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Comparative Genomics of Human Pathogens
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Comparative Genomics of Human Pathogens

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Microbial Genetics and Genomics".

Deadline for manuscript submissions: closed (20 May 2022) | Viewed by 4060

Special Issue Editor

Dr. Brett Pickett

E-Mail Website
Guest Editor
College of Life Sciences, Brigham Young University, Provo, UT 84602-1050, USA
Interests: bioinformatics; comparative genomics; multiple sequence alignments; phylogenetic trees; host–pathogen interactions
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The continued application of modern DNA sequencing approaches has generated large numbers of whole-genome sequences. Past comparative analyses of viral, bacterial, and parasite genomes have identified various components that play a role in the development, progression, and/or severity of human diseases.

A number of genetic mechanisms that contribute to human pathogenesis have been previously identified. Examples of such mechanisms include pathogenicity islands and variants that affect invasiveness, fitness, host range, and evading the host immune response. In addition, genomic analyses enable researchers to trace the evolutionary history, identify emerging variants, and predict the future trajectory of these pathogens. The results from such computational analyses can then be experimentally validated in the wet lab. The continued emergence of novel pathogens, the increased prevalence of drug-resistance genes and variants, as well as the expanded host range of pathogens capable of infecting humans justify maintaining and expanding comparative genomics research.

This Special Issue will cover comparative genomics analyses of viral, bacterial, and parasite sequence data. Submissions describing novel findings for human pathogens using methods not limited to phylogenetic trees, selection pressure, immune epitopes, genotype–phenotype correlations, pathogenicity islands, operons affecting the host range or pathogenicity, and the identification of variants affecting pathogenesis will be evaluated. Submissions using other relevant methods will also be considered. We cordially invite researchers working in these areas to contribute with original research of newly generated data, meta-analyses of existing data, or review papers.

Dr. Brett Pickett
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • comparative genomics
  • multiple sequence alignment
  • genotype–phenotype correlations
  • phylogenetic tree reconstruction
  • meta-analysis
  • public data
  • selection pressure analysis

Published Papers (2 papers)

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Research

17 pages, 1247 KiB  
Article
Mutation in Hemagglutinin Antigenic Sites in Influenza A pH1N1 Viruses from 2015–2019 in the United States Mountain West, Europe, and the Northern Hemisphere
by Craig H. Decker, Naomi Rapier-Sharman and Brett E. Pickett
Genes 2022, 13(5), 909; https://doi.org/10.3390/genes13050909 - 19 May 2022
Cited by 1 | Viewed by 2090
Abstract
H1N1 influenza A virus is a respiratory pathogen that undergoes antigenic shift and antigenic drift to improve viral fitness. Tracking the evolutionary trends of H1N1 aids with the current detection and the future response to new viral strains as they emerge. Here, we [...] Read more.
H1N1 influenza A virus is a respiratory pathogen that undergoes antigenic shift and antigenic drift to improve viral fitness. Tracking the evolutionary trends of H1N1 aids with the current detection and the future response to new viral strains as they emerge. Here, we characterize antigenic drift events observed in the hemagglutinin (HA) sequence of the pandemic H1N1 lineage from 2015–2019. We observed the substitutions S200P, K147N, and P154S, together with other mutations in structural, functional, and/or epitope regions in 2015–2019 HA protein sequences from the Mountain West region of the United States, the larger United States, Europe, and other Northern Hemisphere countries. We reconstructed multiple phylogenetic trees to track the relationships and spread of these mutations and tested for evidence of selection pressure on HA. We found that the prevalence of amino acid substitutions at positions 147, 154, 159, 200, and 233 significantly changed throughout the studied geographical regions between 2015 and 2019. We also found evidence of coevolution among a subset of these amino acid substitutions. The results from this study could be relevant for future epidemiological tracking and vaccine prediction efforts. Similar analyses in the future could identify additional sequence changes that could affect the pathogenicity and/or infectivity of this virus in its human host. Full article
(This article belongs to the Special Issue Comparative Genomics of Human Pathogens)
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15 pages, 6759 KiB  
Article
Conserved Molecular Signatures in the Spike, Nucleocapsid, and Polymerase Proteins Specific for the Genus Betacoronavirus and Its Different Subgenera
by Radhey S. Gupta and Bijendra Khadka
Genes 2022, 13(3), 423; https://doi.org/10.3390/genes13030423 - 25 Feb 2022
Cited by 3 | Viewed by 1560
Abstract
The genus Betacoronavirus, consisting of four main subgenera (Embecovirus, Merbecovirus, Nobecovirus, and Sarbecovirus), encompasses all clinically significant coronaviruses (CoVs), including SARS, MERS, and the SARS-CoV-2 virus responsible for current COVID-19 pandemic. Very few molecular characteristics are known that [...] Read more.
The genus Betacoronavirus, consisting of four main subgenera (Embecovirus, Merbecovirus, Nobecovirus, and Sarbecovirus), encompasses all clinically significant coronaviruses (CoVs), including SARS, MERS, and the SARS-CoV-2 virus responsible for current COVID-19 pandemic. Very few molecular characteristics are known that are specific for the genus Betacoronavirus or its different subgenera. In this study, our analyses of the sequences of four essential proteins of CoVs, viz., spike, nucleocapsid, envelope, and RNA-dependent RNA polymerase (RdRp), identified ten novel molecular signatures consisting of conserved signature indels (CSIs) in these proteins which are specific for the genus Betacoronavirus or its subgenera. Of these CSIs, two 14-aa-conserved deletions found within the heptad repeat motifs 1 and 2 of the spike protein are specific for all betacoronaviruses, except for their shared presence in the highly infectious avian coronavirus. Six additional CSIs present in the nucleocapsid protein and one CSI in the RdRp protein are distinctive characteristics of either the Merbecovirus, Nobecovirus, or Sarbecovirus subgenera. In addition, a 4-aa insert is present in the spike protein, which is uniquely shared by all viruses from the subgenera Merbecovirus, Nobecovirus, and Sarbecovirus, but absent in Embecovirus and all other genera of CoVs. This molecular signature provides evidence that viruses from the three subgenera sharing this CSI are more closely related to each other, and they evolved after the divergence of embecoviruses and other CoVs. As all CSIs specific for different groups of CoVs are flanked by conserved regions, their sequences provide novel means for identifying the above groups of CoVs and for developing novel diagnostic tests. Furthermore, our analyses of the structures of the spike and nucleocapsid proteins show that all identified CSIs are localized in the surface-exposed loops of these protein. It is postulated that these surface loops, through their interactions with other cellular proteins/ligands, play important roles in the biology/pathology of these viruses. Full article
(This article belongs to the Special Issue Comparative Genomics of Human Pathogens)
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