25 Years Responding to Respiratory and Other Viruses with Mass Spectrometry

This review article presents the development and application of mass spectrometry (MS) approaches, developed in the author's laboratory over the past 25 years, to detect; characterise, type and subtype; and distinguish major variants and subvariants of respiratory viruses such as influenza and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). All features make use of matrix-assisted laser desorption ionisation (MALDI) mass maps, recorded for individual viral proteins or whole virus digests. A MALDI-based immunoassay in which antibody-peptide complexes were preserved on conventional MALDI targets without their immobilisation led to an approach that enabled their indirect detection. The site of binding, and thus the molecular antigenicity of viruses, could be determined. The same approach was employed to study antivirals bound to their target viral protein, the nature of the binding residues, and relative binding affinities. The benefits of high-resolution MS were exploited to detect sequence-conserved signature peptides of unique mass within whole virus and single protein digests. These enabled viruses to be typed, subtyped, their lineage determined, and variants and subvariants to be distinguished. Their detection using selected ion monitoring improved analytical sensitivity limits to aid the identification of viruses in clinical specimens. The same high-resolution mass map data, for a wide range of viral strains, were input into a purpose-built algorithm (MassTree) in order to both chart and interrogate viral evolution. Without the need for gene or protein sequences, or any sequence alignment, this phylonumerics approach also determines and displays single-point mutations associated with viral protein evolution in a single-tree building step.

Determination of the epitopic peptides of fig mosaic virus and the single-chain variable fragment antibody by mass spectrometry

The study of antibody-antigen interactions, through epitope mapping, enhances our understanding of antibody neutralization and antigenic determinant recognition. Epitope mapping, employing monoclonal antibodies and mass spectrometry, has emerged as a rapid and precise method to investigate viral antigenic determinants. In this report, we propose an approach to improve the accuracy of epitopic peptide interaction rate recognition. To achieve this, we investigated the interaction between the nucleocapsid protein of fig mosaic virus (FMV-NP) and single-chain variable fragment antibodies (scFv-Ab). These scFv-Ab maintain high specificity similar to whole monoclonal antibodies, but they are smaller in size. We coupled this with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The experimental design involved using two different enzymes to digest FMV-NP separately. The resulting peptides were then incubated separately with the desired scFv-Ab at different incubation times and antibody concentrations. This allowed us to monitor the relative rate of epitopic peptide interaction with the antibody. The results demonstrated that, at a 1:1 ratio and after 2 h of interaction, the residues 122-136, 148-157, and 265-276 exhibited high-rate epitopic peptide binding, with reductions in peak intensity of 78%, 21%, and 22%, respectively. Conversely, the residues 250-264 showed low-rate binding, with a 15% reduction in peak intensity. This epitope mapping approach, utilizing scFv-Ab, two different enzymes, and various incubation times, offers a precise and dependable analysis for monitoring and recognizing the binding kinetics of antigenic determinants. Furthermore, this method can be applied to study any kind of antigens.

High resolution mass spectrometry of respiratory viruses: beyond MALDI-ToF instruments for next generation viral typing, subtyping, variant and sub-variant identification

In the wake of the SARS-CoV2 pandemic, a point has been reached to assess the limitations and strengths of the analytical responses to virus identification and characterisation. Mass spectrometry has played a growing role in this area for over two decades, and this review highlights the benefits of mass spectrometry (MS) over PCR-based methods together with advantages of high mass resolution, high mass accuracy strategies over conventional MALDI-ToF and ESI-MS/MS instrumentation. This review presents the development and application of high resolution mass spectrometry approaches to detect, characterise, type and subtype, and distinguish variants of the influenza and SARS-CoV-2 respiratory viruses. The detection limits for the identification of SARS-CoV2 virus variants in clinical specimens and the future uptake of high resolution instruments in clinical laboratories are discussed. The same high resolution mass data can be used to monitor viral evolution and follow evolutionary trajectories.

Why Glycosylation Matters in Building a Better Flu Vaccine

Low vaccine efficacy against seasonal influenza A virus (IAV) stems from the ability of the virus to evade existing immunity while maintaining fitness. Although most potent neutralizing antibodies bind antigenic sites on the globular head domain of the IAV envelope glycoprotein hemagglutinin (HA), the error-prone IAV polymerase enables rapid evolution of key antigenic sites, resulting in immune escape. Significantly, the appearance of new N-glycosylation consensus sequences (sequons, NXT/NXS, rarely NXC) on the HA globular domain occurs among the more prevalent mutations as an IAV strain undergoes antigenic drift. The appearance of new glycosylation shields underlying amino acid residues from antibody contact, tunes receptor specificity, and balances receptor avidity with virion escape, all of which help maintain viral propagation through seasonal mutations. The World Health Organization selects seasonal vaccine strains based on information from surveillance, laboratory, and clinical observations. Although the genetic sequences are known, mature glycosylated structures of circulating strains are not defined. In this review, we summarize mass spectrometric methods for quantifying site-specific glycosylation in IAV strains and compare the evolution of IAV glycosylation to that of human immunodeficiency virus. We argue that the determination of site-specific glycosylation of IAV glycoproteins would enable development of vaccines that take advantage of glycosylation-dependent mechanisms whereby virus glycoproteins are processed by antigen presenting cells.

Mass spectrometry for the detection of bioterrorism agents: from environmental to clinical applications

In the current context of international conflicts and localized terrorist actions, there is unfortunately a permanent threat of attacks with unconventional warfare agents. Among these, biological agents such as toxins, microorganisms, and viruses deserve particular attention owing to their ease of production and dissemination. Mass spectrometry (MS)-based techniques for the detection and quantification of biological agents have a decisive role to play for countermeasures in a scenario of biological attacks. The application of MS to every field of both organic and macromolecular species has in recent years been revolutionized by the development of soft ionization techniques (MALDI and ESI), and by the continuous development of MS technologies (high resolution, accurate mass HR/AM instruments, novel analyzers, hybrid configurations). New possibilities have emerged for exquisite specific and sensitive detection of biological warfare agents. MS-based strategies for clinical application can now address a wide range of analytical questions mainly including issues related to the complexity of biological samples and their available volume. Multiplexed toxin detection, discovery of new markers through omics approaches, and identification of untargeted microbiological or of novel molecular targets are examples of applications. In this paper, we will present these technological advances along with the novel perspectives offered by omics approaches to clinical detection and follow-up.

Proteotyping for the rapid identification of influenza virus and other biopathogens

The influenza virus is one of the most deadly infectious agents known to man and has been responsible for the deaths of some hundred million lives throughout human history. The need to rapidly and reliably survey circulating virus strains down to the molecular level is ever present. This tutorial describes the development and application of a new proteotyping approach that harnesses the power of high resolution of mass spectrometry to characterise the influenza virus, and by extension other bacterial and viral pathogens. The approach is shown to be able to type, subtype, and determine the lineage of human influenza virus strains through the detection of one or more signature peptide ions in the mass spectrum of whole virus digests. Pandemic strains can be similarly distinguished from seasonal ones, and new computer algorithms have been written to allow reassorted strains that pose the greatest pandemic risk to be rapidly identified from such datasets. The broader application of the approach is further demonstrated here for the parainfluenza virus, a virus which can be life threatening to children and presents similar clinical symptoms to influenza.

Incorporation of a proteotyping approach using mass spectrometry for surveillance of influenza virus in cell-cultured strains

The reemergence of deadly pandemic influenza virus strains has necessitated the development of improved methods for rapid detection and subtyping of influenza viruses that will enable more strains to be characterized at the molecular level. Representative circulating strains of human influenza viruses from primary clinical specimens were grown in cell culture, purified through polyethylene glycol precipitation, proteolytically digested with an endoproteinase, and analyzed and identified by high-resolution mass spectrometry using unique signature peptides that are characteristic of type A H1N1 and H3N2 and type B influenza viruses. This proteotyping approach enabled circulating strains of type A influenza virus to be typed and subtyped, cocirculating seasonal and pandemic H1N1 viruses to be differentiated, and the lineage of type B viruses to be determined through single-ion detection by high-resolution mass spectrometry. Results were obtained using virus titers comparable to those used in reverse transcription (RT)-PCR assays with clinical specimens grown in cell cultures. The methodology represents a more rapid and direct approach than RT-PCR and can be integrated into existing procedures currently used for the surveillance of emerging pandemic and seasonal influenza viruses.

Mass trees: a new phylogenetic approach and algorithm to chart evolutionary history with mass spectrometry

A new phylogenetics approach and algorithm with which to chart the evolutionary history of organisms is presented. It utilizes mass spectral data produced from the proteolytic digestion of proteins, rather than partial or complete gene or translated gene sequences. The concept and validity of the approach is demonstrated herein using both theoretical and experimental mass data, together with the translated gene sequences of the hemagglutinin protein of the influenza virus. A comparison of the mass trees with conventional sequenced-based phylogenetic trees, using two separate tree comparison algorithms, reveals a high degree of similarity and congruence among the trees. Given that the mass map data can be generated more rapidly than gene sequences, even when next generation parallel sequencing is employed, mass trees offer new opportunities and advantages for phylogenetic analysis.

FluShuffle and FluResort: new algorithms to identify reassorted strains of the influenza virus by mass spectrometry

BACKGROUND

Influenza is one of the oldest and deadliest infectious diseases known to man. Reassorted strains of the virus pose the greatest risk to both human and animal health and have been associated with all pandemics of the past century, with the possible exception of the 1918 pandemic, resulting in tens of millions of deaths. We have developed and tested new computer algorithms, FluShuffle and FluResort, which enable reassorted viruses to be identified by the most rapid and direct means possible. These algorithms enable reassorted influenza, and other, viruses to be rapidly identified to allow prevention strategies and treatments to be more efficiently implemented.

RESULTS

The FluShuffle and FluResort algorithms were tested with both experimental and simulated mass spectra of whole virus digests. FluShuffle considers different combinations of viral protein identities that match the mass spectral data using a Gibbs sampling algorithm employing a mixed protein Markov chain Monte Carlo (MCMC) method. FluResort utilizes those identities to calculate the weighted distance of each across two or more different phylogenetic trees constructed through viral protein sequence alignments. Each weighted mean distance value is normalized by conversion to a Z-score to establish a reassorted strain.

CONCLUSIONS

The new FluShuffle and FluResort algorithms can correctly identify the origins of influenza viral proteins and the number of reassortment events required to produce the strains from the high resolution mass spectral data of whole virus proteolytic digestions. This has been demonstrated in the case of constructed vaccine strains as well as common human seasonal strains of the virus. The algorithms significantly improve the capability of the proteotyping approach to identify reassorted viruses that pose the greatest pandemic risk.