Seasonal Genetic Drift of Human Influenza A Virus Quasispecies Revealed by Deep Sequencing

Barbezange, Cyril; Jones, Louis C.; Blanc, Hervé; Isakov, Ofer; Celniker, Gershon; Enouf, Vincent; Shomron, Noam; Vignuzzi, Marco; Werf, Sylvie van der

doi:10.3389/fmicb.2018.02596

Cited by 29 publications

(21 citation statements)

References 74 publications

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“…SAMtools mpileup (version 2.1.0) 48 was used to make SNP calls with minimum base Phred quality score as 25. A reported SNP call was one that satisfied the following criteria at the SNP position: 1) more than 100 reads at that position 49–51 2) reads present from both directions, 3) variant calls exactly at the end of the read eliminated and 4) reads with bases that are different to reference more than 10% of the aligned reads.…”

Section: Methodsmentioning

confidence: 99%

Establishment of a pig influenza challenge model for evaluation of monoclonal antibody delivery platforms

McNee

Smith

Holzer

et al. 2020

Preprint

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31Monoclonal antibodies are a possible adjunct to vaccination and drugs in treatment of 32 influenza virus infection. However questions remain whether small animal models 33 accurately predict efficacy in humans. We have established the pig, a large natural 34 host animal for influenza, with many physiological similarities to humans, as a robust 35 model for testing monoclonal antibodies. We show that a strongly neutralizing 36 monoclonal antibody (2-12C) against the hemagglutinin head administered 37prophylactically at 15 mg/kg reduced viral load and lung pathology after pandemic 38 H1N1 influenza challenge. A lower dose of 1 mg/kg of 2-12C or a DNA plasmid 39 encoded version of 2-12C, reduced pathology and viral load in the lungs, but not viral 40 shedding in nasal swabs. We propose that the pig influenza model will be useful for 41 testing candidate monoclonal antibodies and emerging delivery platforms prior to 42 human trials. 43 therapeutic administration to reduce viral load after infection has been established. 94We went on to evaluate the potential of an in vivo produced 2-12C using synthetic 95 dMAb technology in support of the translation of this technology to humans as an 96 immunoprophylactic. 97 98 Results: 99Establishment of a prophylactic pig influenza challenge model with recombinant 100 2-12C mAb. To establish a positive control protective mAb and delivery method in the 101 pig influenza model we tested the strongly neutralizing human IgG1 anti-head 2-12C 102 mAb 31 in a prophylactic experiment. We administered 15 mg/kg of 2-12C intravenously 103 and the control groups received an isotype matched IgG1 mAb or the diluent. Twenty-104 four hours later the pigs were challenged with pandemic swine H1N1 isolate, 105 A/swine/England/1353/2009 (pH1N1) and 4 days later culled to assess viral load and 106 pathology (Fig. 1a). 2-12C significantly decreased viral load in nasals swabs on each 107 day over the course of infection, although the decrease was less on days 2 and 3 than 108 days 1 and 4 (Fig. 1b). The total viral load in nasal swabs over the 4 days in animals 109 treated with 2-12C was also significantly less as determined by the area under the 110 curve (AUC) compared to diluent and isotype controls (p=0.0267 and p=0.021). Viral 111 load in the 2-12C group was significantly reduced in the BAL and no virus was detected 112 in the lungs at 4 days post infection (DPI). Overall 2-12C had a clear effect on viral 113 load in nasal swabs, BAL and lung. 114The isotype and diluent control groups showed the most severe gross 115 pathology and histopathology scores (Fig. 2a). The red tan areas of pulmonary 116 consolidation were present mainly in the cranial and middle lung lobes of animals from 117 the isotype and diluent groups, but no lesions were found in the 2-12C group (Fig. 2b). 118 6 Similarly, necrotizing bronchiolitis and bronchial and alveolar exudation, and mild 119 thickening of the alveolar septa was shown in the animals from both control groups. 120

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Section: Methodsmentioning

confidence: 99%

Establishment of a pig influenza challenge model for evaluation of monoclonal antibody delivery platforms

McNee

Smith

Holzer

et al. 2020

Preprint

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“…The most feasible explanation for the IC50 variation is quasi-species. Because of the high mutation rate (e.g., 1.8 x 10 4 substitutions per nucleotide per strand replicated for PR8 [46]) specific to RNA viruses, an IAV strain possesses various minor mutants called quasi-species (47). Moreover, some mutations around the NA active site are reported to affect sensitivity to NAI (45,48), which might be demonstratable by sequencing a set of genomes of single IAV particles.…”

Section: Discussionmentioning

confidence: 99%

Multi-dimensional digital bioassay platform based on an air-sealed femtoliter reactor array device

Honda

Minagawa

Noji

et al. 2020

Preprint

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Single-molecule experiments have been helping us to get deeper inside biological phenomena by illuminating how individual molecules actually work. Digital bioassay, in which analyte molecules are individually confined in small compartments to be analyzed, is an emerging technology in single-molecule biology and applies to various biological entities (e.g., cells and virus particles). However, digital bioassay is not compatible with multi-conditional or multi-parametric assays, hindering understanding of analytes. This is because current digital bioassay lacks a repeatable solution-exchange system that keeps analytes inside compartments. To address this challenge, we developed a new digital bioassay platform with easy solution exchanges, called multi-dimensional (MD) digital bioassay, and tested its quantitativity and utility. We immobilized single analytes in arrayed femtoliter (10-15 L) reactors and sealed them with airflow. The solution in each reactor was stable and showed no cross-talk via solution leakage for more than 2 h, and over 30 rounds of perfect solution exchanges were successfully performed. To show the utility of our system, we investigated neuraminidase inhibitor (NAI) sensitivity on single influenza A virus (IAV) particles in a multi-conditional assay. We proved that IAV particles show a heterogeneous response to the NAI. Further, to demonstrate multi-parametric assays, we examined the sensitivity of individual IAV particles or model enzyme molecules to two different inhibitors. Our results support that MD digital bioassay is a versatile platform to unveil heterogeneities of biological entities in unprecedented resolution.

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“…Reassortment can produce new phenotypic traits. It is the main mechanism of antigenic shift of influenza A virusesdoften associated with new influenza pandemics (Webster et al, 1992;Morse, 1994;Gibbs et al, 1995;Domingo et al, 2001)das opposed to antigenic drift, which is mediated by amino acid substitutions in the surface proteins hemagglutinin and neuraminidase (Barbezange et al, 2018). Reassortments occur among the 9e12 doublestranded RNA segments of the widespread Reoviridae family (Tanaka et al, 2012).…”

Section: Genome Segment Reassortmentmentioning

confidence: 99%

Molecular basis of genetic variation of viruses

Domingo

2020

Virus as Populations

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Seasonal Genetic Drift of Human Influenza A Virus Quasispecies Revealed by Deep Sequencing

Cited by 29 publications

References 74 publications

Establishment of a pig influenza challenge model for evaluation of monoclonal antibody delivery platforms

Establishment of a pig influenza challenge model for evaluation of monoclonal antibody delivery platforms

Multi-dimensional digital bioassay platform based on an air-sealed femtoliter reactor array device

Molecular basis of genetic variation of viruses

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