Molecular characterization and comparative analysis of pandemic H1N1/2009 strains with co-circulating seasonal H1N1/2009 strains from eastern India

A computational tool for trend analysis and forecast of the COVID-19 pandemic

Purpose:

This paper proposes a methodology and a computational tool to study the COVID-19 pandemic throughout the world and to perform a trend analysis to assess its local dynamics.

Methods:

Mathematical functions are employed to describe the number of cases and demises in each region and to predict their final numbers, as well as the dates of maximum daily occurrences and the local stabilization date. The model parameters are calibrated using a computational methodology for numerical optimization. Trend analyses are run, allowing to assess the effects of public policies. Easy to interpret metrics over the quality of the fitted curves are provided. Country-wise data from the European Centre for Disease Prevention and Control (ECDC) concerning the daily number of cases and demises around the world are used, as well as detailed data from Johns Hopkins University and from the Brasil.io project describing individually the occurrences in United States counties and in Brazilian states and cities, respectively. U. S. and Brazil were chosen for a more detailed analysis because they are the current focus of the pandemic.

Results:

Illustrative results for different countries, U. S. counties and Brazilian states and cities are presented and discussed.

Conclusion:

The main contributions of this work lie in (i) a straightforward model of the curves to represent the data, which allows automation of the process without requiring interventions from experts; (ii) an innovative approach for trend analysis, whose results provide important information to support authorities in their decision-making process; and (iii) the developed computational tool, which is freely available and allows the user to quickly update the COVID-19 analyses and forecasts for any country, United States county or Brazilian state or city present in the periodic reports from the authorities.

Molecular characterization of Influenza A pandemic H1N1 viruses circulating in eastern India during 2017-19: Antigenic diversity in comparison to the vaccine strains

In the endemic settings of India, high CFR (3.6-7.02%) was observed in the consecutive 2009, 2015 and 2017 A/H1N1pdm09 outbreaks, though in eastern India CFR varied between 0 and 5.5% during same period. Recurrent outbreaks of pandemic Influenza A/H1N1pdm09, fragmented nationwide incidence data, lack of national policy for Influenza vaccination in India underscores the necessity for generating regional level data. Thus, during 2017-19, 4106 referred samples from patients hospitalized with severe acute respiratory illness (SARI) in eastern India were tested for A/H1N1pdm09 infection. Among which 16.5% (n = 677/4106) were found A/H1N1pdm09 positive. Individuals <20 years and middle-aged persons (40-60 years) were most susceptible to A/H1N1pdm09 infection. The vaccine strain (A/human/California/07/2009) which was globally used before 2017, clustered in a different lineage away from the representative eastern Indian strains in the phylogenetic dendrogram. The vaccine strain (A/human/Michigan/45/2015) used in India during the study period and the WHO recommended strain (A/human/Brisbane/02/2018) for 2019-20 flu season for the northern hemisphere, clustered with the circulating isolates in the same lineage-6b. Dissimilarities in the amino acids encompassing the antigenic epitopes were seen to be highest with the vaccine strain- A/human/California/07/2009. The significant amino acid variations in the circulating strains with the current WHO recommended vaccine strain, implies the exigency of continuous pandemic A/H1N1pdm09 surveillance studies in this epidemiological setting. The absence of any Oseltamivir resistant mutation (H275Y) in the neuraminidase gene of the current isolates suggests continuing use of Tamiflu® as an antiviral therapy in suspected subjects in this region.

Epidemiology of influenza viruses from 2009 to 2013 - A sentinel surveillance report from Union territory of Puducherry, India

OBJECTIVE

To report the findings of influenza surveillance programme from Union territory of Puducherry and to document the clinical and epidemiological data of influenza viruses over a five year period from 2009 to 2013.

METHODS

Respiratory samples were collected from patients with influenza-like illness from 2009 to 2013 as part of routine diagnostic and surveillance activity. Detection of pandemic influenza A (H1N1) 2009, influenza A (H3N2) and influenza B was done using Real-time PCR.

RESULTS

Of the total 2247 samples collected from patients with influenza-like illness during the study period 287 (12.7%) and 92 (4.0%) were positive for influenza A (H1N1) 2009 and influenza A (H3N2) respectively. A subset of 557 of these samples were also tested for influenza B and 24 (4.3%) were positive. Significantly higher positivity rate for both viruses was observed in adults when compared with children. The peak positivity of influenza A (H1N1) 2009 was observed in 2009 followed by 2012, while that of influenza A (H3N2) was more uniformly distributed with the exception of 2012. Overall mortality rate due to influenza A (H1N1) 2009 was 7.6% while it was 1% for influenza A (H3N2). Each year influenza-like illness and influenza virus activity coincided with period of high rainfall and low temperature except in the first half of 2012.

CONCLUSIONS

As the sole referral laboratory in this region, the data provides a comprehensive picture of influenza activity. This information will be useful in future planning of the vaccine schedule and influenza pandemic preparedness.

Use of fractional factorial design to study the compatibility of viral ribonucleoprotein gene segments of human H7N9 virus and circulating human influenza subtypes

Avian H7N9 influenza viruses may pose a further threat to humans by reassortment with human viruses, which could lead to generation of novel reassortants with enhanced polymerase activity. We previously established a novel statistical approach to study the polymerase activity of reassorted vRNPs (Influenza Other Respir Viruses. 2013;7:969-78). Here, we report the use of this method to study recombinant vRNPs with subunits derived from human H1N1, H3N2, and H7N9 viruses. Our results demonstrate that some reassortant vRNPs with subunits derived from the H7N9 and other human viruses can have much higher polymerase activities than the wild-type levels.

Whole genome characterization, phylogenetic and genome signature analysis of human pandemic H1N1 virus in Thailand, 2009-2012

BACKGROUND

Three waves of human pandemic influenza occurred in Thailand in 2009-2012. The genome signature features and evolution of pH1N1 need to be characterized to elucidate the aspects responsible for the multiple waves of pandemic.

METHODOLOGY/FINDINGS

Forty whole genome sequences and 584 partial sequences of pH1N1 circulating in Thailand, divided into 1(st), 2(nd) and 3(rd) wave and post-pandemic were characterized and 77 genome signatures were analyzed. Phylogenetic trees of concatenated whole genome and HA gene sequences were constructed calculating substitution rate and d(N)/d(S) of each gene. Phylogenetic analysis showed a distinct pattern of pH1N1 circulation in Thailand, with the first two isolates from May, 2009 belonging to clade 5 while clades 5, 6 and 7 co-circulated during the first wave of pH1N1 pandemic in Thailand. Clade 8 predominated during the second wave and different proportions of the pH1N1 viruses circulating during the third wave and post pandemic period belonged to clades 8, 11.1 and 11.2. The mutation analysis of pH1N1 revealed many adaptive mutations which have become the signature of each clade and may be responsible for the multiple pandemic waves in Thailand, especially with regard to clades 11.1 and 11.2 as evidenced with V731I, G154D of PB1 gene, PA I330V, HA A214T S160G and S202T. The substitution rate of pH1N1 in Thailand ranged from 2.53×10(-3)±0.02 (M2 genes) to 5.27×10(-3)±0.03 per site per year (NA gene).

CONCLUSIONS

All results suggested that this virus is still adaptive, maybe to evade the host's immune response and tends to remain in the human host although the d(N)/d(S) were under purifying selection in all 8 genes. Due to the gradual evolution of pH1N1 in Thailand, continuous monitoring is essential for evaluation and surveillance to be prepared for and able to control future influenza activities.

Full genomic analysis of an influenza A (H1N2) virus identified during 2009 pandemic in Eastern India: evidence of reassortment event between co-circulating A(H1N1)pdm09 and A/Brisbane/10/2007-like H3N2 strains

BACKGROUND

During the pandemic [Influenza A(H1N1)pdm09] period in 2009-2010, an influenza A (Inf-A) virus with H1N2 subtype (designated as A/Eastern India/N-1289/2009) was detected from a 25 years old male from Mizoram (North-eastern India).

OBJECTIVE

To characterize full genome of the H1N2 influenza virus.

METHODS

For initial detection of Influenza viruses, amplification of matrix protein (M) gene of Inf-A and B viruses was carried out by real time RT-PCR. Influenza A positive viruses are then further subtyped with HA and NA gene specific primers. Sequencing and the phylogenetic analysis was performed for the H1N2 strain to understand its origin.

RESULTS

The outcome of this full genome study revealed a unique reassortment event where the N-1289 virus acquired it's HA gene from a 2009 pandemic H1N1 virus with swine origin and the other genes from H3N2-like viruses of human origin.

CONCLUSIONS

This study provides information on possibility of occurrence of reassortment events during influenza season when infectivity is high and two different subtypes of Inf-A viruses co-circulate in same geographical location.

Surveillance in Eastern India (2007-2009) revealed reassortment event involving NS and PB1-F2 gene segments among co-circulating influenza A subtypes

BACKGROUND

Influenza A virus encodes for eleven proteins, of which HA, NA, NS1 and PB1-F2 have been implicated in viral pathogenicity and virulence. Thus, in addition to the HA and NA gene segments, monitoring diversity of NS1 and PB1-F2 is also important.

METHODS

55 out of 166 circulating influenza A strains (31 H1N1 and 24 H3N2) were randomly picked during 2007-2009 and NS and PB1-F2 genes were sequenced. Phylogenetic analysis was carried out with reference to the prototype strains, concurrent vaccine strains and other reference strains isolated world wide.

RESULTS

Comparative analysis of both nucleotide and deduced amino acid sequences, revealed presence of NS gene with A/PR/8/34(H1N1)-like mutations (H4N, Q21R, A22V, K44R, N53D, C59R, V60A, F103S and M106I) in both RNA-binding and effector domain of NS1 protein, and G63E, the HPAI-H5N1-like mutation in NEP/NS2 of five A/H1N1 strains of 2007 and 2009. NS1 of other A/H1N1 strains clustered with concurrent A/H1N1 vaccine strains. Of 31 A/H1N1 strains, five had PB1-F2 similar to the H3N2 strains; six had non-functional PB1-F2 protein (11 amino acids) similar to the 2009 pandemic H1N1 strains and rest 20 strains had 57 amino acids PB1-F2 protein, similar to concurrent A/H1N1 vaccine strain. Interestingly, three A/H1N1 strains with H3N2-like PB1-F2 protein carried primitive PR8-like NS gene. Full gene sequencing of PB1 gene confirmed presence of H3N2-like PB1 gene in these A/H1N1 strains.

CONCLUSION

Overall the study highlights reassortment event involving gene segments other than HA and NA in the co-circulating A/H1N1 and A/H3N2 strains and their importance in complexity of influenza virus genetics. In contrast, NS and PB1-F2 genes of all A/H3N2 eastern India strains were highly conserved and homologous to the concurrent A/H3N2 vaccine strains suggesting that these gene segments of H3N2 viruses are evolutionarily more stable compared to H1N1 viruses.

Comparative analysis of hemagglutinin of 2009 H1N1 influenza A pandemic indicates its evolution to 1918 H1N1 pandemic

To gain insight into the possible origin of the hemagglutinin of 2009 outbreak, we performed its comparative analysis with hemagglutinin of influenza viral strains from 2005 to 2008 and the past pandemics of 1977, 1968, 1957 and 1918. This insilico analysis showed a maximum sequence similarity between 2009 and 1918 pandemics. Primary structure analysis, antigenic and glycosylation site analyses revealed that this protein has evolved from 1918 pandemic. Phylogenetic analysis of HA amino acid sequence of 2009 influenza A(H1N1) viruses indicated that this virus possesses a distinctive evolutionary trait with 1918 influenza A virus. Although the disordered sequences are different among all the isolates, the disordered positions and sequences between 2009 and 1918 isolates show a greater similarity. Thus these analyses contribute to the evidence of the evolution of 2009 pandemic from 1918 influenza pandemic. This is the first computational evolutionary analysis of HA protein of 2009 H1N1 pandemic.

Pandemic and seasonal influenza viruses among patients with acute respiratory illness in Kashmir (India)

Please cite this paper as: Koul PA., et al. (2011) Pandemic and seasonal influenza viruses among patients with acute respiratory illness in Kashmir (India). Influenza and Other Respiratory Viruses 5(6), e521–e527.

Background  With the emergence of pandemic influenza A (2009A/H1N1) virus in India, we sought to determine the prevalence and clinical presentations of seasonal and pandemic influenza viruses among acute respiratory illness (ARI) patients from Srinagar, a temperate climate area in northern India, during the peak winter season.

Methods  Combined throat and nasal swabs, obtained from 194 (108 male) presenting with ARI from January to March 2010 (Week 53‐week 10), were tested by RT‐PCR for influenza A and B, including 2009A/H1N1 viruses. HA1 gene of selected 2009A/H1N1‐positive samples was sequenced, and phylogenetic analysis was carried out.

Results  Twenty‐one (10·8%, age 15–80 years, median age 40 years) patients tested positive for influenza viruses: 13 (62%) for 2009A/H1N1 virus, 6 (28·5%) for seasonal influenza A (H3N2), and 2 (9·5%) for influenza B. Twelve of the 13 patients with 2009A/H1N1 presented with febrile ARI, and eight had associated comorbidities. All of the patients recovered. Phylogenetic analysis of HA gene (n = 8) revealed that all strains from Srinagar clustered in 2009A/H1N1 clade seven along with the other 2009A/H1N1 strains from India. Amino acid substitutions in the HA protein defining clade seven (P83S, S203T, and I321V) were found in almost all isolates from Srinagar.

Conclusions  Both seasonal and 2009A/H1N1 viruses appear to be associated with ARI in Srinagar. The 2009A/H1N1 in Srinagar is genetically similar to globally circulating clade 7 strains, with unique signature sequences in the HA gene. Further investigations into ascertain the role of these mutations in possible alteration of the virulence and transmissibility of the virus are needed.