The Immune Response to SARS-CoV-2 and Variants of Concern

Torbati, Elham Siasi; Krause, Kurt L.; Ussher, James E.

doi:10.3390/v13101911

Cited by 23 publications

(14 citation statements)

References 141 publications

(219 reference statements)

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“…Multiple studies corroborate no significant difference in neutralising antibodies between the alpha variant and the ancestral isolate post mRNA vaccination with BNT162b2 or mRNA-1273. Noteworthy reduction of post-vaccination neutralising sera was observed for the beta variant in persons vaccinated with mRNA-1273(41).…”

Section: Resultsmentioning

confidence: 99%

Characterizing Longitudinal Antibody Responses in Recovered Individuals Following COVID-19 Infection and Single-Dose Vaccination in British Columbia, Canada: a Prospective Cohort Study

Olmstead

Nikiforuk

Schwartz

et al. 2022

Preprint

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Background: Investigating antibody titres in individuals who have been both naturally infected with SARS-CoV-2 and vaccinated can provide insight into antibody dynamics and correlates of protection over time. Methods: Human coronavirus (HCoV) IgG antibodies were measured longitudinally in a prospective cohort of PCR-confirmed, COVID-19 recovered individuals (k=57) in British Columbia pre- and post-vaccination. SARS-CoV-2 and endemic HCoV antibodies were measured in serum collected between Nov. 2020 and Sept. 2021 (n=341). Primary analysis used a linear mixed-effects model to understand the effect of single dose vaccination on antibody concentrations adjusting for biological sex, age, time from infection and vaccination. Secondary analysis investigated the cumulative incidence of high SARS-CoV-2 anti-spike IgG seroreactivity equal to or greater than 5.5 log10 AU/mL up to 105 days post-vaccination. No re-infections were detected in vaccinated participants, post-vaccination by qRT-PCR performed on self-collected nasopharyngeal specimens. Results: Bivariate analysis (complete data for 42 participants, 270 samples over 472 days) found SARS-CoV-2 spike and RBD antibodies increased 14-56 days post-vaccination (p<0.001) and vaccination prevented waning (B=1.66 [95%CI: 1.45-3.46]); while decline of nucleocapsid antibodies over time was observed (B=-0.24 [95%CI: -1.2-(-0.12)]). A non-significant trend towards higher spike antibodies against endemic beta-HCoVs was also noted. On average, SARS-CoV-2 anti-spike IgG concentration increased in participants who received one vaccine dose by 2.06 log10 AU/mL (95%CI: 1.45-3.46) adjusting for age, biological sex, and time. Cumulative incidence of high SARS-CoV-2 spike antibodies (>5.5 log10 AU/mL) was 83% greater in vaccinated compared to unvaccinated individuals. Conclusions: Our study confirms that vaccination post-SARS-CoV-2 infection provides multiple benefits, such as increasing anti-spike IgG titers and preventing decay up to 85 days post-vaccination.

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Section: Resultsmentioning

confidence: 99%

Characterizing Longitudinal Antibody Responses in Recovered Individuals Following COVID-19 Infection and Single-Dose Vaccination in British Columbia, Canada: a Prospective Cohort Study

Olmstead

Nikiforuk

Schwartz

et al. 2022

Preprint

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“…Coronaviruses are known to induce innate and virus‐specific adaptive immune responses to the infection. 13 , 14 These responses are reasoned to provide at least some degree of protection against reinfection. However, protection against the seasonal coronaviruses is limited and diminished with time, concurrent with declining neutralizing antibody titers.…”

Section: Figurementioning

confidence: 99%

Are we moving toward ending SARS‐CoV‐2?

Mishra

Nayak

Byrareddy

2022

Journal of Medical Virology

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To the Editor, In November 2019, the social media app WeChat, the platform used within China, picked up chatter between physicians about a cluster of pneumonia cases reported as an illness in patients of unknown cause. This was followed by a report to the media on December 31, 2019, by the Wuhan Municipal Health Commissioner about a cluster of pneumonia cases in Wuhan, leading to the possibility of a new coronavirus outbreak. Following this report, the World Health Organization (WHO) came into action and announced that the causative agent is a novel coronavirus and issued the initial guidelines. By January 22, 2020, it was confirmed that this novel coronavirus could transmit from human to human. On February 11, the WHO announced the disease caused by the novel coronavirus would be named COVID-19, and due to the widespread global reports of the disease by March 11, the WHO announced COVID-19 as a pandemic. 1 The causative agent of the COVID-19 is the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) virus that has spread from Wuhan, China, to the rest of the world and has been an ongoing pandemic ever since. 2 Approximately 468 million people have been infected with the SARS-CoV-2 and its variant of concerns (VOCs) andand its variants so far, and more than 6.0 million deaths have occurred. Human Coronavirus are classified into four major genera: Alphacoronavirus, Betacoronavirus, Gammacoronavirus, and Deltacoronavirus. Of these, only the Alpha and Beta-CoVs are known to infect humans. In contrast, the Gamma and Delta-CoVs predominantly infect birds. 3 SARS-CoV-2 shares about 89% sequence identity with the other human coronaviruses. 4 The phylogenetic analysis has revealed that the SARS-COV-2 shares 89%-96% homology with the Chinese bat coronavirus (Bat-SL-CoV RaTG13, ZC45, and ZXC21), suggesting potential bat origin that was potentially transmitted to humans 2,5-7 Although the SARS-CoV-2 encodes an RNA proofreading exoribonuclease (nsp14-exon), it has accumulated multiple random mutations over the viral genome during global transmission and led to different variants across the globe. 8,9 The first SARS-CoV2variant of SARS-CoV-2, carrying the mutation at the D614G of Spike protein, emerged throughout the globe and became prevalent, suggesting a fitness advantage. 10 Later on, various variants were identified, including Alpha variant (B.1.1.7; United Kingdom), Beta (B.1.351; South Africa), Gamma (P1; Japan/Brazil), and Delta variants (B.1.617.2; India). As Delta was more transmissible than the other Discipline of Biosciences and Biomedical Engineering,

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“…WHO has defined variants of concern (VOCs) based on reliable evidence of increased phenotypes, including transmissibility ( , accessed on 28 March 2022). Biological approaches have determined the significance of key SARS-CoV-2 VOC mutations that promote transmission, enhance receptor binding affinity [ 14 , 15 ], and antagonize immunity [ 16 , 17 ], however, which lag behind a timely concern about them. The Omicron VOC (B.1.1.529) has dominated the COVID-19 pandemic, spreading worldwide shortly after emerging in South Africa in November 2021 [ 18 ].…”

Section: Introductionmentioning

confidence: 99%

Convolutional Neural Networks Based on Sequential Spike Predict the High Human Adaptation of SARS-CoV-2 Omicron Variants

Nan

Zhang

et al. 2022

Viruses

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The COVID-19 pandemic has frequently produced more highly transmissible SARS-CoV-2 variants, such as Omicron, which has produced sublineages. It is a challenge to tell apart high-risk Omicron sublineages and other lineages of SARS-CoV-2 variants. We aimed to build a fine-grained deep learning (DL) model to assess SARS-CoV-2 transmissibility, updating our former coarse-grained model, with the training/validating data of early-stage SARS-CoV-2 variants and based on sequential Spike samples. Sequential amino acid (AA) frequency was decomposed into serially and slidingly windowed fragments in Spike. Unsupervised machine learning approaches were performed to observe the distribution in sequential AA frequency and then a supervised Convolutional Neural Network (CNN) was built with three adaptation labels to predict the human adaptation of Omicron variants in sublineages. Results indicated clear inter-lineage separation and intra-lineage clustering for SARS-CoV-2 variants in the decomposed sequential AAs. Accurate classification by the predictor was validated for the variants with different adaptations. Higher adaptation for the BA.2 sublineage and middle-level adaptation for the BA.1/BA.1.1 sublineages were predicted for Omicron variants. Summarily, the Omicron BA.2 sublineage is more adaptive than BA.1/BA.1.1 and has spread more rapidly, particularly in Europe. The fine-grained adaptation DL model works well for the timely assessment of the transmissibility of SARS-CoV-2 variants, facilitating the control of emerging SARS-CoV-2 variants.

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The Immune Response to SARS-CoV-2 and Variants of Concern

Cited by 23 publications

References 141 publications

Characterizing Longitudinal Antibody Responses in Recovered Individuals Following COVID-19 Infection and Single-Dose Vaccination in British Columbia, Canada: a Prospective Cohort Study

Characterizing Longitudinal Antibody Responses in Recovered Individuals Following COVID-19 Infection and Single-Dose Vaccination in British Columbia, Canada: a Prospective Cohort Study

Are we moving toward ending SARS‐CoV‐2?

Convolutional Neural Networks Based on Sequential Spike Predict the High Human Adaptation of SARS-CoV-2 Omicron Variants

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