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Vaccines
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Global Analysis of Tracking the Evolution of SARS-CoV-2 Variants
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Global Analysis of Tracking the Evolution of SARS-CoV-2 Variants

A special issue of Vaccines (ISSN 2076-393X). This special issue belongs to the section "COVID-19 Vaccines and Vaccination".

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 9875

Special Issue Editor

Dr. Muhammad Atif Zahoor

E-Mail Website
Guest Editor
Viral Hepatitis Care Network (VIRCAN) Study Group, Toronto Centre for Liver Disease, Toronto, ON M5G 2C, Canada
Interests: host-virus interactions; innate immunity; cell signaling
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

SARS-CoV-2, a positive-sense β-coronavirus, is the etiological agent of COVID-19. As of July 2022, it has caused over 6.43 million deaths worldwide. Although it possesses an error-prone viral RNA-dependent RNA polymerase with limited 3’-5’ exoribonuclease activity, it can cause progeny viruses with new mutations, affecting its infectivity, transmissibility, and virulence. Moreover, recently, a sharp decline in PCR testing due to high cost and reliance on antigen testing kits could lead to the potential underreporting of new emerging variants. Such a situation can possibly promulgate a variant crisis in future and could impact the current ongoing therapeutic approaches. Therefore, the continuous monitoring and tracking of new variants on a globe scale, as well as the characterization of mutations, is crucial because of their effect on adaptive immunity, neutralizing antibody response, and impact on vaccine efficacy.

The detailed maps of mutations highlighting their prospective role in therapeutics and vaccine development can better prepare us for future waves of continuously evolving SARS-CoV-2. With this aim, we invite original research and review articles which address the tracking and genomic surveillance of emerging variants, their virulence, transmissibility, mathematical modeling, and therapeutic aspects of COVID-19.

Dr. Muhammad Atif Zahoor
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. Vaccines is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • SARS-CoV-2
  • COVID-19
  • variants
  • transmission
  • vaccine efficacy
  • immune escape

Published Papers (6 papers)

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Editorial

Jump to: Research, Other

3 pages, 197 KiB  
Editorial
Global Analysis of Tracking the Evolution of SARS-CoV-2 Variants
by Muhammad Atif Zahoor
Vaccines 2023, 11(12), 1812; https://doi.org/10.3390/vaccines11121812 - 04 Dec 2023
Viewed by 964
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), infamously known as Coronavirus Disease 2019 (COVID-19), is responsible for the current pandemic and, to date, has greatly impacted public health and economy globally [...] Full article
(This article belongs to the Special Issue Global Analysis of Tracking the Evolution of SARS-CoV-2 Variants)

Research

Jump to: Editorial, Other

11 pages, 731 KiB  
Article
The Omicron Variant Reinfection Risk among Individuals with a Previous SARS-CoV-2 Infection within One Year in Shanghai, China: A Cross-Sectional Study
by Chuchu Ye, Ge Zhang, Anran Zhang, Hualei Xin, Kang Wu, Zhongjie Li, Yilin Jia, Lipeng Hao, Caoyi Xue, Yuanping Wang, Hongmei Xu, Weiping Zhu and Yixin Zhou
Vaccines 2023, 11(7), 1146; https://doi.org/10.3390/vaccines11071146 - 25 Jun 2023
Cited by 3 | Viewed by 1491
Abstract
Reinfection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants due to immune escape is challenging for the global response to the pandemic. We estimated the Omicron reinfection prevalence among people who had a previous SARS-CoV-2 infection in Shanghai, China. We conducted a [...] Read more.
Reinfection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants due to immune escape is challenging for the global response to the pandemic. We estimated the Omicron reinfection prevalence among people who had a previous SARS-CoV-2 infection in Shanghai, China. We conducted a telephone survey in December 2022 with those who had previously been infected with Omicron between March and May 2022. Information on their demographics, coronavirus disease 2019 (COVID-19) testing, and vaccination history was collected. The overall and subgroup reinfection rates were estimated and compared. Among the 1981 respondents who were infected between March and May 2022, 260 had positive nucleic acid or rapid antigen tests in December 2022, with an estimated reinfection rate of 13.1% (95% confidence interval [95% CI]: 11.6–14.6). The reinfection rate for those who had a booster vaccination was 11.4% (95% CI: 9.2–13.7), which was significantly lower than that for those with an incomplete vaccination series (15.2%, 95% CI: 12.3–18.1) (adjusted odds ratio [aOR]: 0.579; 95% CI: 0.412–0.813). Reinfection with the Omicron variant was lower among individuals with a previous SARS-CoV-2 infection and those who had a booster vaccination, suggesting that hybrid immunity may offer protection against reinfection with Omicron sublineages. Full article
(This article belongs to the Special Issue Global Analysis of Tracking the Evolution of SARS-CoV-2 Variants)
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7 pages, 1918 KiB  
Communication
Deep Mutational Scanning to Predict Escape from Bebtelovimab in SARS-CoV-2 Omicron Subvariants
by Mellissa C. Alcantara, Yusuke Higuchi, Yuhei Kirita, Satoaki Matoba and Atsushi Hoshino
Vaccines 2023, 11(3), 711; https://doi.org/10.3390/vaccines11030711 - 22 Mar 2023
Cited by 4 | Viewed by 1590
Abstract
The major concern with COVID-19 therapeutic monoclonal antibodies is the loss of efficacy against continuously emerging variants of SARS-CoV-2. To predict antibody efficacy against future Omicron subvariants, we conducted deep mutational scanning (DMS) encompassing all single mutations of the receptor-binding domain of the [...] Read more.
The major concern with COVID-19 therapeutic monoclonal antibodies is the loss of efficacy against continuously emerging variants of SARS-CoV-2. To predict antibody efficacy against future Omicron subvariants, we conducted deep mutational scanning (DMS) encompassing all single mutations of the receptor-binding domain of the BA.2 strain utilizing an inverted infection assay with an ACE2-harboring virus and library spike-expressing cells. In the case of bebtelovimab, which preserves neutralization activity against BA.2 and BA.5, a broad range of amino acid substitutions at K444, V445, and G446, and some substitutions at P499 and T500, were indicated to achieve the antibody escape. Among subvariants with current rises in case numbers, BA2.75 with G446S partially evaded neutralization by bebtelovimab, while complete evasion was observed in XBB with V445P and BQ.1 with K444T. This is consistent with the DMS results against BA.2, highlighting the potential of DMS as a predictive tool for antibody escape. Full article
(This article belongs to the Special Issue Global Analysis of Tracking the Evolution of SARS-CoV-2 Variants)
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12 pages, 2593 KiB  
Article
Augmenting Vaccine Efficacy against Delta Variant with ‘Mycobacterium-w’-Mediated Modulation of NK-ADCC and TLR-MYD88 Pathways
by Sarita Rani Jaiswal, Ashraf Saifullah, Jaganath Arunachalam, Rohit Lakhchaura, Dhanir Tailor, Anupama Mehta, Gitali Bhagawati, Hemamalini Aiyer, Subhrajit Biswas, Bakulesh Khamar, Sanjay V. Malhotra and Suparno Chakrabarti
Vaccines 2023, 11(2), 328; https://doi.org/10.3390/vaccines11020328 - 01 Feb 2023
Viewed by 1788
Abstract
Mycobacterium-w (Mw) was shown to boost adaptive natural killer (ANK) cells and protect against COVID-19 during the first wave of the pandemic. As a follow-up of the trial, 50 healthcare workers (HCW) who had received Mw in September 2020 and subsequently received [...] Read more.
Mycobacterium-w (Mw) was shown to boost adaptive natural killer (ANK) cells and protect against COVID-19 during the first wave of the pandemic. As a follow-up of the trial, 50 healthcare workers (HCW) who had received Mw in September 2020 and subsequently received at least one dose of ChAdOx1 nCoV-19 vaccine (Mw + ChAdOx1 group) were monitored for symptomatic COVID-19 during a major outbreak with the delta variant of SARS-CoV-2 (April–June 2021), along with 201 HCW receiving both doses of the vaccine without Mw (ChAdOx1 group). Despite 48% having received just a single dose of the vaccine in the Mw + ChAdOx1 group, only two had mild COVID-19, compared to 36 infections in the ChAdOx1 group (HR-0.46, p = 0.009). Transcriptomic studies revealed an enhanced adaptive NK cell-dependent ADCC in the Mw + ChAdOx1 group, along with downregulation of the TLR2-MYD88 pathway and concomitant attenuation of downstream inflammatory pathways. This might have resulted in robust protection during the pandemic with the delta variant. Full article
(This article belongs to the Special Issue Global Analysis of Tracking the Evolution of SARS-CoV-2 Variants)
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19 pages, 3404 KiB  
Article
Maintenance of Antibody Response in Egyptian Healthcare Workers Vaccinated with ChAdOx1 nCoV-19 Vaccine during Delta and Omicron Variants Pandemic: A Prospective Study
by Noha M. Hammad, Heba M. Kadry, Mai M. Malek, Shereen Mohamed Bahgat, Noha M. Abdelsalam, Amira Hamed Mohamed Afifi and Doaa Alhussein Abo-alella
Vaccines 2022, 10(10), 1706; https://doi.org/10.3390/vaccines10101706 - 12 Oct 2022
Cited by 2 | Viewed by 1587
Abstract
Background: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a constantly evolving virus, resulting in an increased burden on the existing COVID-19 vaccines. Healthcare workers (HCWs) are the first line of defense against the coronavirus disease 2019 (COVID-19) pandemic and have been [...] Read more.
Background: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a constantly evolving virus, resulting in an increased burden on the existing COVID-19 vaccines. Healthcare workers (HCWs) are the first line of defense against the coronavirus disease 2019 (COVID-19) pandemic and have been prioritized among the risk categories receiving the COVID-19 vaccine. This work aimed to investigate the maintenance of antibody response of the Oxford–AstraZeneca vaccine (ChAdOx1/nCoV-19). Methods: Anti-spike immunoglobulin G (IgG) was measured at baseline point (immediately prior to vaccination) and 12- and 24-week (w) points following vaccination. Adverse reactions to the vaccine were reported. Participants were followed up for the incidence of COVID-19 during the 12 w interval between vaccination doses for 24 w after the second dose. Results: A total of 255 HCWs participated in the study. Prior to vaccination, 54.1% experienced COVID-19, 88.2% were seropositive after the first dose, while seropositivity reached 95.7% after the second dose. Following the first and second doses, the anti-spike IgG serum level was significantly higher in subjects with past COVID-19 than in others (p < 0.001 and =0.001, respectively). Conclusions: The Oxford–AstraZeneca vaccine is generally safe and provides a highly effective long-term humoral immune response against the Delta and Omicron variants of SARS-CoV-2. Full article
(This article belongs to the Special Issue Global Analysis of Tracking the Evolution of SARS-CoV-2 Variants)
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Other

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9 pages, 253 KiB  
Brief Report
Monoclonal Antibodies against SARS-CoV-2 Infection: Results from a Real-Life Study before the Omicron Surge
by Riccardo Scotto, Antonio Riccardo Buonomo, Giulia Zumbo, Antonio Di Fusco, Nunzia Esposito, Isabella Di Filippo, Mariano Nobile, Biagio Pinchera, Nicola Schiano Moriello, Riccardo Villari, Ivan Gentile and Federico II COVID Team
Vaccines 2022, 10(11), 1895; https://doi.org/10.3390/vaccines10111895 - 10 Nov 2022
Cited by 3 | Viewed by 1603
Abstract
Despite the lightning-fast advances in the management of SARS-CoV after 2 years of pandemic, COVID-19 continues to pose a challenge for fragile patients, who could benefit from early administration of monoclonal antibodies (mAbs) to reduce the risk of severe disease progression. We conducted [...] Read more.
Despite the lightning-fast advances in the management of SARS-CoV after 2 years of pandemic, COVID-19 continues to pose a challenge for fragile patients, who could benefit from early administration of monoclonal antibodies (mAbs) to reduce the risk of severe disease progression. We conducted a prospective study to evaluate the effectiveness of mAbs against SARS-CoV-2 among patients at risk for severe disease progression, namely elderly and those with comorbidities, before the omicron variant surge. Patients were treated with either casirivimab/imdevimab, sotrovimab, or bamlanivimab/etesevimab. The rates and risk factors for clinical worsening, hospitalization, ICU admission and death (unfavorable outcomes) were evaluated. A stratified analysis according to the presence of SARS-CoV-2 IgG was also performed. Among 185 included patients, we showed low rates of unfavorable outcomes (9.2%), which were more frequent in patients with chronic kidney disease (aOR: 10.44, 95% CI: 1.73–63.03; p < 0.05) and basal D-dimer serum concentrations > 600 ng/mL (aOR 21.74, 95% CI: 1.18–397.70; p < 0.05). Patients with negative SARS-CoV-2 serology at baseline showed higher C-reactive protein values compared with patients with positive serology (p < 0.05) and a trend toward a higher admission rate to SICU and ICU compared with patients with positive serology. Our results thus showed, in a real-life setting, the efficacy of mAbs against SARS-CoV-2 before an Omicron surge when the available mabs become not effective. Full article
(This article belongs to the Special Issue Global Analysis of Tracking the Evolution of SARS-CoV-2 Variants)
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