  
Influenza Viruses ◽  
World Health ◽  
Influenza A H1n1 ◽  
The World ◽  
Health Organization

In March and April 2009, a new strain of influenza A(H1N1) virus has been isolated in Mexico and the United States. Since the initial reports more than 10,000 cases have been reported to the World Health Organization, all around the world. Several hundred isolates have already been sequenced and deposited in public databases. We have studied the genetics of the new strain and identified its closest relatives through a cluster analysis approach. We show that the new virus combines genetic information related to different swine influenza viruses. Segments PB2, PB1, PA, HA, NP and NS are related to swine H1N2 and H3N2 influenza viruses isolated in North America. Segments NA and M are related to swine influenza viruses isolated in Eurasia.

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