Omicron breakthrough infections in wild-type SARS-CoV-2 vaccinees elicit high levels of neutralizing antibodies against pangolin coronavirus GX_P2V

BIC/FTC/TAF Benefits People Living With HIV After Omicron Breakthrough Infection in Shortening Duration of Symptoms, Enhancing Specific Immune Response and Increasing Total CD4 Cells

The clinical manifestations of variability in PLWH with SARS-CoV-2 acquired may be attributed to the use of ART drugs. Omicron breakthrough infection and reinfection in 27 PLWH treated with BIC/FTC/TAF and 51 PLWH treated with TDF/3TC/EFV were investigated, and humoral and cellular immunity after Omicron breakthrough infection were also compared. The results showed that Omicron breakthrough infection symptoms in BIC/FTC/TAF-treated had a shorter duration, and BIC/FTC/TAF could further reduce the duration of symptoms when re-infected. It was also found that the BA.5 specific IgG titers of BIC/FTC/TAF-treated were significantly increased and increased with the extension of the duration of BIC/FTC/TAF. In cellular immunity, the use of BIC/FTC/TAF was also found to increase not only BA.5-specific B lymphocytes and BA.5-specific CD4+T lymphocytes, but also total CD4+T cells. In conclusion, compared to TDF/3TC/EFV, BIC/FTC/TAF can help PLWH shorten the duration of COVID-19 symptoms, enhance SARS-CoV-2 specific humoral and cellular immune responses, help to expand the total CD4+T cells increase in PLWH after Omicron infection and may be more beneficial for PLWH with high risk of infection in the context of COVID-19 normalization.

A Comparative Experimental and Computational Study on the Nature of the Pangolin-CoV and COVID-19 Omicron

The relationship between pangolin-CoV and SARS-CoV-2 has been a subject of debate. Further evidence of a special relationship between the two viruses can be found by the fact that all known COVID-19 viruses have an abnormally hard outer shell (low M disorder, i.e., low content of intrinsically disordered residues in the membrane (M) protein) that so far has been found in CoVs associated with burrowing animals, such as rabbits and pangolins, in which transmission involves virus remaining in buried feces for a long time. While a hard outer shell is necessary for viral survival, a harder inner shell could also help. For this reason, the N disorder range of pangolin-CoVs, not bat-CoVs, more closely matches that of SARS-CoV-2, especially when Omicron is included. The low N disorder (i.e., low content of intrinsically disordered residues in the nucleocapsid (N) protein), first observed in pangolin-CoV-2017 and later in Omicron, is associated with attenuation according to the Shell-Disorder Model. Our experimental study revealed that pangolin-CoV-2017 and SARS-CoV-2 Omicron (XBB.1.16 subvariant) show similar attenuations with respect to viral growth and plaque formation. Subtle differences have been observed that are consistent with disorder-centric computational analysis.

Landscape of T cell epitopes displays hot mutations of SARS-CoV-2 variant spikes evading cellular immunity

The continuous evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been accompanied by the emergence of viral mutations that pose a great challenge to existing vaccine strategies. It is not fully understood with regard to the role of mutations on the SARS-CoV-2 spike protein from emerging viral variants in T cell immunity. In the current study, recombinant eukaryotic plasmids were constructed as DNA vaccines to express the spike protein from multiple SARS-CoV-2 strains. These DNA vaccines were used to immunize BALB/c mice, and cross-T cell responses to the spike protein from these viral strains were quantitated using interferon-γ (IFN-γ) Elispot. Peptides covering the full-length spike protein from different viral strains were used to detect epitope-specific IFN-γ+ CD4+ and CD8+ T cell responses by fluorescence-activated cell sorting. SARS-CoV-2 Delta and Omicron BA.1 strains were found to have broad T cell cross-reactivity, followed by the Beta strain. The landscapes of T cell epitopes on the spike protein demonstrated that at least 30 mutations emerging from Alpha to Omicron BA.5 can mediate the escape of T cell immunity. Omicron and its sublineages have 19 out of these 30 mutations, most of which are new, and a few are inherited from ancient circulating variants of concerns. The cross-T cell immunity between SARS-CoV-2 prototype strain and Omicron strains can be attributed to the T cell epitopes located in the N-terminal domain (181-246 aa [amino acids], 271-318 aa) and C-terminal domain (1171-1273 aa) of the spike protein. These findings provide in vivo evidence for optimizing vaccine manufacturing and immunization strategies for current or future viral variants.

Assessment of vaccinations and breakthrough infections after adjustment of the dynamic zero-COVID-19 strategy in China: an online survey

Coronavirus disease 2019 (COVID-19) cases in China has grown rapidly after adjustment of the dynamic zero-COVID-19 strategy. However, how different vaccination states affect symptoms, severity and post COVID conditions was unclear. Here, we used an online questionnaire to investigate the infection status of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) among 11,897 participants, with 55.55% positive and 28.42% negative. The common COVID-19 symptoms were fatigue (73.31%), cough (70.02%), fever (65.25%) and overall soreness (58.64%); self-reported asymptomatic infection accounted for 0.7% of participants. The persistent symptoms at 1 month after infection included fatigue (48.7%), drowsiness (34.3%), cough (30.1%), decreased exercise ability (23.1%) and pharyngeal discomfort (19.4%), which was reduced by more than 200% at 2 months. Participants with complications such as chronic obstructive pulmonary disease, respiratory diseases, diabetes, hypertension, etc. have a higher proportion of hospitalization and longer recovery time (p < = 0.01). Multiple vaccination statuses reduced the infection (p < 0.001) and severity rates (p = 0.022) by varying degrees as well as reduced the risk of high fever (>39.1 °C), chills, diarrhea and ageusia/anosmia, respectively (p < 0.05). Vaccination may enhance some upper respiratory symptoms, including sore throat, nasal congestion and runny nose, respectively (p < 0.05). Participants who had been vaccinated within 3 months were better protected by helping reduce their risk of overall soreness, chills and ageusia/anosmia, respectively (p < 0.05). In conclusion, our work has updated the epidemic characteristics of the breakthrough infection (BTI) wave after the dynamic zero-COVID-19 strategy, providing data and insights on how different vaccination statuses affect COVID-19 symptoms and disease prognosis.