Prior Vaccination Exceeds Prior Infection in Eliciting Innate and Humoral Immune Responses in Omicron Infected Outpatients

Lee, Hye Kyung; Walter, Mary; Knabl, Ludwig; Dai, Yunchuan; Füßl, Magdalena; Caf, Yasemin; Jeller, Claudia; Knabl, Philipp; Obermoser, Martina; Baurecht, Christof; Kaiser, Norbert; Zabernigg, August; Wurdinger, Gernot M.; Furth, Priscilla A.; Hennighausen, Lothar

doi:10.3389/fimmu.2022.916686

Cited by 26 publications

(27 citation statements)

References 44 publications

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“…In contrast to BA.4 and BA.5, we detected only minor escape of BA.2 from BA.1 elicited immunity in the same cohort of BA.1 infected individuals in a previous study 21 . As we previously reported 21 and confirmed here, BA.1 elicits relatively weak neutralization in the absence of vaccination, consistent with reports showing that Omicron has reduced immunogenicity [24][25][26] . Even with BA.1 breakthrough infection, the FRNT 50 against ancestral virus was about half of that measured in a group composed mostly (Table S1) of people with ancestral infection and vaccination hybrid immunity (Fig.…”

Section: Resultssupporting

confidence: 93%

Omicron BA.4/BA.5 escape neutralizing immunity elicited by BA.1 infection

et al. 2022

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SARS-CoV-2 Omicron (B.1.1.529) BA.4 and BA.5 sub-lineages, first detected in South Africa, have changes relative to Omicron BA.1 including substitutions in the spike receptor binding domain. Here we isolated live BA.4 and BA.5 viruses and measured BA.4/BA.5 neutralization elicited by BA.1 infection either in the absence or presence of previous vaccination as well as from vaccination without BA.1 infection. In BA.1-infected unvaccinated individuals, neutralization relative to BA.1 declines 7.6-fold for BA.4 and 7.5-fold for BA.5. In vaccinated individuals with subsequent BA.1 infection, neutralization relative to BA.1 decreases 3.2-fold for BA.4 and 2.6-fold for BA.5. The fold-drop versus ancestral virus neutralization in this group is 4.0-fold for BA.1, 12.9-fold for BA.4, and 10.3-fold for BA.5. In contrast, BA.4/BA.5 escape is similar to BA.1 in the absence of BA.1 elicited immunity: fold-drop relative to ancestral virus neutralization is 19.8-fold for BA.1, 19.6-fold for BA.4, and 20.9-fold for BA.5. These results show considerable escape of BA.4/BA.5 from BA.1 elicited immunity which is moderated with vaccination and may indicate that BA.4/BA.5 may have the strongest selective advantage in evading neutralization relative to BA.1 in unvaccinated, BA.1 infected individuals.

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Section: Resultssupporting

confidence: 93%

Omicron BA.4/BA.5 escape neutralizing immunity elicited by BA.1 infection

et al. 2022

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“…In this section, we use additional twelve datasets to cross-validate the genes identified in Section 3 . These datasets include GSE152641 [ 35 ], GSE155454 [ 36 ], GSE163151 [ 37 ], GSE166190 [ 38 ], GSE166253 [ 39 ], GSE166530 [ 40 ], GSE177477 [ 41 ], GSE179448 [ 42 ], GSE184401 [ 43 ], GSE189039 [ 44 , 45 ], GSE190680 [ 46 ], and GSE201530 [ 45 , 47 ].…”

Section: Genomic Differences Between Np/op Pcr Swab Samples and Whole...mentioning

confidence: 99%

Genomic Biomarker Heterogeneities between SARS-CoV-2 and COVID-19

Zhang

2022

Vaccines

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Genes functionally associated with SARS-CoV-2 infection and genes functionally related to the COVID-19 disease can be different, whose distinction will become the first essential step for successfully fighting against the COVID-19 pandemic. Unfortunately, this first step has not been completed in all biological and medical research. Using a newly developed max-competing logistic classifier, two genes, ATP6V1B2 and IFI27, stand out to be critical in the transcriptional response to SARS-CoV-2 infection with differential expressions derived from NP/OP swab PCR. This finding is evidenced by combining these two genes with another gene in predicting disease status to achieve better-indicating accuracy than existing classifiers with the same number of genes. In addition, combining these two genes with three other genes to form a five-gene classifier outperforms existing classifiers with ten or more genes. These two genes can be critical in fighting against the COVID-19 pandemic as a new focus and direction with their exceptional predicting accuracy. Comparing the functional effects of these genes with a five-gene classifier with 100% accuracy identified and tested from blood samples in our earlier work, the genes and their transcriptional response and functional effects on SARS-CoV-2 infection, and the genes and their functional signature patterns on COVID-19 antibodies, are significantly different. We will use a total of fourteen cohort studies (including breakthrough infections and omicron variants) with 1481 samples to justify our results. Such significant findings can help explore the causal and pathological links between SARS-CoV-2 infection and the COVID-19 disease, and fight against the disease with more targeted genes, vaccines, antiviral drugs, and therapies.

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“…As the pandemic is now dominated by Omicron variants, especially BA.5, linking the genes identified earlier for other variants to Omicron variants will provide better genomic knowledge of COVID-19 diseases. We found the genes identified from GSE157103 and GSE152418 again led to 100% accuracy with a SARS-CoV-2 Omicron variant BA.1 cohort study GSE201530 37 . The following new Table 3 reports the outcomes.…”

Section: The Data and Our Earlier Resultsmentioning

confidence: 82%

Genomic Benefits and Potential Harms of COVID-19 Vaccines Indicated from High-Performance Genomic Biomarkers

Zhang

2022

Preprint

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COVID-19 vaccines can be the tugboats of preventing SARS-CoV-2 infections when they are practical and, more importantly, without adverse effects. However, the reality is that they may result in short-term or long-term impacts on COVID-19-related diseases and even trigger the formation of new variants of SARS-CoV-2. Using published data, we use a set of high-performance COVID-19 genomic biomarkers (MND1, CDC6, ZNF282) to study the benefits and adverse effects of the BNT162b2 vaccine. We found that the vaccine lowered expression values of genes MND1 and CDC6 while heightening the expression values of ZNF282 of individuals with SARS-CoV-2-naive, which is expected and satisfies the biological equivalence between the COVID-19 disease and the genomic signature patterns established in the literature. However, we also found that the vaccine adversely affected COVID-19 convalescent octogenarians. It heightened the expression values of MND1 and CDC6. In addition, it lowered the expression values of ZNF282. Such adverse effects raise outstanding concerns about whether or not COVID-19 convalescent individuals should take the current vaccine or when they can take it. These findings are new at the genomic level and can provide insights into developing the next-generation vaccines, antiviral drugs, and pandemic management guidance.

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Prior Vaccination Exceeds Prior Infection in Eliciting Innate and Humoral Immune Responses in Omicron Infected Outpatients

Cited by 26 publications

References 44 publications

Omicron BA.4/BA.5 escape neutralizing immunity elicited by BA.1 infection

Omicron BA.4/BA.5 escape neutralizing immunity elicited by BA.1 infection

Genomic Biomarker Heterogeneities between SARS-CoV-2 and COVID-19

Genomic Benefits and Potential Harms of COVID-19 Vaccines Indicated from High-Performance Genomic Biomarkers

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