Life | Special Issue : Virology Applications to COVID-19 Pandemic

Editorial

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5 pages, 169 KiB

Open AccessEditorial

Virology Applications to the COVID-19 Pandemic

by Evangelia Georgia Kostaki

Life 2025, 15(2), 247; https://doi.org/10.3390/life15020247 - 6 Feb 2025

Viewed by 693

Abstract

From the early identification of severe respiratory cases of unknown etiology in Wuhan, China, in late 2019, virology research has played an important role in understanding, management, and prevention of the COVID-19 pandemic [...] Full article

(This article belongs to the Special Issue Virology Applications to COVID-19 Pandemic)

Research

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20 pages, 3610 KiB

Open AccessArticle

Detection of Circulating SARS-CoV-2 Variants of Concern (VOCs) Using a Multiallelic Spectral Genotyping Assay

by Andreas C. Chrysostomou, Antonia Aristokleous, Johana Hezka Rodosthenous, Christina Christodoulou, Georgia Stathi and Leondios G. Kostrikis

Life 2023, 13(2), 304; https://doi.org/10.3390/life13020304 - 21 Jan 2023

Cited by 5 | Viewed by 6073

Abstract

Throughout the coronavirus disease 2019 (COVID-19) pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continuously evolved, resulting in new variants, some of which possess increased infectivity, immune evasion, and virulence. Such variants have been denoted by the World Health Organization as variants [...] Read more.

Throughout the coronavirus disease 2019 (COVID-19) pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continuously evolved, resulting in new variants, some of which possess increased infectivity, immune evasion, and virulence. Such variants have been denoted by the World Health Organization as variants of concern (VOC) because they have resulted in an increased number of cases, posing a strong risk to public health. Thus far, five VOCs have been designated, Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.1.529), including their sublineages. Next-generation sequencing (NGS) can produce a significant amount of information facilitating the study of variants; however, NGS is time-consuming and costly and not efficient during outbreaks, when rapid identification of VOCs is urgently needed. In such periods, there is a need for fast and accurate methods, such as real-time reverse transcription PCR in combination with probes, which can be used for monitoring and screening of the population for these variants. Thus, we developed a molecular beacon-based real-time RT-PCR assay according to the principles of spectral genotyping. This assay employs five molecular beacons that target ORF1a:ΔS3675/G3676/F3677, S:ΔH69/V70, S:ΔE156/F157, S:ΔΝ211, S:ins214EPE, and S:ΔL242/A243/L244, deletions and an insertion found in SARS-CoV-2 VOCs. This assay targets deletions/insertions because they inherently provide higher discrimination capacity. Here, the design process of the molecular beacon-based real-time RT-PCR assay for detection and discrimination of SARS-CoV-2 is presented, and experimental testing using SARS-CoV-2 VOC samples from reference strains (cultured virus) and clinical patient samples (nasopharyngeal samples), which have been previously classified using NGS, were evaluated. Based on the results, it was shown that all molecular beacons can be used under the same real-time RT-PCR conditions, consequently improving the time and cost efficiency of the assay. Furthermore, this assay was able to confirm the genotype of each of the tested samples from various VOCs, thereby constituting an accurate and reliable method for VOC detection and discrimination. Overall, this assay is a valuable tool that can be used for screening and monitoring the population for VOCs or other emerging variants, contributing to limiting their spread and protecting public health. Full article

(This article belongs to the Special Issue Virology Applications to COVID-19 Pandemic)

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11 pages, 1201 KiB

Open AccessArticle

SARS-CoV-2 Neutralizing Responses in Various Populations, at the Time of SARS-CoV-2 Variant Virus Emergence: Evaluation of Two Surrogate Neutralization Assays in Front of Whole Virus Neutralization Test

by Stephane Marot, Djeneba Bocar Fofana, Philippe Flandre, Isabelle Malet, Karen Zafilaza, Valentin Leducq, Diane Vivien, Sarah Mrabet, Corentin Poignon, Vincent Calvez, Laurence Morand-Joubert, Anne-Geneviève Marcelin and Joel Gozlan

Life 2022, 12(12), 2064; https://doi.org/10.3390/life12122064 - 9 Dec 2022

Cited by 3 | Viewed by 1861

Abstract

The SARS-CoV-2 neutralizing antibodies response is the best indicator of effective protection after infection and/or vaccination, but its evaluation requires tedious cell-based experiments using an infectious virus. We analyzed, in 105 patients with various histories of SARS-CoV-2 infection and/or vaccination, the neutralizing response [...] Read more.

The SARS-CoV-2 neutralizing antibodies response is the best indicator of effective protection after infection and/or vaccination, but its evaluation requires tedious cell-based experiments using an infectious virus. We analyzed, in 105 patients with various histories of SARS-CoV-2 infection and/or vaccination, the neutralizing response using a virus neutralization test (VNT) against B.1, Alpha, Beta and Omicron variants, and compared the results with two surrogate assays based on antibody-mediated blockage of the ACE2-RBD interaction (Lateral Flow Boditech and ELISA Genscript). The strongest response was observed for recovered COVID-19 patients receiving one vaccine dose. Naïve patients receiving 2 doses of mRNA vaccine also demonstrate high neutralization titers against B.1, Alpha and Beta variants, but only 34.3% displayed a neutralization activity against the Omicron variant. On the other hand, non-infected patients with half vaccination schedules displayed a weak and inconstant activity against all isolates. Non-vaccinated COVID-19 patients kept a neutralizing activity against B.1 and Alpha up to 12 months after recovery but a decreased activity against Beta and Omicron. Both surrogate assays displayed a good correlation with the VNT. However, an adaptation of the cut-off positivity was necessary, especially for the most resistant Beta and Omicron variants. We validated two simple and reliable surrogate neutralization assays, which may favorably replace cell-based methods, allowing functional analysis on a larger scale. Full article

(This article belongs to the Special Issue Virology Applications to COVID-19 Pandemic)

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10 pages, 625 KiB

Open AccessArticle

The Implementation of a Health Care Worker Screening Program Based on the Advanta RT-qPCR Saliva Assay in a Tertiary Care Referral Hospital in Northern Greece

by Sofia Balaska, Eleftheria Parasidou, Anna Takardaki, Paraskevoula Koutra, Dimitra Chrysafi, Areti Tychala, Simeon Metallidis, Georgios Meletis and Lemonia Skoura

Life 2022, 12(12), 2011; https://doi.org/10.3390/life12122011 - 2 Dec 2022

Cited by 1 | Viewed by 1815

Abstract

Health care workers are at increased risk of acquiring SARS-CoV-2 infection due to different exposures in the community and in hospital settings. Interventions implemented to avoid nosocomial outbreaks include preventive testing strategies. In this report, we present results from the mass screening program [...] Read more.

Health care workers are at increased risk of acquiring SARS-CoV-2 infection due to different exposures in the community and in hospital settings. Interventions implemented to avoid nosocomial outbreaks include preventive testing strategies. In this report, we present results from the mass screening program applied in our hospital to all professionals, irrespective of symptoms or risk of exposure. We processed saliva specimens with real-time reverse transcription polymerase chain reaction. The total number of samples received was 43,726. Positive results were 672 and average positivity rate was 1.21%. The average positivity rate was similar to the positivity rate in the community in Greece and EU. More specifically, 80.5% of the positive participants care for patients in their daily activities, 31% experienced no symptoms before receiving the positive result, 46.1% reported a close contact with a patient or infected coworkers and 32.8% reported a close contact with infected family members. We believe that the identification of asymptomatic carriers has proved the effectiveness of the screening program by preventing the putative nosocomial spread of the virus and the depletion of workforce. In conclusion, in times of high incidence in the community, the periodic testing of health care personnel is wise and relevant for implementation costs. Full article

(This article belongs to the Special Issue Virology Applications to COVID-19 Pandemic)

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10 pages, 1294 KiB

Open AccessArticle

Prediction and Classification of COVID-19 Admissions to Intensive Care Units (ICU) Using Weighted Radial Kernel SVM Coupled with Recursive Feature Elimination (RFE)

by Huda M. Alshanbari, Tahir Mehmood, Waqas Sami, Wael Alturaiki, Mauawia A. Hamza and Bandar Alosaimi

Life 2022, 12(7), 1100; https://doi.org/10.3390/life12071100 - 21 Jul 2022

Cited by 12 | Viewed by 2827

Abstract

Healthcare systems have been under immense pressure since the beginning of the COVID-19 pandemic; hence, studies on using machine learning (ML) methods for classifying ICU admissions and resource allocation are urgently needed. We investigated whether ML can propose a useful classification model for [...] Read more.

Healthcare systems have been under immense pressure since the beginning of the COVID-19 pandemic; hence, studies on using machine learning (ML) methods for classifying ICU admissions and resource allocation are urgently needed. We investigated whether ML can propose a useful classification model for predicting the ICU admissions of COVID-19 patients. In this retrospective study, the clinical characteristics and laboratory findings of 100 patients with laboratory-confirmed COVID-19 tests were retrieved between May 2020 and January 2021. Based on patients’ demographic and clinical data, we analyzed the capability of the proposed weighted radial kernel support vector machine (SVM), coupled with (RFE). The proposed method is compared with other reference methods such as linear discriminant analysis (LDA) and kernel-based SVM variants including the linear, polynomial, and radial kernels coupled with REF for predicting ICU admissions of COVID-19 patients. An initial performance assessment indicated that the SVM with weighted radial kernels coupled with REF outperformed the other classification methods in discriminating between ICU and non-ICU admissions in COVID-19 patients. Furthermore, applying the Recursive Feature Elimination (RFE) with weighted radial kernel SVM identified a significant set of variables that can predict and statistically distinguish ICU from non-ICU COVID-19 patients. The patients’ weight, PCR Ct Value, CCL19, INF-β, BLC, INR, PT, PTT, CKMB, HB, platelets, RBC, urea, creatinine and albumin results were found to be the significant predicting features. We believe that weighted radial kernel SVM can be used as an assisting ML approach to guide hospital decision makers in resource allocation and mobilization between intensive care and isolation units. We model the data retrospectively on a selected subset of patient-derived variables based on previous knowledge of ICU admission and this needs to be trained in order to forecast prospectively. Full article

(This article belongs to the Special Issue Virology Applications to COVID-19 Pandemic)

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14 pages, 2537 KiB

Open AccessArticle

An Enhanced SEIR Model for Prediction of COVID-19 with Vaccination Effect

by Ramesh Chandra Poonia, Abdul Khader Jilani Saudagar, Abdullah Altameem, Mohammed Alkhathami, Muhammad Badruddin Khan and Mozaherul Hoque Abul Hasanat

Life 2022, 12(5), 647; https://doi.org/10.3390/life12050647 - 27 Apr 2022

Cited by 16 | Viewed by 4378

Abstract

Currently, the spread of COVID-19 is running at a constant pace. The current situation is not so alarming, but every pandemic has a history of three waves. Two waves have been seen, and now expecting the third wave. Compartmental models are one of [...] Read more.

Currently, the spread of COVID-19 is running at a constant pace. The current situation is not so alarming, but every pandemic has a history of three waves. Two waves have been seen, and now expecting the third wave. Compartmental models are one of the methods that predict the severity of a pandemic. An enhanced SEIR model is expected to predict the new cases of COVID-19. The proposed model has an additional compartment of vaccination. This proposed model is the SEIRV model that predicts the severity of COVID-19 when the population is vaccinated. The proposed model is simulated with three conditions. The first condition is when social distancing is not incorporated, while the second condition is when social distancing is included. The third one condition is when social distancing is combined when the population is vaccinated. The result shows an epidemic growth rate of about 0.06 per day, and the number of infected people doubles every 10.7 days. Still, with imparting social distancing, the proposed model obtained the value of R₀ is 1.3. Vaccination of infants and kids will be considered as future work. Full article

(This article belongs to the Special Issue Virology Applications to COVID-19 Pandemic)

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9 pages, 1055 KiB

Open AccessArticle

Is the Alpha Variant of SARS-CoV-2 Associated with a Higher Viral Load than the Historical Strain in Saliva Samples in Patients with Mild to Moderate Symptoms?

by Camille Bonnet, Shirley Masse, Hayat Benamar, Ana-Maria Vilcu, Morgane Swital, Thomas Hanslik, Sylvie van der Werf, Xavier Duval, Fabrice Carrat, Alessandra Falchi and Thierry Blanchon

Life 2022, 12(2), 163; https://doi.org/10.3390/life12020163 - 21 Jan 2022

Cited by 4 | Viewed by 3195

Abstract

During the COVID-19 pandemic, several generic variants emerged, including the Alpha variant, with increased transmissibility compared to historical strains. We aimed to compare the evolution of the viral load between patients infected with the Alpha variant and those infected with the historical SARS-CoV-2 [...] Read more.

During the COVID-19 pandemic, several generic variants emerged, including the Alpha variant, with increased transmissibility compared to historical strains. We aimed to compare the evolution of the viral load between patients infected with the Alpha variant and those infected with the historical SARS-CoV-2 strains, while taking into account the time interval between the onset of symptoms and samples. We used data collected from patients with an acute respiratory infection (mild to moderate symptoms) and seen in consultation in primary care, included in a prospective longitudinal study, COVID-A. Patients performed four salivary samples during the follow-up. All patients who had at least one of the saliva samples test positive for SARS-CoV-2 were included in the analysis. Overall, 118 patients were included: 89 infected by the historical strain and 29 infected by the Alpha variant. Even though we tended to observe a higher viral load in the Alpha variant group, we found no significant difference in the evolution of the viral load in saliva samples between patients infected with the Alpha variant of the SARS-CoV-2 and those infected by historical strains when controlling for the time interval between the onset of symptoms and sampling. Full article

(This article belongs to the Special Issue Virology Applications to COVID-19 Pandemic)

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12 pages, 4465 KiB

Open AccessArticle

Evaluation of Three Automated Extraction Systems for the Detection of SARS-CoV-2 from Clinical Respiratory Specimens

by Ho-Jae Lim, Hye-Soo Jung, Min-Young Park, Young-Hyun Baek, Balaji Kannappan, Jin-Young Park, Jae-Hyun Yang, Ja-Hwan Seol, Min-Woo Lee, Sun-Kyung Jung, Sun-Hwa Lee, Jung-Eun Park and Yong-Jin Yang

Life 2022, 12(1), 68; https://doi.org/10.3390/life12010068 - 4 Jan 2022

Cited by 19 | Viewed by 4570

Abstract

Severe acute respiratory syndrome coronavirus (SARS-CoV-2) is highly contagious and causes coronavirus disease 2019 (COVID-19). Reverse transcription quantitative polymerase chain reaction (RT-qPCR) is the most accurate and reliable molecular assay to detect active SARS-CoV-2 infection. However, a rapid increase in test subjects has [...] Read more.

Severe acute respiratory syndrome coronavirus (SARS-CoV-2) is highly contagious and causes coronavirus disease 2019 (COVID-19). Reverse transcription quantitative polymerase chain reaction (RT-qPCR) is the most accurate and reliable molecular assay to detect active SARS-CoV-2 infection. However, a rapid increase in test subjects has created a global bottleneck in testing capacity. Given that efficient nucleic acid extraction greatly affects reliable and accurate testing results, we compared three extraction platforms: MagNA Pure 96 DNA and Viral NA Small Volume kit on MagNA Pure 96 (Roche, Basel, Switzerland), careGENE^TM Viral/Pathogen HiFi Nucleic Acid Isolation kit (WELLS BIO Inc., Seoul, Korea) on KingFisher Flex (Thermo Fisher Scientific, Rocklin, CA, USA), and SGRespi^TM Pure kit (Seegene Inc., Seoul, Korea) on Maelstrom 9600 (Taiwan Advanced Nanotech Inc., Taoyuan, Taiwan). RNA was extracted from 245 residual respiratory specimens from the different types of samples (i.e., NPS, sputum, and saliva) using three different kits. The 95% limits of detection of median tissue culture infectious dose per milliliter (TCID₅₀/mL) for the MagNA Pure 96, KingFisher Flex, and Maelstrom 9600 were 0.37–3.15 × 10¹, 0.41–3.62 × 10¹, and 0.33–1.98 × 10¹, respectively. The KingFisher Flex platform exhibited 99.2% sensitivity and 100% specificity, whereas Maelstrom 9600 exhibited 98.3–100% sensitivity and 100% specificity. Bland–Altman analysis revealed a 95.2% concordance between MagNA Pure 96 and KingFisher Flex and 95.4% concordance between MagNA Pure 96 and Maelstrom 9600, indicating that all three platforms provided statistically reliable results. This suggests that two modifying platforms, KingFisher Flex and Maelstrom 9600, are accurate and scalable extraction platforms for large-scale SARS-CoV-2 clinical detection and could help the management of COVID-19 patients. Full article

(This article belongs to the Special Issue Virology Applications to COVID-19 Pandemic)

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9 pages, 1205 KiB

Open AccessArticle

Emerging Mutations Potentially Related to SARS-CoV-2 Immune Escape: The Case of a Long-Term Patient

by Loredana Capozzi, Domenico Simone, Angelica Bianco, Laura Del Sambro, Valeria Rondinone, Lorenzo Pace, Viviana Manzulli, Michela Iacobellis and Antonio Parisi

Life 2021, 11(11), 1259; https://doi.org/10.3390/life11111259 - 18 Nov 2021

Cited by 4 | Viewed by 2846

Abstract

SARS-CoV-2 isolates from long-term COVID-19 patients play a significant role in understanding the mechanisms of infection and virus persistence. This study describes a SARS-CoV-2 isolate from a 53-year-old woman from Apulia (Italy), who was COVID-19 positive for approximately four months. In this paper [...] Read more.

SARS-CoV-2 isolates from long-term COVID-19 patients play a significant role in understanding the mechanisms of infection and virus persistence. This study describes a SARS-CoV-2 isolate from a 53-year-old woman from Apulia (Italy), who was COVID-19 positive for approximately four months. In this paper we aimed to investigate any potential correlation between genetic mutations and clinical features of this case of infection. The viral isolate was assigned to lineage B.1.177.51 through whole-genome sequencing (WGS) and harbored a novel set of mutations on the Spike protein (V143D, del144/145 and E484K); furthermore, seroneutralization assays showed impaired response of the surveyed strain to BNT162b2 (Comirnaty) Pfizer/BioNTech vaccine-induced (average reduction of 70%) and convalescent sera (average reduction of 19.04%), when compared to VOC P.1. This study highlights the importance of genomic surveillance for the management of the COVID-19 pandemic, the relevance of monitoring of emerging SARS-CoV-2 mutations in all lineages, and the necessity of testing the response of emerging variants to available therapies and vaccines. Full article

(This article belongs to the Special Issue Virology Applications to COVID-19 Pandemic)

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17 pages, 1810 KiB

Open AccessArticle

A Multiallelic Molecular Beacon-Based Real-Time RT-PCR Assay for the Detection of SARS-CoV-2

by Andreas C. Chrysostomou, Johana Hezka Rodosthenous, Cicek Topcu, Christina Papa, Antonia Aristokleous, Georgia Stathi, Christina Christodoulou, Christina Eleftheriou, Dora C. Stylianou and Leondios G. Kostrikis

Life 2021, 11(11), 1146; https://doi.org/10.3390/life11111146 - 27 Oct 2021

Cited by 6 | Viewed by 4211

Abstract

Emerging infectious viruses have led to global advances in the development of specific and sensitive detection techniques. Viruses have an inherent potential to easily mutate, presenting major hurdles for diagnostics and requiring methods capable of detecting genetically diverse viral strains. One such infectious [...] Read more.

Emerging infectious viruses have led to global advances in the development of specific and sensitive detection techniques. Viruses have an inherent potential to easily mutate, presenting major hurdles for diagnostics and requiring methods capable of detecting genetically diverse viral strains. One such infectious agent is severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which emerged in December 2019 and has resulted in the global coronavirus disease 2019 (COVID-19) pandemic. This study presents a real-time reverse transcription PCR (RT-PCR) detection assay for SARS-CoV-2, taking into account its intrinsic polymorphic nature that arises due to genetic drift and recombination, as well as the possibility of continuous and multiple introductions of genetically nonidentical strains into the human population. This advance was achieved by using mismatch-tolerant molecular beacons designed to specifically detect the SARS-CoV-2 S, E, M, and N genes. These were applied to create a simple and reproducible real-time RT-PCR assay, which was validated using external quality control panels (QCMD: CVOP20, WHO: SARS-CoV-2-EQAP-01) and clinical samples. This assay was designed for high target detection accuracy and specificity and can also be readily adapted for the detection of other emerging and rapidly mutating pathogens. Full article

(This article belongs to the Special Issue Virology Applications to COVID-19 Pandemic)

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9 pages, 1939 KiB

Open AccessEditor’s ChoiceCommunication

Robust Neutralizing Antibody Responses 6 Months Post Vaccination with BNT162b2: A Prospective Study in 308 Healthy Individuals

by Evangelos Terpos, Vangelis Karalis, Ioannis Ntanasis-Stathopoulos, Maria Gavriatopoulou, Sentiljana Gumeni, Panagiotis Malandrakis, Eleni-Dimitra Papanagnou, Efstathios Kastritis, Ioannis P. Trougakos and Meletios A. Dimopoulos

Life 2021, 11(10), 1077; https://doi.org/10.3390/life11101077 - 12 Oct 2021

Cited by 24 | Viewed by 3229

Abstract

Elucidating long-term immunity following COVID-19 vaccination is essential for decision-making regarding booster shots. The aim of this study was to investigate the kinetics of neutralizing antibodies (Nabs) against SARS-CoV-2 up to six months after the second vaccination dose with the BNT162b2 mRNA vaccine. [...] Read more.

Elucidating long-term immunity following COVID-19 vaccination is essential for decision-making regarding booster shots. The aim of this study was to investigate the kinetics of neutralizing antibodies (Nabs) against SARS-CoV-2 up to six months after the second vaccination dose with the BNT162b2 mRNA vaccine. Nabs levels were measured on days 1 (before the first vaccine shot), 8, 22 (before the second shot), 36, 50, and 3 and 6 months after the second vaccination (NCT04743388). Three hundred and eight healthy individuals without malignant disease were included in this study. At six months, 2.59% of the participants had a Nabs value less than 30%, while 11.9% had Nabs values of less than 50%. Importantly, 58% of the subjects had Nabs values of more than 75%. Nabs were initially eliminated at a relatively slow rate, but after three months their elimination was 5.7 times higher. Older age was inversely associated with Nabs levels at all examined timepoints. Interestingly, a population modeling analysis estimated that half of the subjects will have Nabs values less than 73.8% and 64.6% at 9 and 12 months, respectively, post vaccination completion. In conclusion, we found a persistent but declining anti-SARS-CoV-2 humoral immunity at six months following full vaccination with BNT162b2 in healthy individuals, which was more pronounced among older persons. These data may inform the public health policies regarding the prioritization of booster vaccine shots. Full article

(This article belongs to the Special Issue Virology Applications to COVID-19 Pandemic)

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10 pages, 228 KiB

Open AccessArticle

Demographic, Clinical and Immunogenetic Profiles of a Greek Cohort of COVID-19 Patients

by Maria. G. Detsika, Chara Giatra, Vasiliki Kitsiou, Edison Jahaj, Theofilos Athanassiades, Diamanto Kouniaki, Stylianos E. Orfanos, Ioanna Dimopoulou, Maria Pagoni, Katerina Tarassi, Alexandra Tsirogianni and Anastasia Kotanidou

Life 2021, 11(10), 1017; https://doi.org/10.3390/life11101017 - 27 Sep 2021

Cited by 7 | Viewed by 2224

Abstract

The present cross-sectional study consists of a comprehensive analysis of epidemiological, laboratory, and clinical characteristics of COVID-19 patients in relation to their immunogenetic profiles. We studied 125 COVID-19 patients comprising different stages of disease severity; non-hospitalized (mild n = 69) and hospitalized ( [...] Read more.

The present cross-sectional study consists of a comprehensive analysis of epidemiological, laboratory, and clinical characteristics of COVID-19 patients in relation to their immunogenetic profiles. We studied 125 COVID-19 patients comprising different stages of disease severity; non-hospitalized (mild n = 69) and hospitalized (n = 56). Analysis of disease characteristics revealed no major differences between males and females of each group of patients while hospitalized patients were older and presented with comorbidities. A positive allele association was observed for HLA-DRB1*01 in total COVID-19 patients versus healthy controls. Subgrouping of COVID-19 patients in mild and hospitalized further identified a statistically significant increase in HLA-DRB1*01 in mild COVID-19 patients versus controls. The frequency of A*11, A*23, and DRB1*09 alleles was higher, while the frequency of C*12 was lower, in hospitalized patients versus healthy controls albeit with uncorrected statistical significance. The identification of specific allele associations may provide useful future markers for disease susceptibility in order to allow successful clinical management of COVID-19 patients. Full article

(This article belongs to the Special Issue Virology Applications to COVID-19 Pandemic)

12 pages, 2240 KiB

Open AccessEditor’s ChoiceArticle

A Novel Real-Time RT-PCR-Based Methodology for the Preliminary Typing of SARS-CoV-2 Variants, Employing Non-Extendable LNA Oligonucleotides and Three Signature Mutations at the Spike Protein Receptor-Binding Domain

by Serafeim C. Chaintoutis, Taxiarchis Chassalevris, Sofia Balaska, Evangelia Mouchtaropoulou, George Tsiolas, Ioannis Vlatakis, Areti Tychala, Dimitris Koutsioulis, Anagnostis Argiriou, Lemonia Skoura and Chrysostomos I. Dovas

Life 2021, 11(10), 1015; https://doi.org/10.3390/life11101015 - 27 Sep 2021

Cited by 7 | Viewed by 2900

Abstract

Mutations resulting in amino-acid substitutions of the SARS-CoV-2 spike protein receptor-binding domain (RBD) have been associated with enhanced transmissibility and immune escape of the respective variants, namely Alpha, Beta, Gamma or Delta. Rapid identification of the aforementioned variants of concern and their discrimination [...] Read more.

Mutations resulting in amino-acid substitutions of the SARS-CoV-2 spike protein receptor-binding domain (RBD) have been associated with enhanced transmissibility and immune escape of the respective variants, namely Alpha, Beta, Gamma or Delta. Rapid identification of the aforementioned variants of concern and their discrimination of other variants is thus of importance for public health interventions. For this reason, a one-step real-time RT-PCR assay employing four locked nucleic acid (LNA) modified TaqMan probes was developed, to target signature mutations associated with amino-acid substitutions at positions 478, 484 and 501 present in the receptor-binding motif (RBM) of the spike protein RBD. This region contains most contacting residues of SARS-CoV-2 that bind to ACE2. A novel strategy employing the use of non-extendable LNA oligonucleotide blockers that can reduce non-specific hybridization of probes increased the number of different mutated sites examined in a multiplex PCR. The combinatory analysis of the different fluorescence signals obtained enabled the preliminary differentiation of SARS-CoV-2 variants of concern. The assay is sensitive with a LOD of 263 copies/reaction for the Delta variant, 170 copies/reaction for the Beta variant, amplification efficiencies > 91% and a linear range of >5 log₁₀ copies/reaction against all targets. Validation of the assay using known SARS-CoV-2-positive and negative samples from humans and animals revealed its ability to correctly identify the targeted mutations and preliminary characterize the SARS-CoV-2 variants. The novel approach for mutation typing using LNA oligonucleotide blockers can be modified to target signature mutations at four different sites in the RBM and further expand the range of variants detected. Full article

(This article belongs to the Special Issue Virology Applications to COVID-19 Pandemic)

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13 pages, 2351 KiB

Open AccessEditor’s ChoiceArticle

Evidence of Long-Lasting Humoral and Cellular Immunity against SARS-CoV-2 Even in Elderly COVID-19 Convalescents Showing a Mild to Moderate Disease Progression

by Bastian Fischer, Christopher Lindenkamp, Christoph Lichtenberg, Ingvild Birschmann, Cornelius Knabbe and Doris Hendig

Life 2021, 11(8), 805; https://doi.org/10.3390/life11080805 - 9 Aug 2021

Cited by 9 | Viewed by 5071

Abstract

We here evaluate the humoral and cellular immune response against SARS-CoV-2 in 41 COVID-19 convalescents. As previous studies mostly included younger individuals, one advantage of our study is the comparatively high mean age of the convalescents included in the cohort considered (54 ± [...] Read more.

We here evaluate the humoral and cellular immune response against SARS-CoV-2 in 41 COVID-19 convalescents. As previous studies mostly included younger individuals, one advantage of our study is the comparatively high mean age of the convalescents included in the cohort considered (54 ± 8.4 years). While anti-SARS-CoV-2 antibodies were still detectable in 95% of convalescents up to 8 months post infection, an antibody-decay over time was generally observed in most donors. Using a multiplex assay, our data additionally reveal that most convalescents exhibit a broad humoral immunity against different viral epitopes. We demonstrate by flow cytometry that convalescent donors show a significantly elevated number of natural killer cells when compared to healthy controls, while no differences were found concerning other leucocyte subpopulations. We detected a specific long-lasting cellular immune response in convalescents by stimulating immune cells with SARS-CoV-2-specific peptides, covering domains of the viral spike, membrane and nucleocapsid protein, and measuring interferon-γ (IFN-γ) release thereafter. We modified a commercially available ELISA assay for IFN-γ determination in whole-blood specimens of COVID-19 convalescents. One advantage of this assay is that it does not require special equipment and can, thus, be performed in any standard laboratory. In conclusion, our study adds knowledge regarding the persistence of immunity of convalescents suffering from mild to moderate COVID-19. Moreover, our study provides a set of simple methods to characterize and confirm experienced COVID-19. Full article

(This article belongs to the Special Issue Virology Applications to COVID-19 Pandemic)

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Review

Jump to: Editorial, Research

12 pages, 576 KiB

Open AccessReview

Effect of Vaccination against SARS-CoV-2 on Long COVID-19: A Narrative Review

by Andreas G. Tofarides, Eirini Christaki, Haralampos Milionis and Georgios K. Nikolopoulos

Life 2022, 12(12), 2057; https://doi.org/10.3390/life12122057 - 8 Dec 2022

Cited by 17 | Viewed by 3366

Abstract

Vaccines against SARS-CoV-2 have saved millions of lives and played an important role in containing the COVID-19 pandemic. Vaccination against SARS-CoV-2 is also associated with reduced disease severity and, perhaps, with COVID-19 symptom burden. In this narrative review, we present, in a clinically [...] Read more.

Vaccines against SARS-CoV-2 have saved millions of lives and played an important role in containing the COVID-19 pandemic. Vaccination against SARS-CoV-2 is also associated with reduced disease severity and, perhaps, with COVID-19 symptom burden. In this narrative review, we present, in a clinically relevant question-and-answer manner, the evidence regarding the association between vaccination against SARS-CoV-2 and long COVID-19. We discuss how the mechanism of action of vaccines could interplay with the pathophysiology of post-COVID-19 condition. Furthermore, we describe how specific factors, such as the number of vaccine doses and the type of SARS-CoV-2 variants, may affect post-COVID-19 condition. We also discuss the role of timing for vaccination in relation to the onset of long COVID-19 symptoms, as it seems to affect the frequency and severity of the condition. Additionally, we describe the potential modifying effect of age, as well as the association of type and level of immune response with long COVID-19. We also describe how system-specific long COVID-19 sequelae, namely neurocognitive-psychologic symptoms and cardiovascular pathology, could be altered by vaccination. Last, we address the question of whether seasonal influenza vaccination has a meaningful impact on the frequency of long COVID-19. Full article

(This article belongs to the Special Issue Virology Applications to COVID-19 Pandemic)

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Virology Applications to COVID-19 Pandemic

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