Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
3.6
3.6
Journals
Diagnostics
Special Issues
Monitoring and Detection for SARS-CoV-2 and Its Variants
share announcement

Monitoring and Detection for SARS-CoV-2 and Its Variants

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 November 2022) | Viewed by 14676

Special Issue Editor

Dr. Federica Novazzi

E-Mail Website
Guest Editor
1. Department of Medicine and Surgery, University of Insubria, Varese, Italy
2. Clinical Microbiology Laboratory, Hospital of Circolo and Estabilshment Macchi, Varese, Italy
Interests: clinical microbiology; SARS-COV-2 immunity; SARS-COV-2 variants; HCV; HIV; respiratory viruses
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues, 

Since the beginning of the COVID-19 pandemic in 2020, SARS-COV-2 has changed and continues to mutate like all RNA viruses. Therefore, we must constantly stay updated on new mutations, especially on the clinical impact that these mutations of the virus can have on populations. Some mutations may affect the virus’s properties, such as how easily it spreads, the associated disease severity, or the performance of vaccines, therapeutic medicines, diagnostic tools, or other public health and social measures. Monitoring SARS COV-2 is still of paramount importance to understand how the virus behaves in the population following recent immunizations with the vaccine. The surveillance of SARS-COV-2 variants through sequencing is proving to be a valid method to monitor and control the distribution of variants in different local realities that have a potential global impact. Another important aspect is the mutations that arise as a result of monoclonal antibody therapy, which can lead to therapeutic failure. This Special Issue welcomes research concerning all aspects of monitoring the viral variants and epidemiology of SARS-COV-2 and the possible impact on COVID-19. In particular, we encourage submissions that focus on cases or clusters of viral variants in both small and large communities and the detection of unusual epidemiological events.

Dr. Federica Novazzi
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.

Published Papers (8 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

Jump to: Review

5 pages, 1602 KiB  
Communication
Rise of the BQ.1.1.37 SARS-CoV-2 Sublineage, Italy
by Daniele Focosi, Pietro Giorgio Spezia, Anna-Lisa Capria, Federico Gueli, Scott McConnell, Federica Novazzi and Mauro Pistello
Diagnostics 2023, 13(5), 1000; https://doi.org/10.3390/diagnostics13051000 - 06 Mar 2023
Cited by 1 | Viewed by 1996
Abstract
BQ.1.1 has dominated the Europe and Americas COVID-19 wave across the 2022–2023 winter, and further viral evolution is expected to escape the consolidating immune responses. We report here the emergence of the BQ.1.1.37 variant in Italy, peaking in January 2022 before suffering competition [...] Read more.
BQ.1.1 has dominated the Europe and Americas COVID-19 wave across the 2022–2023 winter, and further viral evolution is expected to escape the consolidating immune responses. We report here the emergence of the BQ.1.1.37 variant in Italy, peaking in January 2022 before suffering competition by XBB.1.*. We attempted to correlate the potential fitness of BQ.1.1.37 with a unique two-amino acid insertion within the Spike protein. Full article
(This article belongs to the Special Issue Monitoring and Detection for SARS-CoV-2 and Its Variants)
►▼ Show Figures

Figure 1

13 pages, 257 KiB  
Article
Investigation of SARS-CoV-2 Variants and Their Effect on SARS-CoV-2 Monoclonal Antibodies, Convalescent and Vaccine Plasma by a Novel Web Tool
by Ayse Arikan and Murat Sayan
Diagnostics 2022, 12(11), 2869; https://doi.org/10.3390/diagnostics12112869 - 19 Nov 2022
Cited by 1 | Viewed by 1471
Abstract
(1) Background: SARS-CoV-2 variants possess specific mutations throughout their genome; however, the effect of these mutations on pathogenesis is little known. The study aimed to identify SARS-CoV-2 variants and their susceptibility rate against monoclonal antibodies, convalescent, and vaccine plasma. (2) Methods: Strains isolated [...] Read more.
(1) Background: SARS-CoV-2 variants possess specific mutations throughout their genome; however, the effect of these mutations on pathogenesis is little known. The study aimed to identify SARS-CoV-2 variants and their susceptibility rate against monoclonal antibodies, convalescent, and vaccine plasma. (2) Methods: Strains isolated from COVID-19 cases in Turkey in April and September 2021 were involved. Illuma Nextera XT was processed for NGS, followed by virtual phenotyping (Coronavirus Antiviral and Resistance Database (CoV-RDB) by Stanford University). (3) Results: Among 211 strains, 79% were SARS-CoV-2 variants. B.1.1.7 (Alpha) was the most dominant, followed by B.1.617.2 (Delta), B.1.351 (Beta), and B.1.525 (Eta). Alpha and Delta were less susceptible to Etesevimab—Sotrovimab and Bamlanivimab—Etesevimab, respectively. Reduced efficacy was observed for convalescent plasma in Beta and Delta; AstraZeneca, Comirnaty plus AstraZeneca in Alpha; Comirnaty, Moderna, Novovax in Beta; Comirnaty in Delta. (4) Conclusion: CoV-RDB analysis is an efficient, rapid, and helpful web tool for SARS-CoV-2 variant detection and susceptibility analysis. Full article
(This article belongs to the Special Issue Monitoring and Detection for SARS-CoV-2 and Its Variants)
10 pages, 442 KiB  
Article
Fuzzy-Based PROMETHEE Method for Performance Ranking of SARS-CoV-2 IgM Antibody Tests
by Ayse Arikan, Tamer Sanlidag, Murat Sayan, Berna Uzun and Dilber Uzun Ozsahin
Diagnostics 2022, 12(11), 2830; https://doi.org/10.3390/diagnostics12112830 - 17 Nov 2022
Cited by 5 | Viewed by 1331
Abstract
Antibody tests, widely used as a complementary approach to reverse transcriptase–polymerase chain reaction testing in identifying COVID-19 cases, are used to measure antibodies developed for COVID-19. This study aimed to evaluate the different parameters of the FDA-authorized SARS-CoV-2 IgM antibody tests and to [...] Read more.
Antibody tests, widely used as a complementary approach to reverse transcriptase–polymerase chain reaction testing in identifying COVID-19 cases, are used to measure antibodies developed for COVID-19. This study aimed to evaluate the different parameters of the FDA-authorized SARS-CoV-2 IgM antibody tests and to rank them according to their performance levels. In the study, we involved 27 antibody tests, and the analyzes were performed using the fuzzy preference ranking organization method for the enrichment evaluation model, a multi-criteria decision-making model. While criteria such as analytical sensitivity, specificity, positive predictive value, and negative predictive value were evaluated in the study, the ranking was reported by determining the importance levels of the criteria. According to our evaluation, Innovita 2019-nCoV Ab Test (colloidal gold) was at the top of the ranking. While Cellex qSARS-CoV-2 IgG/IgM Rapid Test and Assure COVID-19 IgG/IgM Rapid Tester ranked second and third on the list, the InBios-SCoV 2 Detect Ig M ELISA Rapid Test Kit was determined as the least preferable. The fuzzy preference ranking organization method for enrichment evaluation, which has been applied to many fields, can help decision-makers choose the appropriate antibody test for managing COVID-19 in controlling the global pandemic. Full article
(This article belongs to the Special Issue Monitoring and Detection for SARS-CoV-2 and Its Variants)
►▼ Show Figures

Figure 1

10 pages, 1559 KiB  
Article
A Simplified Sanger Sequencing Method for Detection of Relevant SARS-CoV-2 Variants
by Felice Deminco, Sara N. Vaz, Daniele S. Santana, Celia Pedroso, Jean Tadeu, Andreas Stoecker, Sueli M. Vieira, Eduardo Netto and Carlos Brites
Diagnostics 2022, 12(11), 2609; https://doi.org/10.3390/diagnostics12112609 - 27 Oct 2022
Cited by 2 | Viewed by 1503
Abstract
Molecular surveillance of the new coronavirus through new genomic sequencing technologies revealed the circulation of important variants of SARS-CoV-2. Sanger sequencing has been useful in identifying important variants of SARS-CoV-2 without the need for whole-genome sequencing. A sequencing protocol was constructed to cover [...] Read more.
Molecular surveillance of the new coronavirus through new genomic sequencing technologies revealed the circulation of important variants of SARS-CoV-2. Sanger sequencing has been useful in identifying important variants of SARS-CoV-2 without the need for whole-genome sequencing. A sequencing protocol was constructed to cover a region of 1000 base pairs, from a 1120 bp product generated after a two-step RT-PCR assay in samples positive for SARS-CoV-2. Consensus sequence construction and mutation identification were performed. Of all 103 samples sequenced, 69 contained relevant variants represented by 20 BA.1, 13 delta, 22 gamma, and 14 zeta, identified between June 2020 and February 2022. All sequences found were aligned with representative sequences of the variants. Using the Sanger sequencing methodology, we were able to develop a more accessible protocol to assist viral surveillance with a more accessible platform. Full article
(This article belongs to the Special Issue Monitoring and Detection for SARS-CoV-2 and Its Variants)
►▼ Show Figures

Figure 1

10 pages, 1135 KiB  
Article
Molecular Detection of Human Papillomaviruses in Formalin Fixed Paraffin Embedded Sections from Different Anogenital Lesions in Duhok-Iraq
by Adil Othman, Amer Goreal and Intisar Pity
Diagnostics 2022, 12(10), 2496; https://doi.org/10.3390/diagnostics12102496 - 15 Oct 2022
Cited by 1 | Viewed by 1691
Abstract
Human Papilloma virus infection is the fundamental reason for the development of ano-genital malignancies and knowing the best tool for diagnostic purposes is mandatory. This study investigated the prevalence and genotype distribution of HPV genotypes in formalin-fixed paraffin-embedded (FFPE) blocks from patients with [...] Read more.
Human Papilloma virus infection is the fundamental reason for the development of ano-genital malignancies and knowing the best tool for diagnostic purposes is mandatory. This study investigated the prevalence and genotype distribution of HPV genotypes in formalin-fixed paraffin-embedded (FFPE) blocks from patients with different anogenital lesions. In this cross-sectional retrospective study, 125 blocks from patients with different anogenital lesions were collected. Three internal sections were taken for HPV detection and genotyping using the paraffin tissue processing kit and HPV Direct Flow CHIP. HPV positivity was detected in 90 (72.0%), with 77 (85.6%) females and 13 (14.4%) males as follows: SCC 64.0%, CINIII 66.7%, CINII 100.0%, CINI 83.3%, KA 83.7%, NILM 44.0%, Anus 66.6%. A total of 44% of histologically unremarkable (negative) cases were positive for HPV genotypes while in only 64% of SCC were HPV genotypes detected. Sixty-six (73.3%) cases were low-risk, and 16 (17.8%) cases were high-risk genotypes, mostly cervical lesions, while seven (7.8%) cases showed a mixed viral detection. The most frequent low-risk genotype was HPV6 genotype (62–68.9%), while the prevalent high-risk HPV was HPV16 genotype (12–13.3%). In this study, HPV16 was more frequently detected than HR-HPV, but mainly in cervical lesion, while HPV6 topped the LR-HPV infections amongst different anogenital lesions in Duhok-Iraq. Higher HPV positivity among cytological unremarkable and abnormal cases may reflect the higher sensitivity of the direct flow CHIP diagnostic technique. The results demonstrate that screening for HPV is essential to reduce cancer development and planning for the vaccine’s introduction in Iraq. Full article
(This article belongs to the Special Issue Monitoring and Detection for SARS-CoV-2 and Its Variants)
►▼ Show Figures

Figure 1

9 pages, 1309 KiB  
Article
SARS-CoV-2 Variants Monitoring Using Real-Time PCR
by Anna Esman, Anna Cherkashina, Konstantin Mironov, Dmitry Dubodelov, Svetlana Salamaikina, Anna Golubeva, Gasan Gasanov, Kamil Khafizov, Natalya Petrova, Evgeniy Cherkashin and Vasiliy Akimkin
Diagnostics 2022, 12(10), 2388; https://doi.org/10.3390/diagnostics12102388 - 01 Oct 2022
Cited by 4 | Viewed by 1713
Abstract
According to the temporary recommendations of the 2021 World Health Organization (WHO), in addition to whole-genome sequencing, laboratories in various countries can also screen for known mutations utilizing targeted RT-PCR-based mutation detection assays. The aim of this work was to generate a laboratory [...] Read more.
According to the temporary recommendations of the 2021 World Health Organization (WHO), in addition to whole-genome sequencing, laboratories in various countries can also screen for known mutations utilizing targeted RT-PCR-based mutation detection assays. The aim of this work was to generate a laboratory technique to differentiate the main circulating SARS-CoV-2 variants in 2021–2022, when a sharp increase in morbidity was observed with the appearance of the Omicron variant. Real-time PCR methodology is available for use in the majority of scientific and diagnostic institutions in Russia, which makes it possible to increase the coverage of monitoring of variants in the territories of all 85 regions in order to accumulate information for the Central Services and make epidemiological decisions. With the methodology developed by the Central Research Institute of Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing (FSSCRP Human Wellbeing) (CRIE), more than 6000 biological samples have been typed, and 7% of samples with the Delta variant and 92% of samples with the Omicron variant have been identified as of 25 August 2022. Reagents for 140,000 definitions have been supplied to regional organizations. Full article
(This article belongs to the Special Issue Monitoring and Detection for SARS-CoV-2 and Its Variants)
►▼ Show Figures

Figure 1

11 pages, 1850 KiB  
Article
Molecular Characterization of Whole-Genome SARS-CoV-2 from the First Suspected Cases of the XE Variant in the Lazio Region, Italy
by Martina Rueca, Emanuela Giombini, Giulia Gramigna, Cesare Ernesto Maria Gruber, Lavinia Fabeni, Angela Corpolongo, Valentina Mazzotta, Luisella Corso, Ornella Butera, Maria Beatrice Valli, Fabrizio Carletti, Stefano Pignalosa, Francesco Vairo, Emanuele Nicastri, Andrea Antinori, Enrico Girardi, Francesco Vaia, Fabrizio Maggi and SARS CoV-2 Lazio Surveillance Study Group
Diagnostics 2022, 12(9), 2219; https://doi.org/10.3390/diagnostics12092219 - 14 Sep 2022
Viewed by 1278
Abstract
We report two cases of SARS-CoV-2 recombinant variant XE detected in nasopharyngeal swabs (NPS) of hospitalized patients with no evident epidemiological link in Lazio, Central Italy. Whole-Genome Sequencing (WGS) performed on an Ion Torrent GSS5 platform according to Italian flash surveys showed genomes [...] Read more.
We report two cases of SARS-CoV-2 recombinant variant XE detected in nasopharyngeal swabs (NPS) of hospitalized patients with no evident epidemiological link in Lazio, Central Italy. Whole-Genome Sequencing (WGS) performed on an Ion Torrent GSS5 platform according to Italian flash surveys showed genomes corresponding to the PANGOLIN unclassified lineage and the Nextclade XE clade. Further analyses were then carried out to investigate more deeply the genetic characteristics of these XE-like sequences. When phylogenetic trees, by using IQ-TREE, were built splitting the genome into two regions according to the putative XE recombination site, the upstream and downstream regions were seen to be clustered near BA.1 and BA.2 sequences, respectively. However, our XE-like sequences clustered separately, with a significant bootstrap, from the classified European and Italian XE strains, although the recombination site between BA.1 and BA.2 was identified at the nucleotide site 11556 by RDP4 software, consistent with the putative XE breakpoint. These findings show the risk of the introduction of novel recombinant variants of SARS-CoV-2 and the existence of XE-like strains, phylogenetically separated, that could make their exact taxonomy difficult. It follows the need for continued SARS-CoV-2 surveillance by WGS. Full article
(This article belongs to the Special Issue Monitoring and Detection for SARS-CoV-2 and Its Variants)
►▼ Show Figures

Figure 1

Review

Jump to: Research

16 pages, 950 KiB  
Review
SARS-CoV-2 Omicron (B.1.1.529) Variant: A Challenge with COVID-19
by Zeinab Mohseni Afshar, Ali Tavakoli Pirzaman, Bardia Karim, Shiva Rahimipour Anaraki, Rezvan Hosseinzadeh, Elaheh Sanjari Pireivatlou, Arefeh Babazadeh, Dariush Hosseinzadeh, Seyed Rouhollah Miri, Terence T. Sio, Mark J. M. Sullman, Mohammad Barary and Soheil Ebrahimpour
Diagnostics 2023, 13(3), 559; https://doi.org/10.3390/diagnostics13030559 - 02 Feb 2023
Cited by 11 | Viewed by 2823
Abstract
Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic, there have been multiple peaks of the SARS-CoV-2 (severe acute respiratory syndrome coronavirus virus 2) infection, mainly due to the emergence of new variants, each with a new set of mutations in the [...] Read more.
Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic, there have been multiple peaks of the SARS-CoV-2 (severe acute respiratory syndrome coronavirus virus 2) infection, mainly due to the emergence of new variants, each with a new set of mutations in the viral genome, which have led to changes in the pathogenicity, transmissibility, and morbidity. The Omicron variant is the most recent variant of concern (VOC) to emerge and was recognized by the World Health Organization (WHO) on 26 November 2021. The Omicron lineage is phylogenetically distinct from earlier variants, including the previously dominant Delta SARS-CoV-2 variant. The reverse transcription–polymerase chain reaction (RT–PCR) test, rapid antigen assays, and chest computed tomography (CT) scans can help diagnose the Omicron variant. Furthermore, many agents are expected to have therapeutic benefits for those infected with the Omicron variant, including TriSb92, molnupiravir, nirmatrelvir, and their combination, corticosteroids, and interleukin-6 (IL-6) receptor blockers. Despite being milder than previous variants, the Omicron variant threatens many lives, particularly among the unvaccinated, due to its higher transmissibility, pathogenicity, and infectivity. Mounting evidence has reported the most common clinical manifestations of the Omicron variant to be fever, runny nose, sore throat, severe headache, and fatigue. This review summarizes the essential features of the Omicron variant, including its history, genome, transmissibility, clinical manifestations, diagnosis, management, and the effectiveness of existing vaccines against this VOC. Full article
(This article belongs to the Special Issue Monitoring and Detection for SARS-CoV-2 and Its Variants)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-8
Back to TopTop