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Diagnostics
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Genomic Analysis of Infectious Diseases
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Genomic Analysis of Infectious Diseases

A special issue of Diagnostics (ISSN 2075-4418). This special issue belongs to the section "Diagnostic Microbiology and Infectious Disease".

Deadline for manuscript submissions: closed (30 September 2023) | Viewed by 12559

Special Issue Editor

Prof. Dr. Sayed Sartaj Sohrab

E-Mail Website
Guest Editor
Joined King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
Interests: molecular virology; diagnosis; genomic analysis; vaccine development

Special Issue Information

Dear Colleagues,

Infectious diseases are a leading cause of death and a serious concern for the human population globally. The disease is mainly caused by pathogenic microorganisms, like viruses, bacteria, fungi, and parasites, and rarely by Prions. Infectious diseases can be transmitted from person to person via vectors, animals, bug bites, environmental conditions, and contaminated food and water.

The genomic analysis of infectious disease plays an important role in the detection, identification, genetic variations, prediction of new pathogen emergence, drug resistance, functional element annotation, disease spread, transmission pattern, vaccine development, therapeutics, designing of control measures, and disease management. Additionally, the genomic information offers an opportunity to analyze host-pathogen interaction, treatment, and prevention in both clinical practices as well as public health settings.

For rapid detection and genomic analysis of infectious agents, various advanced technologies and methods have emerged. These technologies significantly contribute to the development of disease-control measures and the prediction of new threats and outbreaks.

The Special Issue: ‘Genomic Analysis of Infectious Diseases’ invite eminent researchers/clinicians to submit their original research papers, review papers, brief and case reports. The main objectives of this Special Issue are to provide updated information about advanced molecular diagnostic techniques and genomic analysis of infectious diseases.

This Special Issue will explore, but is not restricted to, the following topics:

  1. Advanced diagnostic technologies for infectious diseases.
  2. Genomic analysis of Infectious agents.
  3. Bioinformatics-based diagnostic tools for early detection of pathogens.
  4. Comparative diagnostics techniques and promotion of optimal practices of infectious diseases.
  5. Emergence/ re-emergence of new isolates/strains/variants of pathogens.
  6. Metagenomic analysis of infectious diseases.

Prof. Dr. Sayed Sartaj Sohrab
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. Diagnostics is an international peer-reviewed open access semimonthly 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

  • infectious agents
  • diagnosis
  • genome analysis
  • bioinformatics
  • metagenomics

Published Papers (6 papers)

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Research

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10 pages, 638 KiB  
Article
Genetic Association Studies of MICB and PLCE1 with Severity of Dengue in Indonesian and Taiwanese Populations
by Imaniar Noor Faridah, Haafizah Dania, Rita Maliza, Wan-Hsuan Chou, Wen-Hung Wang, Yen-Hsu Chen, Dyah Aryani Perwitasari and Wei-Chiao Chang
Diagnostics 2023, 13(21), 3365; https://doi.org/10.3390/diagnostics13213365 - 1 Nov 2023
Viewed by 913
Abstract
Dengue is an arboviral disease that has spread globally and become a major public health concern. A small proportion of patients may progress from symptomatic dengue fever (DF) to dengue hemorrhagic fever (DHF) or dengue shock syndrome (DSS). Findings from a previous genome-wide [...] Read more.
Dengue is an arboviral disease that has spread globally and become a major public health concern. A small proportion of patients may progress from symptomatic dengue fever (DF) to dengue hemorrhagic fever (DHF) or dengue shock syndrome (DSS). Findings from a previous genome-wide association study (GWAS) demonstrated that variations in the major histocompatibility complex (MHC) class I chain-related B (MICB) and the phospholipase C epsilon 1 (PLCE1) genes were related to DSS in a Vietnamese population. This study investigated associations of variations in MICB (rs3132468) and PLCE1 (rs3740360, rs3765524) with dengue severity and thrombocytopenia in both the Indonesian and Taiwanese populations. We sampled 160 patients from the Indonesian population and 273 patients from the Taiwanese population. None of the patients had DSS in the Taiwanese population. Based on age demographics, we found that dengue is more prevalent among younger individuals in the Indonesian population, whereas it has a greater impact on adults in the Taiwanese population. Our results showed the association between MICB rs3132468 and DSS. In addition, an association was identified between PLCE1 rs3740360 and DHF in secondary dengue in Indonesian patients. However, there is no association of MICB or PLCE1 variants with thrombocytopenia. This study highlights the value of genetic testing, which might be included in the clinical pathway for specific patients who can be protected from severe dengue. Full article
(This article belongs to the Special Issue Genomic Analysis of Infectious Diseases)
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18 pages, 2359 KiB  
Article
Molecular Mechanisms of Resistance to Direct-Acting Antiviral (DAA) Drugs for the Treatment of Hepatitis C Virus Infections
by Mohammad Asrar Izhari
Diagnostics 2023, 13(19), 3102; https://doi.org/10.3390/diagnostics13193102 - 30 Sep 2023
Cited by 3 | Viewed by 1303
Abstract
Hepatitis C virus (HCV) is a hepatotropic virus that affects millions of human lives worldwide. Direct-acting antiviral (DAA) regimens are the most effective HCV treatment option. However, amino acid substitution-dependent resistance to DAAs has been a major challenge. This study aimed to determine [...] Read more.
Hepatitis C virus (HCV) is a hepatotropic virus that affects millions of human lives worldwide. Direct-acting antiviral (DAA) regimens are the most effective HCV treatment option. However, amino acid substitution-dependent resistance to DAAs has been a major challenge. This study aimed to determine the increasing risk of DAA resistance due to substitutions in DAA target non-structural proteins (NS3/4A, NS5A, and NS5B). Using a Sequence Retrieval System (SRS) at the virus pathogen resource (ViPR/BV-BRC), n = 32763 target protein sequences were retrieved and analyzed for resistance-associated amino acid substitutions (RAASs) by the Sequence Feature Variant Type (SFVT) antiviral-resistance assessment modeling tool. Reference target protein sequences with 100% identity were retried from UniProt following NCBI BLAST. The types and locations of RAASs were identified and visualized by AlphaFold and PyMol. Linux-r-base/R-studio was used for the data presentation. Multi-drug-resistant variants of NS3/4A in genotype 1 (n = 9) and genotype 5 (n = 5) along with DAA-specific NS3/4A, NS5A, and NS5B variants were identified pan-genotypically. A total of 27 variants (RAASs) of all the targets were identified. Fourteen genotype 1-specific substitutions: V1196A, V1158I, D1194A/T/G, R1181K, T1080S, Q1106R, V1062A, S1148G, A1182V, Y2065N, M2000T, and L2003V were identified. The most frequent substitutions were V1062L and L2003M, followed by Q2002H. L2003V, Q2002H, M2000T, Y2065N, and NL2003M of NS5A and L2003M of NS5B conferred resistance to daclatasvir. S2702T NS5B was the sofosbuvir-resistant variant. D1194A NS3/4A was triple DAA (simeprevir, faldaprevir, and asunaprevir) resistant. The double-drug resistant variants R1181K (faldaprevir and asunaprevir), A1182V and Q1106K/R (faldaprevir and simeprevir), T1080S (faldaprevir and telaprevir), and single drug-resistant variants V1062L (telaprevir), D1194E/T (simeprevir), D1194G (asunaprevir), S1148A/G (simeprevir), and Q1106L (Boceprevir) of NS3/4A were determined. The molecular phenomenon of DAA resistance is paramount in the development of HCV drug candidates. RAASs in NS3, NS5A, and NS5B reduce the susceptibility to DAAs; therefore, continuous RAAS-dependent resistance profiling in HCV is recommended to minimize the probability of DAA therapeutic failure. Full article
(This article belongs to the Special Issue Genomic Analysis of Infectious Diseases)
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11 pages, 831 KiB  
Article
Distribution of Human Papillomavirus Genotypes among the Women of South Andaman Island, India
by Rehnuma Parvez, Paluru Vijayachari, Mrinmoy Kumar Saha, Lipika Biswas, Jawahar Ramasamy, Alwin Vins, Nisha Beniwal, S. Vasanthi, Sasikala Ramadoss, Harpreet Kaur and Muruganandam Nagarajan
Diagnostics 2023, 13(17), 2765; https://doi.org/10.3390/diagnostics13172765 - 25 Aug 2023
Viewed by 1299
Abstract
Background: Human Papillomavirus (HPV) causes various types of cancer in both men and women. Woman with HPV infection has a risk of developing invasive cervical cancer. Globally, HPV 16 and 18 were predominant. This study aims to find the distribution of various HPV [...] Read more.
Background: Human Papillomavirus (HPV) causes various types of cancer in both men and women. Woman with HPV infection has a risk of developing invasive cervical cancer. Globally, HPV 16 and 18 were predominant. This study aims to find the distribution of various HPV types in South Andaman. Methods: A cross-sectional study was conducted among women in South Andaman, where cervical scrapes were collected after collecting written informed consent. Detection of HPV genotypes was carried out by using a PCR assay. Further, sequencing analysis was performed using MEGA11 to identify various genotypes in this territory. Result: Of these 1000 samples, 32 were positive for HR-HPV 16, and four were positive for HR-HPV 18. Fifteen HPV genotypes were detected using molecular evolutionary analysis. Six cases were identified with multiple genotypes. The most prevalent genotype is HPV 16 which belongs to Lineage-A and sub-lineage A2. HPV 18 identified in South Andaman belonged to the lineage A1 to A5. Discussion: Various HPV types were identified among women in South Andaman. Global burden of cervical cancer associated with various HPV sub-lineages. HPV-16 A1 sub-lineage was globally widespread, whereas sub-lineages A1, A2 and D1 prevailed in South Andaman. Conclusions: HR-HPV identified in this study enlightens the importance of HPV vaccination among women in remote places. These findings will help to strengthen public health awareness programs and prevention strategies for women in remote areas. Full article
(This article belongs to the Special Issue Genomic Analysis of Infectious Diseases)
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19 pages, 2414 KiB  
Article
Helicobacter pylori (H. pylori) Infection-Associated Anemia in the Asir Region, Saudi Arabia
by Omar A. Al Mutawa, Mohammad Asrar Izhari, Raed A. Alharbi, Abdulmajeed Abdulghani A. Sindi, Abdullah M. Alqarni, Foton E. Alotaibi, Ahmed R. A. Gosady, Daifallah M. M. Dardari, Abdulrahman M. Almutairi, Mohammed Alshehri and Ahmed I. E. Athathi
Diagnostics 2023, 13(14), 2404; https://doi.org/10.3390/diagnostics13142404 - 18 Jul 2023
Cited by 3 | Viewed by 1856
Abstract
H. pylori (ubiquitous) and anemia together represent one of the growing health concerns globally. Gastroduodenal sequelae of H. pylori infection are distinguished; however, for the H. pylori infection and its implication in the development of anemia, iron has a significant health impact. We [...] Read more.
H. pylori (ubiquitous) and anemia together represent one of the growing health concerns globally. Gastroduodenal sequelae of H. pylori infection are distinguished; however, for the H. pylori infection and its implication in the development of anemia, iron has a significant health impact. We aimed to evaluate H. pylori infection-associated anemia by employing a logistic regression analysis model. A retrospective (case–control) study design-based assessment of the H. pylori associated-anemia. The study area was geo-referenced by QGIS/QuickMapServies. Descriptive and inferential statistical analyses were accomplished using the R-base–R-studio (v-4.0.2)-tidyverse. A p-value < 0.05 was the statistical significance cut-off value. A ggplot2 package was used for data representation and visualization. Mean ± SD age, Hb, MCV, ferritin, and RBC for overall study participants were measured to be 44.0 ± 13.58, 13.84 ± 2.49, 83.02 ± 8.31, 59.42 ± 68.37, and 5.14 ± 0.75, respectively. Decreased levels of Hb (infected vs. uninfected: 13.26 ± 2.92 vs. 14.42 ± 1.75, p < 0.001) ferritin (infected vs. uninfected: 48.11 ± 63.75 vs. 71.17 ± 71.14, p < 0.001), and MCV (infected vs. uninfected: 81.29 ± 9.13 vs. and 84.82 ± 6.93, p < 0.05) were measured to be associated with H. pylori infection when compared with H. pylori uninfected control group. Moreover, the magnitude (prevalence) of anemia (infected vs. uninfected: 78% vs. 21%, p < 0.001), iron deficiency anemia (IDA) (infected vs. uninfected: 63.3% vs. 36.6%, p < 0.001), and microcytic anemia (infected vs. uninfected: 71.6% vs. 46.1%, p < 0.001) were significantly different among the H. pylori-infected participants. The higher likelihood of developing anemia (AOR; 4.98, 95% CI; 3.089–8.308, p < 0.001), IDA (AOR; 3.061, 95% CI; 2.135–4.416, p < 0.001), and microcytic anemia (AOR; 3.289, 95% CI; 2.213–4.949, p < 0.001) by 398%, 206.1%, and 229%, respectively, was associated with H. pylori-infected. We recommend the regular monitoring of hematological parameters and eradication of H. pylori infection to minimize the extra-gastric health consequences of H. pylori infection. Full article
(This article belongs to the Special Issue Genomic Analysis of Infectious Diseases)
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13 pages, 1270 KiB  
Article
Comprehensive In Silico Characterization of the Coding and Non-Coding SNPs in Human Dectin-1 Gene with the Potential of High-Risk Pathogenicity Associated with Fungal Infections
by Hakeemah H. Al-nakhle and Aiah M. Khateb
Diagnostics 2023, 13(10), 1785; https://doi.org/10.3390/diagnostics13101785 - 18 May 2023
Viewed by 1667
Abstract
The human C-type lectin domain family 7 member A (CLEC7A) gene encodes a Dectin-1 protein that recognizes beta-1,3-linked and beta-1,6-linked glucans, which form the cell walls of pathogenic bacteria and fungi. It plays a role in immunity against fungal infections through [...] Read more.
The human C-type lectin domain family 7 member A (CLEC7A) gene encodes a Dectin-1 protein that recognizes beta-1,3-linked and beta-1,6-linked glucans, which form the cell walls of pathogenic bacteria and fungi. It plays a role in immunity against fungal infections through pathogen recognition and immune signaling. This study aimed to explore the impact of nsSNPs in the human CLEC7A gene through computational tools (MAPP, PhD-SNP, PolyPhen-1, PolyPhen-2, SIFT, SNAP, and PredictSNP) to identify the most deleterious and damaging nsSNPs. Further, their effect on protein stability was checked along with conservation and solvent accessibility analysis by I-Mutant 2.0, ConSurf, and Project HOPE and post-translational modification analysis using MusiteDEEP. Out of the 28 nsSNPs that were found to be deleterious, 25 nsSNPs affected protein stability. Some SNPs were finalized for structural analysis with Missense 3D. Seven nsSNPs affected protein stability. Results from this study predicted that C54R, L64P, C120G, C120S, S135C, W141R, W141S, C148G, L155P, L155V, I158M, I158T, D159G, D159R, I167T, W180R, L183F, W192R, G197E, G197V, C220S, C233Y, I240T, E242G, and Y3D were the most structurally and functionally significant nsSNPs in the human CLEC7A gene. No nsSNPs were found in the predicted sites for post-translational modifications. In the 5′ untranslated region, two SNPs, rs536465890 and rs527258220, showed possible miRNA target sites and DNA binding sites. The present study identified structurally and functionally significant nsSNPs in the CLEC7A gene. These nsSNPs may potentially be used for further evaluation as diagnostic and prognostic biomarkers. Full article
(This article belongs to the Special Issue Genomic Analysis of Infectious Diseases)
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Review

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17 pages, 1924 KiB  
Review
Metabolomics: A New Era in the Diagnosis or Prognosis of B-Cell Non-Hodgkin’s Lymphoma
by Abdullah Alfaifi, Mohammed Y. Refai, Mohammed Alsaadi, Salem Bahashwan, Hafiz Malhan, Waiel Al-Kahiry, Enas Dammag, Ageel Ageel, Amjed Mahzary, Raed Albiheyri, Hussein Almehdar and Ishtiaq Qadri
Diagnostics 2023, 13(5), 861; https://doi.org/10.3390/diagnostics13050861 - 23 Feb 2023
Cited by 2 | Viewed by 4204
Abstract
A wide range of histological as well as clinical properties are exhibited by B-cell non-Hodgkin’s lymphomas. These properties could make the diagnostics process complicated. The diagnosis of lymphomas at an initial stage is essential because early remedial actions taken against destructive subtypes are [...] Read more.
A wide range of histological as well as clinical properties are exhibited by B-cell non-Hodgkin’s lymphomas. These properties could make the diagnostics process complicated. The diagnosis of lymphomas at an initial stage is essential because early remedial actions taken against destructive subtypes are commonly deliberated as successful and restorative. Therefore, better protective action is needed to improve the condition of those patients who are extensively affected by cancer when diagnosed for the first time. The development of new and efficient methods for early detection of cancer has become crucial nowadays. Biomarkers are urgently needed for diagnosing B-cell non-Hodgkin’s lymphoma and assessing the severity of the disease and its prognosis. New possibilities are now open for diagnosing cancer with the help of metabolomics. The study of all the metabolites synthesised in the human body is called “metabolomics.” A patient’s phenotype is directly linked with metabolomics, which can help in providing some clinically beneficial biomarkers and is applied in the diagnostics of B-cell non-Hodgkin’s lymphoma. In cancer research, it can analyse the cancerous metabolome to identify the metabolic biomarkers. This review provides an understanding of B-cell non-Hodgkin’s lymphoma metabolism and its applications in medical diagnostics. A description of the workflow based on metabolomics is also provided, along with the benefits and drawbacks of various techniques. The use of predictive metabolic biomarkers for the diagnosis and prognosis of B-cell non-Hodgkin’s lymphoma is also explored. Thus, we can say that abnormalities related to metabolic processes can occur in a vast range of B-cell non-Hodgkin’s lymphomas. The metabolic biomarkers could only be discovered and identified as innovative therapeutic objects if we explored and researched them. In the near future, the innovations involving metabolomics could prove fruitful for predicting outcomes and bringing out novel remedial approaches. Full article
(This article belongs to the Special Issue Genomic Analysis of Infectious Diseases)
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