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Viruses
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Bioinformatics Research on SARS-CoV-2
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Bioinformatics Research on SARS-CoV-2

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "SARS-CoV-2 and COVID-19".

Deadline for manuscript submissions: closed (31 October 2022) | Viewed by 34904

Special Issue Editors

Dr. Kimberly A. Bishop-Lilly

E-Mail Website
Guest Editor
Genomics & Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD 21702, USA
Interests: virus discovery; phage genomics; metagenomic sequencing; biosurveillance; RNA virus biology; virus entry
Dr. Irina Maljkovic Berry

E-Mail Website
Guest Editor
Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
Interests: SARS-CoV-2; bioinformatics; viral genetics; phylogenetics; evolution
Dr. Todd J. Treangen

E-Mail Website
Guest Editor
Department of Computer Science, Rice University, Houston, TX 77005, USA
Interests: ‪bioinformatics‬; computational genomics‬; ‪metagenomics‬

Special Issue Information

Dear Colleagues,

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), the causative agent of the COVID-19 pandemic, emerged at a time when high-throughput sequencing is finally cost-effective enough to be used routinely not only in industry, but also in government and academic laboratories around the world.  COVID-19 has brought into focus the importance of genomic surveillance through sequencing and has aided in the improvement of global sequencing capabilities to support public health and research. Bioinformatics, a crucial component of the sequencing process, is however often an issue for smaller or newer laboratories.  Remarkably, there are over 9 million SARS-CoV-2 genomes available, but this deluge of genomic data has outpaced the development of user-friendly and cost-effective bioinformatic solutions, in terms of both hardware and software solutions.  Despite these challenges, the COVID-19 pandemic has been met with an unprecedented widespread application of molecular detection methods, to include sequencing-based analyses for molecular epidemiology as well as to monitor variant emergence and resistance to medical countermeasures.  The data produced will likely provide lasting impact on our understanding of how a novel virus spreads and adapts.

This Special Issue will focus on bioinformatic research on SARS-CoV-2, to include challenges, best practices, and novel applications of bioinformatic research to pandemic response.

Dr. Kimberly A. Bishop-Lilly
Dr. Irina Maljkovic Berry
Dr. Todd J. Treangen
Guest Editors

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. Viruses 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

  • SARS-CoV-2
  • bioinformatics
  • computational biology
  • phylogenetics
  • evolution
  • genomic surveillance
  • metagenomics

Published Papers (15 papers)

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14 pages, 1608 KiB  
Article
SARSMutOnto: An Ontology for SARS-CoV-2 Lineages and Mutations
by Jamal Bakkas, Mohamed Hanine, Abderrahman Chekry, Said Gounane, Isabel de la Torre Díez, Vivian Lipari, Nohora Milena Martínez López and Imran Ashraf
Viruses 2023, 15(2), 505; https://0-doi-org.brum.beds.ac.uk/10.3390/v15020505 - 11 Feb 2023
Cited by 1 | Viewed by 1678
Abstract
Mutations allow viruses to continuously evolve by changing their genetic code to adapt to the hosts they infect. It is an adaptive and evolutionary mechanism that helps viruses acquire characteristics favoring their survival and propagation. The COVID-19 pandemic declared by the WHO in [...] Read more.
Mutations allow viruses to continuously evolve by changing their genetic code to adapt to the hosts they infect. It is an adaptive and evolutionary mechanism that helps viruses acquire characteristics favoring their survival and propagation. The COVID-19 pandemic declared by the WHO in March 2020 is caused by the SARS-CoV-2 virus. The non-stop adaptive mutations of this virus and the emergence of several variants over time with characteristics favoring their spread constitute one of the biggest obstacles that researchers face in controlling this pandemic. Understanding the mutation mechanism allows for the adoption of anticipatory measures and the proposal of strategies to control its propagation. In this study, we focus on the mutations of this virus, and we propose the SARSMutOnto ontology to model SARS-CoV-2 mutations reported by Pango researchers. A detailed description is given for each mutation. The genes where the mutations occur and the genomic structure of this virus are also included. The sub-lineages and the recombinant sub-lineages resulting from these mutations are additionally represented while maintaining their hierarchy. We developed a Python-based tool to automatically generate this ontology from various published Pango source files. At the end of this paper, we provide some examples of SPARQL queries that can be used to exploit this ontology. SARSMutOnto might become a ‘wet bench’ machine learning tool for predicting likely future mutations based on previous mutations. Full article
(This article belongs to the Special Issue Bioinformatics Research on SARS-CoV-2)
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14 pages, 3195 KiB  
Article
Tracking of Mutational Signature of SARS-CoV-2 Omicron on Distinct Continents and Little Difference was Found
by Shu-Yue Zheng, Yun-Peng Zhang, Yu-Xin Liu, Wei Zhao, Xiang-Lei Peng, Yan-Peng Zheng, Yuan-Hui Fu, Jie-Mei Yu and Jin-Sheng He
Viruses 2023, 15(2), 321; https://0-doi-org.brum.beds.ac.uk/10.3390/v15020321 - 23 Jan 2023
Cited by 1 | Viewed by 1539
Abstract
The Omicron variant is currently ravaging the world, raising serious concern globally. Monitoring genomic variations and determining their influence on biological features are critical for tracing its ongoing transmission and facilitating effective measures. Based on large-scale sequences from different continents, this study found [...] Read more.
The Omicron variant is currently ravaging the world, raising serious concern globally. Monitoring genomic variations and determining their influence on biological features are critical for tracing its ongoing transmission and facilitating effective measures. Based on large-scale sequences from different continents, this study found that: (i) The genetic diversity of Omicron is much lower than that of the Delta variant. Still, eight deletions (Del 1–8) and 1 insertion, as well as 130 SNPs, were detected on the Omicron genomes, with two deletions (Del 3 and 4) and 38 SNPs commonly detected on all continents and exhibiting high-occurring frequencies. (ii) Four groups of tightly linked SNPs (linkage I–IV) were detected, among which linkage I, containing 38 SNPs, with 6 located in the RBD, increased its occurring frequency remarkably over time. (iii) The third codons of the Omicron shouldered the most mutation pressures, while the second codons presented the least flexibility. (iv) Four major mutants with amino acid substitutions in the RBD were detected, and further structural analysis suggested that the substitutions did not alter the viral receptor binding ability greatly. It was inferred that though the Omicron genome harbored great changes in antigenicity and remarkable ability to evade immunity, it was immune-pressure selected. This study tracked mutational signatures of Omicron variant and the potential biological significance of the SNPs, and the linkages await further functional verification. Full article
(This article belongs to the Special Issue Bioinformatics Research on SARS-CoV-2)
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14 pages, 8746 KiB  
Article
Comparison of the Diagnostic Performance of Deep Learning Algorithms for Reducing the Time Required for COVID-19 RT–PCR Testing
by Yoonje Lee, Yu-Seop Kim, Da In Lee, Seri Jeong, Gu Hyun Kang, Yong Soo Jang, Wonhee Kim, Hyun Young Choi and Jae Guk Kim
Viruses 2023, 15(2), 304; https://0-doi-org.brum.beds.ac.uk/10.3390/v15020304 - 22 Jan 2023
Cited by 1 | Viewed by 1629
Abstract
(1) Background: Rapid and accurate negative discrimination enables efficient management of scarce isolated bed resources and adequate patient accommodation in the majority of areas experiencing an explosion of confirmed cases due to Omicron mutations. Until now, methods for artificial intelligence or deep learning [...] Read more.
(1) Background: Rapid and accurate negative discrimination enables efficient management of scarce isolated bed resources and adequate patient accommodation in the majority of areas experiencing an explosion of confirmed cases due to Omicron mutations. Until now, methods for artificial intelligence or deep learning to replace time-consuming RT-PCR have relied on CXR, chest CT, blood test results, or clinical information. (2) Methods: We proposed and compared five different types of deep learning algorithms (RNN, LSTM, Bi-LSTM, GRU, and transformer) for reducing the time required for RT-PCR diagnosis by learning the change in fluorescence value derived over time during the RT-PCR process. (3) Results: Among the five deep learning algorithms capable of training time series data, Bi-LSTM and GRU were shown to be able to decrease the time required for RT–PCR diagnosis by half or by 25% without significantly impairing the diagnostic performance of the COVID-19 RT–PCR test. (4) Conclusions: The diagnostic performance of the model developed in this study when 40 cycles of RT–PCR are used for diagnosis shows the possibility of nearly halving the time required for RT–PCR diagnosis. Full article
(This article belongs to the Special Issue Bioinformatics Research on SARS-CoV-2)
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11 pages, 3400 KiB  
Article
Origin and Reversion of Omicron Core Mutations in the Evolution of SARS-CoV-2 Genomes
by Xinwei Zhao, Luyao Qin, Xiao Ding, Yudi Zhang, Xuefeng Niu, Feng Gao, Taijiao Jiang and Ling Chen
Viruses 2023, 15(1), 30; https://0-doi-org.brum.beds.ac.uk/10.3390/v15010030 - 21 Dec 2022
Cited by 3 | Viewed by 2052
Abstract
Genetic analyses showed nearly 30 amino acid mutations occurred in the spike protein of the Omicron variant of SARS-CoV-2. However, how these mutations occurred and changed during the generation and development of Omicron remains unclear. In this study, 6.7 million (all publicly available [...] Read more.
Genetic analyses showed nearly 30 amino acid mutations occurred in the spike protein of the Omicron variant of SARS-CoV-2. However, how these mutations occurred and changed during the generation and development of Omicron remains unclear. In this study, 6.7 million (all publicly available data from 2020/04/01 to 2022/04/01) SARS-CoV-2 genomes were analyzed to track the origin and evolution of Omicron variants and to reveal the genetic pathways of the generation of core mutations in Omicron. The haplotype network visualized the pre-Omicron, intact-Omicron, and post-Omicron variants and revealed their evolutionary direction. The correlation analysis showed the correlation feature of the core mutations in Omicron. Moreover, we found some core mutations, such as 142D, 417N, 440K, and 764K, reversed to ancestral residues (142G, 417K, 440N, and 764N) in the post-Omicron variant, suggesting the reverse mutations provided sources for the emergence of new variants. In summary, our analysis probed the origin and further evolution of Omicron sub-variants, which may add to our understanding of new variants and facilitate the control of the pandemic. Full article
(This article belongs to the Special Issue Bioinformatics Research on SARS-CoV-2)
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16 pages, 3828 KiB  
Article
Exploration of Potent Antiviral Phytomedicines from Lauraceae Family Plants against SARS-CoV-2 Main Protease
by Himashree Bora, Madhu Kamle, Hesham Hassan, Ahmed Al-Emam, Sidharth Chopra, Nikhil Kirtipal, Shiv Bharadwaj and Pradeep Kumar
Viruses 2022, 14(12), 2783; https://0-doi-org.brum.beds.ac.uk/10.3390/v14122783 - 14 Dec 2022
Cited by 2 | Viewed by 2075
Abstract
A new Coronaviridae strain, Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), emerged from Wuhan city of China and caused one of the substantial global health calamities in December 2019. Even though several vaccines and drugs have been developed worldwide since COVID-19, a cost-effective drug [...] Read more.
A new Coronaviridae strain, Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), emerged from Wuhan city of China and caused one of the substantial global health calamities in December 2019. Even though several vaccines and drugs have been developed worldwide since COVID-19, a cost-effective drug with the least side effects is still unavailable. Currently, plant-derived compounds are mostly preferred to develop antiviral therapeutics due to its less toxicity, easy access, and cost-effective characteristics. Therefore, in this study, 124 phytochemical compounds from plants of Lauraceae family with medicinal properties were virtually screened against SARS-CoV-2 Mpro. Identification of four phytomolecules, i.e., cassameridine, laetanine, litseferine and cassythicine, with docking scores −9.3, −8.8, −8.6, and −8.6 kcal/mol, respectively, were undertaken by virtual screening, and molecular docking. Furthermore, the molecular dynamic simulation and essential dynamics analysis have contributed in understanding the stability and inhibitory effect of these selected compounds. These phytomolecules can be considered for further in vitro and in vivo experimental study to develop anti-SARS-CoV-2 therapeutics targeting the main protease (Mpro). Full article
(This article belongs to the Special Issue Bioinformatics Research on SARS-CoV-2)
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17 pages, 2034 KiB  
Article
Bayesian Molecular Dating Analyses Combined with Mutational Profiling Suggest an Independent Origin and Evolution of SARS-CoV-2 Omicron BA.1 and BA.2 Sub-Lineages
by Naveen Kumar, Rahul Kaushik, Ashutosh Singh, Vladimir N. Uversky, Kam Y. J. Zhang, Upasana Sahu, Sandeep Bhatia and Aniket Sanyal
Viruses 2022, 14(12), 2764; https://0-doi-org.brum.beds.ac.uk/10.3390/v14122764 - 12 Dec 2022
Cited by 3 | Viewed by 2106
Abstract
The ongoing evolution of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has resulted in the recent emergence of a highly divergent variant of concern (VOC) defined as Omicron or B.1.1.529. This VOC is of particular concern because it has the potential to evade most therapeutic [...] Read more.
The ongoing evolution of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has resulted in the recent emergence of a highly divergent variant of concern (VOC) defined as Omicron or B.1.1.529. This VOC is of particular concern because it has the potential to evade most therapeutic antibodies and has undergone a sustained genetic evolution, resulting in the emergence of five distinct sub-lineages. However, the evolutionary dynamics of the initially identified Omicron BA.1 and BA.2 sub-lineages remain poorly understood. Herein, we combined Bayesian phylogenetic analysis, mutational profiling, and selection pressure analysis to track the virus’s genetic changes that drive the early evolutionary dynamics of the Omicron. Based on the Omicron dataset chosen for the improved temporal signals and sampled globally between November 2021 and January 2022, the most recent common ancestor (tMRCA) and substitution rates for BA.1 were estimated to be that of 18 September 2021 (95% highest posterior density (HPD), 4 August–22 October 2021) and 1.435 × 10−3 (95% HPD  =  1.021 × 10−3 − 1.869 × 10−3) substitution/site/year, respectively, whereas 3 November 2021 (95% highest posterior density (HPD) 26 September–28 November 2021) and 1.074 × 10−3 (95% HPD  =  6.444 × 10−4 − 1.586 × 10−3) substitution/site/year were estimated for the BA.2 sub-lineage. The findings of this study suggest that the Omicron BA.1 and BA.2 sub-lineages originated independently and evolved over time. Furthermore, we identified multiple sites in the spike protein undergoing continued diversifying selection that may alter the neutralization profile of BA.1. This study sheds light on the ongoing global genomic surveillance and Bayesian molecular dating analyses to better understand the evolutionary dynamics of the virus and, as a result, mitigate the impact of emerging variants on public health. Full article
(This article belongs to the Special Issue Bioinformatics Research on SARS-CoV-2)
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27 pages, 1689 KiB  
Article
Immunoinformatics Identification of the Conserved and Cross-Reactive T-Cell Epitopes of SARS-CoV-2 with Human Common Cold Coronaviruses, SARS-CoV, MERS-CoV and Live Attenuated Vaccines Presented by HLA Alleles of Indonesian Population
by Marsia Gustiananda, Vivi Julietta, Angelika Hermawan, Gabriella Gita Febriana, Rio Hermantara, Lidya Kristiani, Elizabeth Sidhartha, Richard Sutejo, David Agustriawan, Sita Andarini and Arli Aditya Parikesit
Viruses 2022, 14(11), 2328; https://0-doi-org.brum.beds.ac.uk/10.3390/v14112328 - 24 Oct 2022
Cited by 1 | Viewed by 2325
Abstract
Reports on T-cell cross-reactivity against SARS-CoV-2 epitopes in unexposed individuals have been linked with prior exposure to the human common cold coronaviruses (HCCCs). Several studies suggested that cross-reactive T-cells response to live attenuated vaccines (LAVs) such as BCG (Bacillus Calmette–Guérin), OPV (Oral Polio [...] Read more.
Reports on T-cell cross-reactivity against SARS-CoV-2 epitopes in unexposed individuals have been linked with prior exposure to the human common cold coronaviruses (HCCCs). Several studies suggested that cross-reactive T-cells response to live attenuated vaccines (LAVs) such as BCG (Bacillus Calmette–Guérin), OPV (Oral Polio Vaccine), and MMR (measles, mumps, and rubella) can limit the development and severity of COVID-19. This study aims to identify potential cross-reactivity between SARS-CoV-2, HCCCs, and LAVs in the context of T-cell epitopes peptides presented by HLA (Human Leukocyte Antigen) alleles of the Indonesian population. SARS-CoV-2 derived T-cell epitopes were predicted using immunoinformatics tools and assessed for their conservancy, variability, and population coverage. Two fully conserved epitopes with 100% similarity and nine heterologous epitopes with identical T-cell receptor (TCR) contact residues were identified from the ORF1ab fragment of SARS-CoV-2 and all HCCCs. Cross-reactive epitopes from various proteins of SARS-CoV-2 and LAVs were also identified (15 epitopes from BCG, 7 epitopes from MMR, but none from OPV). A majority of the identified epitopes were observed to belong to ORF1ab, further suggesting the vital role of ORF1ab in the coronaviruses family and suggesting it as a candidate for a potential universal coronavirus vaccine that protects against severe disease by inducing cell mediated immunity. Full article
(This article belongs to the Special Issue Bioinformatics Research on SARS-CoV-2)
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28 pages, 3979 KiB  
Article
Systems Bioinformatics Reveals Possible Relationship between COVID-19 and the Development of Neurological Diseases and Neuropsychiatric Disorders
by Anna Onisiforou and George M. Spyrou
Viruses 2022, 14(10), 2270; https://0-doi-org.brum.beds.ac.uk/10.3390/v14102270 - 16 Oct 2022
Cited by 2 | Viewed by 2825
Abstract
Coronavirus Disease 2019 (COVID-19) is associated with increased incidence of neurological diseases and neuropsychiatric disorders after infection, but how it contributes to their development remains under investigation. Here, we investigate the possible relationship between COVID-19 and the development of ten neurological disorders and [...] Read more.
Coronavirus Disease 2019 (COVID-19) is associated with increased incidence of neurological diseases and neuropsychiatric disorders after infection, but how it contributes to their development remains under investigation. Here, we investigate the possible relationship between COVID-19 and the development of ten neurological disorders and three neuropsychiatric disorders by exploring two pathological mechanisms: (i) dysregulation of host biological processes via virus–host protein–protein interactions (PPIs), and (ii) autoreactivity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epitopes with host “self” proteins via molecular mimicry. We also identify potential genetic risk factors which in combination with SARS-CoV-2 infection might lead to disease development. Our analysis indicated that neurodegenerative diseases (NDs) have a higher number of disease-associated biological processes that can be modulated by SARS-CoV-2 via virus–host PPIs than neuropsychiatric disorders. The sequence similarity analysis indicated the presence of several matching 5-mer and/or 6-mer linear motifs between SARS-CoV-2 epitopes with autoreactive epitopes found in Alzheimer’s Disease (AD), Parkinson’s Disease (PD), Myasthenia Gravis (MG) and Multiple Sclerosis (MS). The results include autoreactive epitopes that recognize amyloid-beta precursor protein (APP), microtubule-associated protein tau (MAPT), acetylcholine receptors, glial fibrillary acidic protein (GFAP), neurofilament light polypeptide (NfL) and major myelin proteins. Altogether, our results suggest that there might be an increased risk for the development of NDs after COVID-19 both via autoreactivity and virus–host PPIs. Full article
(This article belongs to the Special Issue Bioinformatics Research on SARS-CoV-2)
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16 pages, 1451 KiB  
Article
Intrahost SARS-CoV-2 k-mer Identification Method (iSKIM) for Rapid Detection of Mutations of Concern Reveals Emergence of Global Mutation Patterns
by Ashley Thommana, Migun Shakya, Jaykumar Gandhi, Christian K. Fung, Patrick S. G. Chain, Irina Maljkovic Berry and Matthew A. Conte
Viruses 2022, 14(10), 2128; https://0-doi-org.brum.beds.ac.uk/10.3390/v14102128 - 27 Sep 2022
Viewed by 1716
Abstract
Despite unprecedented global sequencing and surveillance of SARS-CoV-2, timely identification of the emergence and spread of novel variants of concern (VoCs) remains a challenge. Several million raw genome sequencing runs are now publicly available. We sought to survey these datasets for intrahost variation [...] Read more.
Despite unprecedented global sequencing and surveillance of SARS-CoV-2, timely identification of the emergence and spread of novel variants of concern (VoCs) remains a challenge. Several million raw genome sequencing runs are now publicly available. We sought to survey these datasets for intrahost variation to study emerging mutations of concern. We developed iSKIM (“intrahost SARS-CoV-2 k-mer identification method”) to relatively quickly and efficiently screen the many SARS-CoV-2 datasets to identify intrahost mutations belonging to lineages of concern. Certain mutations surged in frequency as intrahost minor variants just prior to, or while lineages of concern arose. The Spike N501Y change common to several VoCs was found as a minor variant in 834 samples as early as October 2020. This coincides with the timing of the first detected samples with this mutation in the Alpha/B.1.1.7 and Beta/B.1.351 lineages. Using iSKIM, we also found that Spike L452R was detected as an intrahost minor variant as early as September 2020, prior to the observed rise of the Epsilon/B.1.429/B.1.427 lineages in late 2020. iSKIM rapidly screens for mutations of interest in raw data, prior to genome assembly, and can be used to detect increases in intrahost variants, potentially providing an early indication of novel variant spread. Full article
(This article belongs to the Special Issue Bioinformatics Research on SARS-CoV-2)
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13 pages, 1699 KiB  
Article
SARS-CoV-2 Infections in Vaccinated and Unvaccinated Populations in Camp Lemonnier, Djibouti, from April 2020 to January 2022
by Catherine E. Arnold, Logan J. Voegtly, Emily K. Stefanov, Matthew R. Lueder, Andrea E. Luquette, Robin H. Miller, Haven L. Miner, Andrew J. Bennett, Lindsay Glang, Tara N. McGinnis, Kristie E. Reisinger, Jae W. Dugan, Michael A. Mangat, Daniel J. Silberger, Rebecca L. Pavlicek, Chaselynn M. Watters, Gregory K. Rice, Francisco Malagon, Regina Z. Cer, Stephen M. Eggan and Kimberly A. Bishop-Lillyadd Show full author list remove Hide full author list
Viruses 2022, 14(9), 1918; https://0-doi-org.brum.beds.ac.uk/10.3390/v14091918 - 30 Aug 2022
Viewed by 1681
Abstract
The global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted the disparity between developed and developing countries for infectious disease surveillance and the sequencing of pathogen genomes. The majority of SARS-CoV-2 sequences published are from Europe, North America, and [...] Read more.
The global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted the disparity between developed and developing countries for infectious disease surveillance and the sequencing of pathogen genomes. The majority of SARS-CoV-2 sequences published are from Europe, North America, and Asia. Between April 2020 and January 2022, 795 SARS-CoV-2-positive nares swabs from individuals in the U.S. Navy installation Camp Lemonnier, Djibouti, were collected, sequenced, and analyzed. In this study, we described the results of genomic sequencing and analysis for 589 samples, the first published viral sequences for Djibouti, including 196 cases of vaccine breakthrough infections. This study contributes to the knowledge base of circulating SARS-CoV-2 lineages in the under-sampled country of Djibouti, where only 716 total genome sequences are available at time of publication. Our analysis resulted in the detection of circulating variants of concern, mutations of interest in lineages in which those mutations are not common, and emerging spike mutations. Full article
(This article belongs to the Special Issue Bioinformatics Research on SARS-CoV-2)
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25 pages, 4657 KiB  
Article
The Flexible, Extended Coil of the PDZ-Binding Motif of the Three Deadly Human Coronavirus E Proteins Plays a Role in Pathogenicity
by Dewald Schoeman, Ruben Cloete and Burtram C. Fielding
Viruses 2022, 14(8), 1707; https://0-doi-org.brum.beds.ac.uk/10.3390/v14081707 - 2 Aug 2022
Cited by 4 | Viewed by 3681
Abstract
The less virulent human (h) coronaviruses (CoVs) 229E, NL63, OC43, and HKU1 cause mild, self-limiting respiratory tract infections, while the more virulent SARS-CoV-1, MERS-CoV, and SARS-CoV-2 have caused severe outbreaks. The CoV envelope (E) protein, an important contributor to the pathogenesis of severe [...] Read more.
The less virulent human (h) coronaviruses (CoVs) 229E, NL63, OC43, and HKU1 cause mild, self-limiting respiratory tract infections, while the more virulent SARS-CoV-1, MERS-CoV, and SARS-CoV-2 have caused severe outbreaks. The CoV envelope (E) protein, an important contributor to the pathogenesis of severe hCoV infections, may provide insight into this disparate severity of the disease. We, therefore, generated full-length E protein models for SARS-CoV-1 and -2, MERS-CoV, HCoV-229E, and HCoV-NL63 and docked C-terminal peptides of each model to the PDZ domain of the human PALS1 protein. The PDZ-binding motif (PBM) of the SARS-CoV-1 and -2 and MERS-CoV models adopted a more flexible, extended coil, while the HCoV-229E and HCoV-NL63 models adopted a less flexible alpha helix. All the E peptides docked to PALS1 occupied the same binding site and the more virulent hCoV E peptides generally interacted more stably with PALS1 than the less virulent ones. We hypothesize that the increased flexibility of the PBM in the more virulent hCoVs facilitates more stable binding to various host proteins, thereby contributing to more severe disease. This is the first paper to model full-length 3D structures for both the more virulent and less virulent hCoV E proteins, providing novel insights for possible drug and/or vaccine development. Full article
(This article belongs to the Special Issue Bioinformatics Research on SARS-CoV-2)
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19 pages, 4626 KiB  
Article
Sequence Similarity Network Analysis Provides Insight into the Temporal and Geographical Distribution of Mutations in SARS-CoV-2 Spike Protein
by Shruti S. Patil, Helen N. Catanese, Kelly A. Brayton, Eric T. Lofgren and Assefaw H. Gebremedhin
Viruses 2022, 14(8), 1672; https://0-doi-org.brum.beds.ac.uk/10.3390/v14081672 - 29 Jul 2022
Viewed by 1840
Abstract
Severe acute respiratory syndrome-related coronavirus (SARS-CoV-2), which still infects hundreds of thousands of people globally each day despite various countermeasures, has been mutating rapidly. Mutations in the spike (S) protein seem to play a vital role in viral stability, transmission, and adaptability. Therefore, [...] Read more.
Severe acute respiratory syndrome-related coronavirus (SARS-CoV-2), which still infects hundreds of thousands of people globally each day despite various countermeasures, has been mutating rapidly. Mutations in the spike (S) protein seem to play a vital role in viral stability, transmission, and adaptability. Therefore, to control the spread of the virus, it is important to gain insight into the evolution and transmission of the S protein. This study deals with the temporal and geographical distribution of mutant S proteins from sequences gathered across the US over a period of 19 months in 2020 and 2021. The S protein sequences are studied using two approaches: (i) multiple sequence alignment is used to identify prominent mutations and highly mutable regions and (ii) sequence similarity networks are subsequently employed to gain further insight and study mutation profiles of concerning variants across the defined time periods and states. Additionally, we tracked the variants using visualizations on geographical maps. The visualizations produced using the Directed Weighted All Nearest Neighbors (DiWANN) networks and maps provided insights into the transmission of the virus that reflect well the statistics reported for the time periods studied. We found that the networks created using DiWANN are superior to commonly used approximate distance networks created using BLAST bitscores. The study offers a richer computational approach to analyze the transmission profile of the prominent S protein mutations in SARS-CoV-2 and can be extended to other proteins and viruses. Full article
(This article belongs to the Special Issue Bioinformatics Research on SARS-CoV-2)
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16 pages, 467 KiB  
Article
SARS-CoV-2 Whole-Genome Sequencing by Ion S5 Technology—Challenges, Protocol Optimization and Success Rates for Different Strains
by Maria Szargut, Sandra Cytacka, Karol Serwin, Anna Urbańska, Romain Gastineau, Miłosz Parczewski and Andrzej Ossowski
Viruses 2022, 14(6), 1230; https://0-doi-org.brum.beds.ac.uk/10.3390/v14061230 - 6 Jun 2022
Cited by 1 | Viewed by 2256
Abstract
The COVID-19 pandemic demonstrated how rapidly various molecular methods can be adapted for a Public Health Emergency. Whether a need arises for whole-genome studies (next-generation sequencing), fast and high-throughput diagnostics (reverse-transcription real-time PCR) or global immunization (construction of mRNA or viral vector vaccines), [...] Read more.
The COVID-19 pandemic demonstrated how rapidly various molecular methods can be adapted for a Public Health Emergency. Whether a need arises for whole-genome studies (next-generation sequencing), fast and high-throughput diagnostics (reverse-transcription real-time PCR) or global immunization (construction of mRNA or viral vector vaccines), the scientific community has been able to answer all these calls. In this study, we aimed at the assessment of effectiveness of the commercially available solution for full-genome SARS-CoV-2 sequencing (AmpliSeq™ SARS-CoV-2 Research Panel and Ion AmpliSeq™ Library Kit Plus, Thermo Fisher Scientific). The study is based on 634 samples obtained from patients from Poland, with varying viral load, assigned to a number of lineages. Here, we also present the results of protocol modifications implemented to obtain high-quality genomic data. We found that a modified library preparation protocol required less viral RNA input in order to obtain the optimal library quantity. Concurrently, neither concentration of cDNA nor reamplification of libraries from low-template samples improved the results of sequencing. On the basis of the amplicon success rates, we propose one amplicon to be redesigned, namely, the r1_1.15.1421280, for which less than 50 reads were produced by 44% of samples. Additionally, we found several mutations within different SARS-CoV-2 lineages that cause the neighboring amplicons to underperform. Therefore, due to constant SARS-CoV-2 evolution, we support the idea of conducting ongoing sequence-based surveillance studies to continuously validate commercially available RT-PCR and whole-genome sequencing solutions. Full article
(This article belongs to the Special Issue Bioinformatics Research on SARS-CoV-2)
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Review

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14 pages, 2009 KiB  
Review
Development of Single-Cell Transcriptomics and Its Application in COVID-19
by Chaochao Wang, Ting Huyan, Xiaojie Zhou, Xuanshuo Zhang, Suyang Duan, Shan Gao, Shanfeng Jiang and Qi Li
Viruses 2022, 14(10), 2271; https://0-doi-org.brum.beds.ac.uk/10.3390/v14102271 - 16 Oct 2022
Cited by 1 | Viewed by 2184
Abstract
Over the last three years, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-related health crisis has claimed over six million lives and caused USD 12 trillion losses to the global economy. SARS-CoV-2 continuously mutates and evolves with a high basic reproduction number (R0), [...] Read more.
Over the last three years, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-related health crisis has claimed over six million lives and caused USD 12 trillion losses to the global economy. SARS-CoV-2 continuously mutates and evolves with a high basic reproduction number (R0), resulting in a variety of clinical manifestations ranging from asymptomatic infection to acute respiratory distress syndrome (ARDS) and even death. To gain a better understanding of coronavirus disease 2019 (COVID-19), it is critical to investigate the components that cause various clinical manifestations. Single-cell sequencing has substantial advantages in terms of identifying differentially expressed genes among individual cells, which can provide a better understanding of the various physiological and pathological processes. This article reviewed the use of single-cell transcriptomics in COVID-19 research, examined the immune response disparities generated by SARS-CoV-2, and offered insights regarding how to improve COVID-19 diagnosis and treatment plans. Full article
(This article belongs to the Special Issue Bioinformatics Research on SARS-CoV-2)
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15 pages, 4217 KiB  
Review
Immune Escape Associated with RBD Omicron Mutations and SARS-CoV-2 Evolution Dynamics
by Aleksandr V. Kudriavtsev, Anna V. Vakhrusheva, Valery N. Novoseletsky, Marine E. Bozdaganyan, Konstantin V. Shaitan, Mikhail P. Kirpichnikov and Olga S. Sokolova
Viruses 2022, 14(8), 1603; https://0-doi-org.brum.beds.ac.uk/10.3390/v14081603 - 22 Jul 2022
Cited by 23 | Viewed by 3543
Abstract
The evolution and the emergence of new mutations of viruses affect their transmissibility and/or pathogenicity features, depending on different evolutionary scenarios of virus adaptation to the host. A typical trade-off scenario of SARS-CoV-2 evolution has been proposed, which leads to the appearance of [...] Read more.
The evolution and the emergence of new mutations of viruses affect their transmissibility and/or pathogenicity features, depending on different evolutionary scenarios of virus adaptation to the host. A typical trade-off scenario of SARS-CoV-2 evolution has been proposed, which leads to the appearance of an Omicron strain with lowered lethality, yet enhanced transmissibility. This direction of evolution might be partly explained by virus adaptation to therapeutic agents and enhanced escape from vaccine-induced and natural immunity formed by other SARS-CoV-2 strains. Omicron’s high mutation rate in the Spike protein, as well as its previously described high genome mutation rate (Kandeel et al., 2021), revealed a gap between it and other SARS-CoV-2 strains, indicating the absence of a transitional evolutionary form to the Omicron strain. Therefore, Omicron has emerged as a new serotype divergent from the evolutionary lineage of other SARS-CoV-2 strains. Omicron is a rapidly evolving variant of high concern, whose new subvariants continue to manifest. Its further understanding and the further monitoring of key mutations that provide virus immune escape and/or high affinity towards the receptor could be useful for vaccine and therapeutic development in order to control the evolutionary direction of the COVID-19 pandemic. Full article
(This article belongs to the Special Issue Bioinformatics Research on SARS-CoV-2)
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