Whole-Genome Analysis of Influenza B Viruses of Multiple Genotypes Cocirculating in India

Patil, Kunal; Bhise, Atul B.; Dakhave, Minal; Kadam, Archana; Chadha, Mandeep S.; Potdar, Varsha

doi:10.1128/genomea.00951-13

Cited by 4 publications

(5 citation statements)

References 7 publications

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“…Furthermore, phylogenetic analysis of the NS gene showed that all viruses clustered together to form a distinct Lineage IV. The incongruent phylogenetic patterns observed at the lineage level corroborated with previous reports [ 7 , 13 , 15 , 16 ], which suggest that the phylogenies of eight gene segments could be divided into three distinct evolutionary profiles: (i) PB1, PB2 and HA genes derived from either Lineage II or III; (ii) PA, NP, NA and MP genes derived from Lineage II; and (iii) NS genes derived from Lineage IV. Firstly, the consistent grouping of Yam-like or Vic-like viruses in Lineage II or III, respectively, in the tree topology of PB1, PB2 and HA genes could be attributed to possible genetic linkage between these three gene segments, which has been described [ 8 ].…”

Section: Resultssupporting

confidence: 89%

“…In conclusion, this present study highlights the strategy used for the phylogenetic classification of all gene segments of influenza B viruses, which classifies all genes at the lineage, clade and sub-clade level. This strategy for lineage classification was adapted from previously reported methods [ 7 , 13 , 15 , 16 ], while the strategy for clade and sub-clade classification was adapted from the WHO interim reports [ 11 , 12 ] and criteria used for H5N1 classification [ 30 ], respectively. Adaptation of this approach in future studies with a larger dataset of whole-genome sequences may perhaps allow a better understanding of the complexity of segment reassortments in influenza B evolution which may contribute to future vaccine design, and also for better monitoring of unique reassortants in surveillance studies.…”

Section: Resultsmentioning

confidence: 99%

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Whole-Genome Phylogenetic Analysis of Influenza B/Phuket/3073/2013-Like Viruses and Unique Reassortants Detected in Malaysia between 2012 and 2014

Oong

Tan

et al. 2017

PLoS ONE

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Reassortment of genetic segments between and within influenza B lineages (Victoria and Yamagata) has been shown to generate novel reassortants with unique genetic characteristics. Based on hemagglutinin (HA) and neuraminidase (NA) genes, recent surveillance study has identified reassortment properties in B/Phuket/3073/2013-like virus, which is currently used in the WHO-recommended influenza vaccine. To understand the potential reassortment patterns for all gene segments, four B/Phuket/3073/2013-like viruses and two unique reassortants (one each from Yamagata and Victoria) detected in Malaysia from 2012–2014 were subjected to whole-genome sequencing. Each gene was phylogenetically classified into lineages, clades and sub-clades. Three B/Phuket/3073/2013-like viruses from Yamagata lineage were found to be intra-clade reassortants, possessing PA and NA genes derived from Stockholm/12-like sub-clade, while the remaining genes from Wisconsin/01-like sub-clade (both sub-clades were within Yamagata Clade 3/Yam-3). However, the other B/Phuket/3073/2013-like virus had NS gene that derived from Stockholm/12-like sub-clade instead of Wisconsin/01-like sub-clade. One inter-clade reassortant had Yamagata Clade 2/Yam-2-derived HA and NP, and its remaining genes were Yam-3-derived. Within Victoria Clade 1/Vic-1 in Victoria lineage, one virus had intra-clade reassortment properties: HA and PB2 from Vic-1B sub-clade, MP and NS from a unique sub-clade “Vic-1C”, and the remaining genes from Vic-1A sub-clade. Although random reassortment event may generate unique reassortants, detailed phylogenetic classification of gene segments showed possible genetic linkage between PA and NA genes in B/Phuket/3073/2013-like viruses, which requires further investigation. Understanding on reassortment patterns in influenza B evolution may contribute to future vaccine design.

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Section: Resultssupporting

confidence: 89%

Section: Resultsmentioning

confidence: 99%

Whole-Genome Phylogenetic Analysis of Influenza B/Phuket/3073/2013-Like Viruses and Unique Reassortants Detected in Malaysia between 2012 and 2014

Oong

Tan

et al. 2017

PLoS ONE

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“…49 In our study, both Yamagata and Victoria lineage strains of influenza B were found in this region, similar to other reports of co-circulation of both the lineages from India, China and Singapore. [50][51][52] Globally, Victoria lineage of influenza B viruses is considered the predominant type of influenza B viruses 53 and the current influenza vaccine contains only the Victoria-like lineage virus (B/Brisbane/60/ 2008). However, previous studies conducted in humans have proved that this vaccine could not provide immunity against the Yamagata lineage viruses 54 and hence recently, CDC has approved the usage of Quadrivalent vaccine with both the types of influenza B viruses.…”

Section: Discussionmentioning

confidence: 99%

Epidemiology and phylogenetic analysis of respiratory viruses from 2012 to 2015 – A sentinel surveillance report from union territory of Puducherry, India

Palani

Sistla

2020

Clinical Epidemiology and Global Health

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Background: Acute respiratory infections (ARI) are the most common illnesses affecting people of all ages worldwide. Viruses contribute to 30-70% of acute respiratory infections. Identification of these respiratory viruses is not given high priority except influenza; however, the knowledge about prevalence of non-influenza viruses, their seasonal pattern and genetic evolution have significant epidemiological value. Methods: As a part of National Influenza-like illness surveillance programme, respiratory specimens were collected children and adults with symptoms of ILI or ARI, between January 2012 and March 2015 (including SARI cases). Real-time PCR was done to identify 13 respiratory viruses. Sequencing was done for representative isolates of each virus using ABI 3730 Genetic Analyzer. Results: During the study period between January 2012 and March 2015, a total of 648 patients with symptoms of ARI were included in this study. The mean age of the patients was 20.2 years (SD = 19.13, median = 18); 292 (45.1%) were children (≤13 years) and 356 (54.9%) were adults. Respiratory viruses were identified in 44% (287/648) of all patients. Influenza accounted for the maximum number of cases-179/648 (27.6%). Among the non-influenza viruses, RSV predominated with 34 cases (5.2%), followed by HMPV 24 (3.7%) and PIV-3 20 (3%). Four patients died due to INF A/H1N1 (2012-2, 2015-2) as a result of acute respiratory distress syndrome (ARDS) (CFR 3.7%). Among the non-influenza viruses, no particular seasonality pattern was observed over the different months of the study period. Conclusion: Antibiotic usage in treating acute respiratory infections empirically is not justified as nearly half of ARI are due to viruses; nearly 28% of them were due to influenza viruses. Among the non-influenza viruses, RSV predominated, followed by HMPV. This study is based on an active influenza surveillance initiated after 2009 pandemic influenza outbreak, in the Union territory of Puducherry which has contributed significantly to the knowledge of the burden of influenza and non-influenza viruses among children and adults. Such surveillance network has paved the way for better diagnosis and timely therapeutic interventions.

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“…Similar to this study various studies are being carried out in India. The National Institute of Virology has continued research work on isolation, genetic characterization and drug susceptibility monitoring of pdmH1N1 isolates from India under national surveillance program as well as [12] which revealed the co-circulation of type B lineages. The genetic diversity of influenza B viruses was observed when full-genome analysis was performed.…”

Section: Rt-pcr Methodsmentioning

confidence: 99%

“…Annual influenza epidemics are responsible for the death of 250,000-500,000 people worldwide and cause illness in (5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15) % of the total population each year [22]. Human influenza occurs all over the world with annual global attack rate of fever or myalgia, headache, malaise or non productive cough.…”

Section: Introductionmentioning

confidence: 99%

The emergence and consistency of influenza strains causing influenza like illness in Himachal Pradesh, India

et al. 2016

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The present study offers the status of ongoing surveillance influenza at National Influenza Surveillance Centre (NISC), Central Research Institute (CRI), Kasauli for the emergence and consistency of influenza strains for current as well as over a period of three decades in Solan, Himachal Pradesh. From 1980 to 2015, various clinical centers of Himachal reported counts of influenza-like illness (fever including cough or sore throat). During these years, the respiratory specimens of 6581 patients showing influenza-like illness were collected. The incidence of visits had been calculated for influenza-like illness using the size of the patient population, and the incidence attributable to influenza was extrapolated from the proportion of patients with positive tests. Up to 2008 the egg inoculation method was used for the isolation and detection of influenza strains but in 2009 a RT-PCR equipped, fabricated BSL-3 laboratory was implanted at CRI for the isolation and detection of influenza strains. The reagents, primers and probes were supplied by NCDC, Delhi. Since 1980, 319 influenza isolates has been identified and isolated at NISC. Among these 282 were isolated by egg propagation method while 37 were processed by RT-PCR. Influenza incidence varied with age groups and by season after the pandemic of 2009 influenza A, H1N1. High levels of influenza virus circulation, especially in young children, emphasize the need for additional efforts to increase the uptake of influenza vaccines and anti-virals.

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Whole-Genome Analysis of Influenza B Viruses of Multiple Genotypes Cocirculating in India

Cited by 4 publications

References 7 publications

Whole-Genome Phylogenetic Analysis of Influenza B/Phuket/3073/2013-Like Viruses and Unique Reassortants Detected in Malaysia between 2012 and 2014

Whole-Genome Phylogenetic Analysis of Influenza B/Phuket/3073/2013-Like Viruses and Unique Reassortants Detected in Malaysia between 2012 and 2014

Epidemiology and phylogenetic analysis of respiratory viruses from 2012 to 2015 – A sentinel surveillance report from union territory of Puducherry, India

The emergence and consistency of influenza strains causing influenza like illness in Himachal Pradesh, India

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