Genomic profile of SARS-CoV-2 Omicron variant and its correlation with disease severity in Rajasthan

Comparative transcriptome analysis of SARS-CoV-2, SARS-CoV, MERS-CoV, and HCoV-229E identifying potential IFN/ISGs targets for inhibiting virus replication

Introduction

Since its outbreak in December 2019, SARS-CoV-2 has spread rapidly across the world, posing significant threats and challenges to global public health. SARS-CoV-2, together with SARS-CoV and MERS-CoV, is a highly pathogenic coronavirus that contributes to fatal pneumonia. Understanding the similarities and differences at the transcriptome level between SARS-CoV-2, SARS-CoV, as well as MERS-CoV is critical for developing effective strategies against these viruses.

Methods

In this article, we comparatively analyzed publicly available transcriptome data of human cell lines infected with highly pathogenic SARS-CoV-2, SARS-CoV, MERS-CoV, and lowly pathogenic HCoV-229E. The host gene expression profiles during human coronavirus (HCoV) infections were generated, and the pathways and biological functions involved in immune responses, antiviral efficacy, and organ damage were intensively elucidated.

Results

Our results indicated that SARS-CoV-2 induced a stronger immune response versus the other two highly pathogenic HCoVs. Specifically, SARS-CoV-2 induced robust type I and type III IFN responses, marked by higher upregulation of type I and type III IFNs, as well as numerous interferon-stimulated genes (ISGs). Further Ingenuity Pathway Analysis (IPA) revealed the important role of ISGs for impeding SARS-CoV-2 infection, and the interferon/ISGs could be potential targets for therapeutic interventions. Moreover, our results uncovered that SARS-CoV-2 infection was linked to an enhanced risk of multi-organ toxicity in contrast to the other two highly pathogenic HCoVs.

Discussion

These findings provided valuable insights into the pathogenic mechanism of SARS-CoV-2, which showed a similar pathological feature but a lower fatality rate compared to SARS-CoV and MERS-CoV.

Comparative Evaluation of the Clinical Severity of COVID-19 of Vaccinated and Unvaccinated Patients in Southeastern Romania in the First 6 Months of 2022, during the Omicron Wave

(1) Background: The pandemic wave produced by SARS-CoV-2 Omicron was characterized by milder clinical forms and high contagiousness. The vaccination rate against COVID-19 in Romania was approximately 42%. (2) Objectives: Comparison of the clinical severity in vaccinated patients compared to unvaccinated ones. (3) Methods: A retrospective cohort study was conducted on a group of 699 adult patients confirmed with COVID-19 who presented in the "Sf. Cuvioasa Parascheva" Infectious Diseases Clinical Hospital of Galati, Romania, between 1 January 2022 and 30 June 2022. The study compared the need for hospitalization, reinfections, demographic and comorbidity data, clinical and paraclinical parameters from the initial evaluation, and the ratio of unfavorable developments on subgroups chosen according to the vaccination status. (4) Results and Conclusions: Our study reveals that unvaccinated patients required hospitalization in 54.68% of cases, while fully vaccinated patients had a hospitalization rate of 40.72%, which was significantly lower than that of the unvaccinated group (p = 0.01); patients who received a booster dose had a hospitalization rate of 27.84% (p < 0.01, significantly lower than unvaccinated individuals; p = 0.01, significantly lower than fully vaccinated individuals); and among the four patients who received four doses, none required hospitalization. From the analysis of the two subgroups of hospitalized patients, we observed a significantly higher prevalence of radiological lesions, such as pulmonary opacities in the group of unvaccinated patients and a higher average duration of hospitalization, and serum values of D-dimers and blood-sugar at admission were significantly higher in unvaccinated patients. The higher presence of these parameters, which are indicators of severe progression in clinical studies, in the group of unvaccinated patients suggests the need to include them in the initial evaluation of the unvaccinated patients with COVID-19.The cumulative share of deaths and transfers in the ICU was higher in the group of unvaccinated patients, but the difference between the groups had no statistical significance. This study draws attention to the possibility of severe clinical forms among both vaccinated and unvaccinated populations, especially in the elderly and in patients with multiple comorbidities.

Role of previous infection with SARS-CoV-2 in protecting against omicron reinfections and severe complications of COVID-19 compared to pre-omicron variants: a systematic review

BACKGROUND

The SARS-CoV-2 virus elicited a major public concern worldwide since December 2019 due to the high number of infections and deaths caused by COVID-19. The Omicron variant was detected in October 2021 which evolved from the wild-type SARS-CoV-2 and was found to possess many mutations. Omicron exhibited high transmissibility and immune evasion as well as reduced severity when compared to the earlier variants. Although vaccinated individuals were largely protected against infections in previous waves, the high prevalence of both reinfections and breakthrough infections with Omicron was observed. The aim of this review is to understand the effectiveness of previous infection on subsequent reinfection, given its significance in driving public health policy, including vaccination prioritization and lockdown requirements.

METHODS

A comprehensive literature search was conducted using several databases to target studies reporting data related to the effectiveness of the previous infection with SARS-CoV-2 in protecting against the Omicron variant. Screening of the studies, quality assessment and data extraction were conducted by two reviewers for each study.

RESULTS

Only 27 studies met our inclusion criteria. It was observed that previous infection was less effective in preventing reinfections with the Omicron variant compared to the Delta variant irrespective of vaccination status. Furthermore, being fully vaccinated with a booster dose provided additional protection from the Omicron variant. Additionally, most infections caused by Omicron were asymptomatic or mild and rarely resulted in hospitalizations or death in comparison to the Delta wave.

CONCLUSION

A majority of the studies reached a consensus that although previous infection provides some degree of immunity against Omicron reinfection, it is much lower in comparison to Delta. Full vaccination with two doses was more protective against Delta than Omicron. Receiving a booster dose provided additional protection against Omicron. It is therefore clear that neither vaccination nor previous infection alone provide optimal protection; hybrid immunity has shown the best results in terms of protecting against either Omicron or Delta variants. However, additional research is needed to quantify how long immunity from vaccination versus previous infection lasts and whether individuals will benefit from variant-specific vaccinations to enhance protection from infection.

Prevalence of Olfactory Dysfunction with the Omicron Variant of SARS-CoV-2: A Systematic Review and Meta-analysis

The omicron variant is thought to cause less olfactory dysfunction than previous variants of SARS-CoV-2, but the reported prevalence differs greatly between populations and studies. Our systematic review and meta-analysis provide information about regional differences in prevalence as well as an estimate of the global prevalence of olfactory dysfunction based on 62 studies reporting on 626,035 patients infected with the omicron variant. Our estimate of the omicron-induced prevalence of olfactory dysfunction in populations of European ancestry is 11.7%, while it is significantly lower in all other populations, ranging between 1.9% and 4.9%. When ethnic differences and population sizes are taken into account, the global prevalence of omicron-induced olfactory dysfunction in adults is estimated at 3.7%. Omicron’s effect on olfaction is twofold to tenfold lower than that of the alpha or delta variant, according to previous meta-analyses and our analysis of studies that directly compared prevalence of olfactory dysfunction between omicron and previous variants. The profile of prevalence differences between ethnicities mirrors the results of a recent genome-wide association study that implicated a gene locus encoding an odorant-metabolizing enzyme, UDP glycosyltransferase, to be linked to the extent of COVID-related loss of smell. Our analysis is consistent with the hypothesis that this enzyme contributes to the observed population differences.