Detection and Assessment of SARS-CoV-2 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 (31 August 2023) | Viewed by 8354

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Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
Interests: clinical pathology; molecular diagnosis; genome; epidemiology
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Dear Colleagues,

Since the first severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant Alpha was identified in England in late November 2021, mutations in the viral genome can increase transmissibility, facilitate escape from the human immune system, and/or alter biologically important phenotypes. The SARS-CoV-2 variants are classified as variants being monitored (VBMs), variants of interest (VOIs), variants of concern (VOCs), and variants of high consequence (VOHCs). There are two currently circulating SARS-CoV-2 VOCs (Delta and Omicron), and three previously circulating VOCs (Alpha, Beta, and Gamma) in a way that confers a fitness advantage to the virus, such as mutations in the spike (S) gene that affect antigenicity. Each characterized variant has mutations in the gene encoding the S protein (Omicron: 30 mutations; Delta: 10 mutations; Alpha: 7 mutations and 2 deletions; Beta: 9 mutations and 1 deletion; and Gamma: >10 mutations), compared to the sequence of the wild type index virus (Wuhan-Hu-1).

Previous studies have pointed out that viral genomic mutations leading to new variants of SARS-CoV-2 are a real challenge in tackling the global coronavirus disease (COVID-19). Understanding SARS-CoV-2 variants remains an issue of concern for all local government authorities and are critical for establishing and implementing effective public health measures.

This Special Issue on “Detection and Assessment of SARS-CoV-2 Variants” will cover all related areas, such as diagnostic applications, VOC pathogen detection, biomarker monitoring, and others of concern.

Prof. Dr. Hung-Sheng Shang
Guest Editor

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Keywords

  • variant of concerns
  • Omicron
  • pathogen detection
  • biomarker

Published Papers (6 papers)

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Research

11 pages, 1235 KiB  
Article
Clinical Evaluation of Direct Reverse Transcription PCR for Detection of SARS-CoV-2 Compared to Conventional RT-PCR in Patients with Positive Rapid Antigen Test Results during Circulation of Emerging Viral Variants
by Ming-Jr Jian, Chi-Sheng Chen, Hsing-Yi Chung, Chih-Kai Chang, Cherng-Lih Perng and Hung-Sheng Shang
Diagnostics 2023, 13(24), 3668; https://doi.org/10.3390/diagnostics13243668 - 14 Dec 2023
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Abstract
The emergence of the Omicron (B.1.1.529) variant of SARS-CoV-2 has precipitated a new global wave of the COVID-19 pandemic. The rapid identification of SARS-CoV-2 infection is imperative for the effective mitigation of transmission. Diagnostic modalities such as rapid antigen testing and real-time reverse [...] Read more.
The emergence of the Omicron (B.1.1.529) variant of SARS-CoV-2 has precipitated a new global wave of the COVID-19 pandemic. The rapid identification of SARS-CoV-2 infection is imperative for the effective mitigation of transmission. Diagnostic modalities such as rapid antigen testing and real-time reverse transcription polymerase chain reaction (RT-PCR) offer expedient turnaround times of 10–15 min and straightforward implementation. This preliminary study assessed the correlation between outcomes of commercially available rapid antigen tests for home use and conventional reverse transcription polymerase chain reaction (RT-PCR) assays using a limited set of clinical specimens. Patients aged 5–99 years presenting to the emergency department for SARS-CoV-2 testing were eligible for enrollment (n = 5652). Direct PCR and conventional RT-PCR were utilized for the detection of SARS-CoV-2. The entire cohort of 5652 clinical specimens was assessed by both modalities to determine the clinical utility of the direct RT-PCR assay. Timely confirmation of SARS-CoV-2 infection may attenuate viral propagation and guide therapeutic interventions. Additionally, direct RT-PCR as a secondary confirmatory test for at-home rapid antigen test results demonstrated sensitivity comparable to conventional RT-PCR, indicating utility for implementation in laboratories globally, especially in resource-limited settings with constraints on reagents, equipment, and skilled personnel. In summary, direct RT-PCR enables the detection of SARS-CoV-2 with a sensitivity approaching that of conventional RT-PCR while offering expedient throughput and shorter turnaround times. Moreover, direct RT-PCR provides an open-source option for diagnostic laboratories worldwide, particularly in low- and middle-income countries. Full article
(This article belongs to the Special Issue Detection and Assessment of SARS-CoV-2 Variants)
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8 pages, 573 KiB  
Communication
No Association between SARS-CoV-2 Infection and the Polymorphism of the Toll-like Receptor 7 (TLR7) Gene in Female Population
by Mohammed Zayed, Yong-Chan Kim, Chang-Seop Lee and Byung-Hoon Jeong
Diagnostics 2023, 13(23), 3510; https://doi.org/10.3390/diagnostics13233510 - 23 Nov 2023
Viewed by 821
Abstract
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a single-stranded RNA virus. Toll-like receptor 7 (TLR7) recognizes single-stranded RNA viruses. The TLR7 gene plays a critical role in the human innate and adaptive immune response [...] Read more.
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a single-stranded RNA virus. Toll-like receptor 7 (TLR7) recognizes single-stranded RNA viruses. The TLR7 gene plays a critical role in the human innate and adaptive immune response to SARS-CoV-2 infections. Genetic factors probably affect SARS-CoV-2 infection susceptibility. In the current study, our aim was to search for genetic variations associated with COVID-19 patients in the TLR7 gene of a Korean population. We designed five gene-specific primers to cover the coding region of the human TLR7 gene. Using amplicon sequencing, we screened the genetic polymorphisms in the coding region of the TLR7 gene in COVID-19 patients and healthy controls. The genotype frequencies, allele frequencies, and Hardy–Weinberg equilibrium (HWE) were examined. We identified a low-frequency synonymous single nucleotide polymorphism (SNP) (rs864058) in the coding region of the TLR7 gene. There were no significant differences in the genotype or allele frequencies of the TLR7 rs864058 polymorphism between COVID-19 female patients and healthy controls (p = 1.0). In conclusion, TLR7 (rs864058) polymorphism is low frequency in Korean populations and is not associated with SARS-CoV-2 infection. Full article
(This article belongs to the Special Issue Detection and Assessment of SARS-CoV-2 Variants)
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12 pages, 1777 KiB  
Article
Detection of SARS-CoV-2 Variants via Different Diagnostics Assays Based on Single-Nucleotide Polymorphism Analysis
by Eliana Specchiarello, Giulia Matusali, Fabrizio Carletti, Cesare Ernesto Maria Gruber, Lavinia Fabeni, Claudia Minosse, Emanuela Giombini, Martina Rueca, Fabrizio Maggi, Alessandra Amendola and Anna Rosa Garbuglia
Diagnostics 2023, 13(9), 1573; https://doi.org/10.3390/diagnostics13091573 - 27 Apr 2023
Cited by 4 | Viewed by 1375
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is characterized by fast evolution with the appearance of several variants. Next-Generation Sequencing (NGS) technology is considered the gold standard for monitoring known and new SARS-CoV-2 variants. However, the complexity of this technology renders this approach [...] Read more.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is characterized by fast evolution with the appearance of several variants. Next-Generation Sequencing (NGS) technology is considered the gold standard for monitoring known and new SARS-CoV-2 variants. However, the complexity of this technology renders this approach impracticable in laboratories located in areas with limited resources. We analyzed the capability of the ThermoFisher TaqPath COVID-19 RT-PCR (TaqPath) and the Seegene Novaplex SARS-CoV-2 Variant assay (Novaplex) to detect Omicron variants; the Allplex VariantII (Allplex) was also evaluated for Delta variants. Sanger sequencing (SaS) was the reference method. The results obtained with n = 355 nasopharyngeal samples were: negative with TaqPath, although positive with other qualitative molecular assays (n = 35); undetermined (n = 40) with both the assays; negative for the ∆69/70 mutation and confirmed as the Delta variant via SaS (n = 100); positive for ∆69/70 and confirmed as Omicron BA.1 via SaS (n = 80); negative for ∆69/70 and typed as Omicron BA.2 via SaS (n = 80). Novaplex typed 27.5% of samples as undetermined with TaqPath, 11.4% of samples as negative with TaqPath, and confirmed 100% of samples were Omicron subtypes. In total, 99/100 samples were confirmed as the Delta variant with Allplex with a positive per cent agreement (PPA) of 98% compared to SaS. As undermined samples with Novaplex showed RdRp median Ct values (Ct = 35.4) statistically higher than those of typed samples (median Ct value = 22.0; p < 0.0001, Mann–Whitney test), the inability to establish SARS-CoV-2 variants was probably linked to the low viral load. No amplification was obtained with SaS among all 35 negative TaqPath samples. Overall, 20% of samples which were typed as negative or undetermined with TaqPath, and among them, twelve were not typed even by SaS, but they were instead correctly identified with Novaplex. Although full-genome sequencing remains the elected method to characterize new strains, our data show the high ability of a SNP-based assay to identify VOCs, also resolving samples typed as undetermined with TaqPath. Full article
(This article belongs to the Special Issue Detection and Assessment of SARS-CoV-2 Variants)
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19 pages, 4824 KiB  
Article
Virus-Specific Stem Cell Memory CD8+ T Cells May Indicate a Long-Term Protection against Evolving SARS-CoV-2
by Milena Aleksova, Yana Todorova, Radoslava Emilova, Magdalena Baymakova, Nina Yancheva, Radina Andonova, Anelia Zasheva, Alba Grifoni, Daniela Weiskopf, Alessandro Sette and Maria Nikolova
Diagnostics 2023, 13(7), 1280; https://doi.org/10.3390/diagnostics13071280 - 28 Mar 2023
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Abstract
Immune memory to SARS-CoV-2 is key for establishing herd immunity and limiting the spread of the virus. The duration and qualities of T-cell-mediated protection in the settings of constantly evolving pathogens remain an open question. We conducted a cross-sectional study of SARS-CoV-2-specific CD4+ [...] Read more.
Immune memory to SARS-CoV-2 is key for establishing herd immunity and limiting the spread of the virus. The duration and qualities of T-cell-mediated protection in the settings of constantly evolving pathogens remain an open question. We conducted a cross-sectional study of SARS-CoV-2-specific CD4+ and CD8+ T-cell responses at several time points over 18 months (30–750 days) post mild/moderate infection with the aim to identify suitable methods and biomarkers for evaluation of long-term T-cell memory in peripheral blood. Included were 107 samples from 95 donors infected during the periods 03/2020–07/2021 and 09/2021–03/2022, coinciding with the prevalence of B.1.1.7 (alpha) and B.1.617.2 (delta) variants in Bulgaria. SARS-CoV-2-specific IFNγ+ T cells were measured in ELISpot in parallel with flow cytometry detection of AIM+ total and stem cell-like memory (TSCM) CD4+ and CD8+ T cells after in vitro stimulation with peptide pools corresponding to the original and delta variants. We show that, unlike IFNγ+ T cells, AIM+ virus-specific CD4+ and CD8+ TSCM are more adequate markers of T cell memory, even beyond 18 months post-infection. In the settings of circulating and evolving viruses, CD8+ TSCM is remarkably stable, back-differentiated into effectors, and delivers immediate protection, regardless of the initial priming strain. Full article
(This article belongs to the Special Issue Detection and Assessment of SARS-CoV-2 Variants)
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12 pages, 276 KiB  
Article
Association between Vitamin D Status and Secondary Infections in Patients with Severe COVID-19 Admitted in the Intensive Care Unit of a Tertiary-Level Hospital in Turkey
by Lutfiye Karcioglu Batur and Suna Koç
Diagnostics 2023, 13(1), 59; https://doi.org/10.3390/diagnostics13010059 - 26 Dec 2022
Cited by 1 | Viewed by 1583
Abstract
There are several studies showing that the vitamin D status can determine risk of COVID-19 infections, severity and mortality from coronavirus disease 2019 (COVID-19). However, the association between vitamin D (25(OH)D) and secondary infections in the prognosis of COVID-19 patients has not been [...] Read more.
There are several studies showing that the vitamin D status can determine risk of COVID-19 infections, severity and mortality from coronavirus disease 2019 (COVID-19). However, the association between vitamin D (25(OH)D) and secondary infections in the prognosis of COVID-19 patients has not been reported yet. The aim was to investigate whether the vitamin D status affects the rates of secondary infections in patients with severe COVID-19 hospitalized in the intensive care unit (ICU) of a tertiary-level hospital in Turkey. The data of 194 patients with diagnosis of severe COVID-19 who were admitted to the ICU from March 2020 to June 2021 and older than 18 years were evaluated in this retrospective study. The patients were divided into two groups according to total serum 25(OH)D level as normal group (≥20 ng/mL) and low group (<20 ng/mL). The 25(OH)D level was low in 118 (60.8%) and normal in 76 (39.2%) patients. The mean age of the low group was significantly higher than that of the normal group (67.02 ± 14.47 vs. 61.70 ± 14.38; p = 0.013). The systolic and diastolic blood pressure as well as the Glasgow coma scale score of the low group were significantly lower than that of the normal group (p = 0.004, 0.002 and 0.001, respectively). The intubation rate and APACHE (Acute Physiology and Chronic Health Evaluation) score of the low group was significantly higher than that of the normal group (p = 0.001). The platelets number and blood pH decreased, and the neutrophil/lymphocyte ratio, procalcitonin, lactate, urea, creatinine and lactate dehydrogenase concentrations increased significantly in the low group (p < 0.05). The mortality rate was 79.7% in the low group and 22.4% in the normal group (p < 0.001). Microbiological growth was observed in 68.6% of the normal group and 52.6% of the normal group (p = 0.025). The number of cultures with resistant bacteria was significantly higher in the low group (25.9%) than that in the normal group (17.5%) (p = 0.035). The severe COVID-19 patients hospitalized with vitamin D deficiency may have increased risks of poor prognosis and mortality due to secondary infections in the ICU. Full article
(This article belongs to the Special Issue Detection and Assessment of SARS-CoV-2 Variants)
7 pages, 217 KiB  
Communication
SARS-CoV-2 RT-PCR to Screen for B.1.617.2 (Delta) Variant of Concern
by Kym Lowry, Claire Wang, Amanda Bordin, Cameron Buckley, Steven Badman, Patrick Harris, Ian Mackay and David Whiley
Diagnostics 2022, 12(9), 2056; https://doi.org/10.3390/diagnostics12092056 - 24 Aug 2022
Cited by 2 | Viewed by 1467
Abstract
The continuous transmission and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has required that diagnostic capabilities be constantly monitored and updated as new variants emerge and prior variants disappear. Although whole genome sequencing provides full characterisation of SARS-CoV-2 directly from patient [...] Read more.
The continuous transmission and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has required that diagnostic capabilities be constantly monitored and updated as new variants emerge and prior variants disappear. Although whole genome sequencing provides full characterisation of SARS-CoV-2 directly from patient samples, this has limited throughput and requires sufficient resources. To enhance screening for circulating variants, we designed a rapid in-house RT-PCR assay to target a spike mutation (D950N) in Delta variants, which is not detected in the remaining variants of concern (VOCs). Assay sensitivity for detecting Delta variants was 93% and specificity was 100% using a sequenced sample bank of several lineages. As the D950N mutation is prevalent in >95% of the global Delta variant sequences deposited in GISAID, this assay has the potential to provide rapid results to determine if the samples are presumptively Delta variants and can support clinicians in timely clinical decision-making for effective treatments and surveillance. Full article
(This article belongs to the Special Issue Detection and Assessment of SARS-CoV-2 Variants)
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