Comparison of Omicron and Delta Variants of SARS-CoV-2: A Systematic Review of Current Evidence

INTRODUCTION

Severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) caused the outbreak of coronavirus disease 2019 (COVID-19) in late 2019 in Wuhan, China. In early 2020, the disease spread rapidly around the world. Since the pandemic, SARS-CoV-2 has evolved dramatically into a wide variety of variants endowed with devastating properties. As of March 6, 2022, five SARS-CoV-2 variants of concern, including Alpha, Beta, Gamma, Delta, and Omicron strains have been identified. Due to the crucial importance of understanding the differences between the Omicron and Delta variants, this systematic review was conducted.

METHODS

This systematic review investigated new variants of Omicron SARS-CoV-2 based on cur-rent studies. Online databases were searched for English articles as of January 03, 2023. Selection of publications was a two-step process of title/abstract and full-text assessment against eligibility crite-ria. The relevant data from the included articles were systematically collected and organized in a designed table for analysis. To ensure the quality of the review, the PRISMA checklist and Newcas-tle-Ottawa Scale (NOS) of quality assessment were utilized.

RESULTS

The data extracted from 58 articles were analyzed, including 10003 pieces of evidence. Lower risk of hospitalization, ICU admission, and mortality after vaccination were reported in the Omicron variant compared to the Delta variant. Additionally, the Delta variant led to more severe clinical symptoms in comparison to the Omicron variant.

CONCLUSION

The Omicron variant of SARS-CoV-2 results in less severe disease outcomes as com-pared to Delta. Nevertheless, it remains crucial to maintain ongoing monitoring, implement contain-ment measures, and adapt vaccination protocols to effectively address the evolving variants.

Characteristics of Critically Ill COVID-19 Patients in Busan, Republic of Korea

BACKGROUND

This study aimed to improve the clinical course of patients through rapid response by analyzing the characteristics of critically ill patients with confirmed coronavirus disease 2019 (COVID-19) in Busan between December 1, 2020, and December 31, 2021.

METHODS

We divided patients diagnosed with COVID-19 into mild-to-moderate and critical groups based on their clinical severity. The critically ill patients were further sub-divided into delta and delta variant non-epidemic group.

RESULTS

The following factors were significantly more frequent in critically ill patients than in patients with mild-tomoderate symptoms: male sex, age ≥60 years, symptoms at the time of diagnosis, and those with underlying diseases. The following factors were significantly more common in the non-delta variant epidemic group than in the delta variant epidemic group in critically ill patients: male sex, age ≥60 years, underlying diseases, and not being vaccinated. In the delta variant epidemic group, the duration between confirmation of disease and its progression to critically ill status was significantly shorter than that in the non-delta variant epidemic group.

CONCLUSION

COVID-19 is characterized by the emergence of new variants and repeated epidemics. Therefore, it is necessary to analyze the characteristics of critically ill patients to efficiently distribute and manage medical resources.

Recombinant Protein Micelles to Block Transduction by SARS-CoV-2 Pseudovirus

The continuing emergence of variants of the SARS-CoV-2 virus requires the development of modular molecular therapies. Here, we engineered a recombinant amphiphilic protein, oleosin, to spontaneously self-assemble into multivalent micellar nanostructures which can block the Spike S1 protein of SARS-CoV-2 pseudoviruses (PVs). Short recombinant proteins like oleosin can be formulated more easily than antibodies and can be functionalized with precision through genetic engineering. We cloned S1-binding mini-protein genes called LCBx, previously designed by David Baker's laboratory (UW Seattle), to the N-terminus of oleosin, expressing Oleo-LCBx proteins in E. coli. These proteins largely formed 10-100 nm micelles as verified by dynamic light scattering. Two proteins, Oleo-LCB1 and Oleo-LCB3, were seen to completely and irreversibly block transduction by both wild-type and delta variant PVs into 293T-hsACE2 cells at 10 μM. Presented in multivalent micelles, these proteins reduced transduction by PVs down to a functional protein concentration of 5 nM. Additionally, Oleo-LCB1 micelles outperformed corresponding synthetic LCB1 mini-proteins in reducing transduction by PVs. Tunable aqueous solubility of recombinant oleosin allowed incorporation of peptides/mini-proteins at high concentrations within micelles, thus enhancing drug loading. To validate the potential multifunctionality of the micelles, we showed that certain combinations of Oleo-LCB1 and Oleo-LCB3 performed much better than the individual proteins at the same concentration. These micelles, which we showed to be non-toxic to human cells, are thus a promising step toward the design of modular, multifunctional therapeutics that could bind to and inactivate multiple receptors and proteins necessary for the infection of the SARS-CoV-2 virus.

Does the "Delta Variant" affect the nonlinear dynamic characteristics of SARS-CoV-2 transmission?

In this paper, we analyzed the difference of nonlinear dynamic characteristics of SARS-CoV-2 transmission caused by 'Delta Variant'. We selected the daily new diagnostic data of SARS-CoV-2 from 15 countries. Four different kinds of complexity metrics such as Kolmogorov complexity, Higuchi's Hurst exponent, Shannon entropy, and multifractal degrees were selected to explore the features of information content, persistence, randomness, multifractal complexity. Afterwards, Student's t-tests were performed to assess the presence of differences of these nonlinear dynamic characteristics for periods before and after "Delta Variant" appearance. The results of two-tailed Student's t-test showed that for all the nonlinear dynamic characteristics, the null hypothesis of equality of mean values were strongly rejected for the two periods. In addition, by one-tailed Student's t-test, we concluded that time series in "Delta period" exhibit higher value of Kolmogorov complexity and Shannon entropy, indicating a higher level of information content and randomness. On the other hand, the Higuchi's Hurst exponent in "Delta period" was lower, which showed the weaker persistent in this period. Moreover, the multifractal specturm width after "Delta" emergence were reduced, representing a more stable multifractality. The sources for the formation of multifractal features are also investigated.

Clinical Manifestations of COVID-19 Breakthrough Infections: A Systematic Review and Meta-Analysis

To provide a comparative meta‐analysis and systematic review of the risk and clinical outcomes of coronavirus 2019 (COVID‐19) infection between fully vaccinated and unvaccinated groups. Eighteen studies of COVID‐19 infections in fully vaccinated (“breakthrough infections”) and unvaccinated individuals were reviewed from Medline/PubMed, Scopus, Embase, and Web of Science databases. The meta‐analysis examined the summary effects and between‐study heterogeneity regarding differences in the risk of infection, hospitalization, treatments, and mortality between vaccinated and unvaccinated individuals. he overall risk of infection was lower for the fully vaccinated compared to that of the unvaccinated (relative risk [RR] 0.20, 95% confidence interval [CI]: 0.19−0.21), especially for variants other than Delta (Delta: RR 0.29, 95% CI: 0.13−0.65; other variants: RR 0.06, 95% CI: 0.04−0.08). The risk of asymptomatic infection was not statistically significantly different between fully vaccinated and unvaccinated (RR 0.56, 95% CI: 0.27−1.19). There were neither statistically significant differences in risk of hospitalization (RR 1.06, 95% CI: 0.38−2.93), invasive mechanical ventilation (RR 1.65, 95% CI: 0.90−3.06), or mortality (RR 1.19, 95% CI: 0.79−1.78). Conversely, the risk of supplemental oxygen during hospitalization was significantly higher for the unvaccinated (RR 1.40, 95% CI: 1.08−1.82). Unvaccinated people were more vulnerable to COVID‐19 infection than fully vaccinated for all variants. Once infected, there were no statistically significant differences in the risk of hospitalization, invasive mechanical ventilation, or mortality. Still, unvaccinated showed an increased need for oxygen supplementation. Further prospective analysis, including patients’ risk factors, COVID‐19 variants, and the utilized treatment strategies, would be warranted.

Cardiac involvement in patients recovering from Delta Variant of COVID-19: a prospective multi-parametric MRI study

AIMS

The cardiac injury and sequelae of Delta Variant of coronavirus disease 2019 (COVID-19) remain unknown. This study aimed to evaluate the presence of cardiac involvement in patients recovering from Delta Variant of COVID-19 based on multi-parametric cardiac magnetic resonance imaging (MRI).

METHODS AND RESULTS

We prospectively assessed patients recovering from Delta Variant of COVID-19 using multi-parametric cardiac magnetic resonance imaging (MRI) between June 2021 and July 2021. Comparison was made with 25 healthy controls. Forty-four patients (median age 51 years, 28 women) recovering from Delta Variant were recruited and had a median time of 35 days between diagnosis and cardiac MRI. There were no patients with chest pain (0/44, 0%) and high sensitivity cardiac troponin T troponin elevation (median levels 2.20 pg/mL, IQR levels 0.85-4.40 pg/mL). Regarding the cardiac imaging findings, a total of 14 (32%) patients presented cardiac tissue feature abnormalities, and a total of 9 (20%) patients had a myocarditis-like injury based on cardiac MRI 2018 Lake Louise criteria. When we further assessed the T1 and T2 mapping values for of patients' individual, abnormal raised global native T1, T2, and extracellular volume were seen in 6 (14%), 6 (14%), and 4 (9%) patients, respectively. Comparing with controls, the patients had lower LV global longitudinal strain and (-22.2 ± 2.8% vs. -24.6 ± 2.0%, P < 0.001) and global circumferential strain (-20.7 ± 6.8% vs. -24.3 ± 2.9%, P = 0.014), but higher global native T1 (1318.8 ± 55.5 ms vs. 1282.9 ± 38.1 ms, P = 0.006). Four (9%) patients presented myocardial late gadolinium enhancement with subepicardial pattern mostly common seen, and two (5%) patients presented pericardial enhancement.

CONCLUSIONS

The cardiac MRI could detect subclinical functional and myocardial tissue characteristic abnormalities in individuals who were recovering from Delta Variant without cardiac-related clinical findings. The native T1 mapping and strain imaging may be a sensitive tool for the noninvasive detection of a subset of patients who are at risk for cardiac sequelae and more prone to myocardial damage in survivors with Delta Variant.

Impact of SARS-CoV-2 Vaccination and Paediatric Age on Delta Variant Household Transmission

Background

The impact of SARS-CoV-2 vaccination status and paediatric age on transmission of the Delta variant is key to preventing COVID-19 spread. In Singapore, quarantine of all close-contacts, and quarantine-entry and exit PCR testing, enabled evaluation of these factors.

Methods

This retrospective cohort study included all household close-contacts between March 1, 2021 and August 31, 2021. Logistic regression using generalized estimating equations was used to determine risk factors associated with SARS-CoV-2 acquisition and symptomatic disease.

Findings

Among 8470 Delta variant-exposed household close-contacts linked to 2583 indices, full-vaccination of the index with BNT162b2 or mRNA-1273 was associated with significant reduction in SARS-CoV-2 acquisition by contacts (adjusted odds ratio [aOR]:0.56, 95% robust confidence interval [RCI]:0.44–0.71 and aOR:0.51, 95%RCI:0.27–0.96 respectively).

Compared to young adults (18–29y), children (0–11y) were significantly more likely to transmit (aOR:2.37 [95%RCI:1.57–3.60]) and acquire (aOR:1.43 [95%RCI:1.07–1.93]) infection, taking into account vaccination status.

Longer duration from completion of vaccination among contacts was associated with decline in protection against acquisition (first-month aOR:0.42, 95%RCI:0.33–0.55; fifth-month aOR:0.84, 95%RCI:0.55–0.98; p<0.0001 for trend) and symptomatic disease (first-month aOR:0.30, 95%RCI:0.23–0.41; fifth-month aOR;0.62, 95%RCI:0.38–1.02; p<0.0001 for trend). Contacts immunized with mRNA-1273 had significant reduction in acquisition (aOR:0.73, 95%RCI:0.58–0.91) compared to BNT162b2.

Conclusions

Among household close-contacts, vaccination prevented onward SARS-CoV-2 transmission and there was increased risk of SARS-CoV-2 acquisition and transmission among children compared with young adults. Time after completion of vaccination and vaccine type affected SARS-CoV-2 acquisition.

Kinetics of Neutralizing Antibody Responses Against SARS-CoV-2 Delta Variant in Patients Infected at the Beginning of the Pandemic

We investigated the kinetics of the neutralizing antibody responses to the severe acute respiratory syndrome-coronavirus-2 delta variant over the course of 1 year in 16 patients infected at the beginning of the pandemic. In patients with severe disease, neutralizing responses to the delta variant were detectable, albeit at lower levels than responses to the wild type. Neutralizing responses to the delta variant were undetectable, however, in asymptomatic persons. This finding implies that the vaccination strategy for persons with past natural infection should depend on the severity of the previous infection.

Analyses of Confirmed COVID-19 Cases Among Korean Military Personnel After Mass Vaccination

BACKGROUND

The military was one of the first groups in Korea to complete mass vaccination against the coronavirus disease 2019 (COVID-19) due to their high vulnerability to COVID-19. To confirm the effect of mass vaccination, this study analyzed the patterns of confirmed cases within Korean military units.

METHODS

From August 1 to September 15, 2021, all epidemiological data regarding confirmed COVID-19 cases in military units were reviewed. The number of confirmed cases in the units that were believed to have achieved herd immunity (i.e., ≥ 70% vaccination) was compared with the number of cases in the units that were not believed to have reached herd immunity (< 70% vaccination). Additionally, trends in the incidence rates of COVID-19 in the military and the entire Korean population were compared.

RESULTS

By August 2021, 85.60% of military personnel were fully vaccinated. During the study period, a total of 174 COVID-19 cases were confirmed in the 39 units. More local transmission (herd immunity group vs. non-herd immunity group [%], 1 [0.91] vs. 39 [60.94]) and hospitalizations (12 [11.01] vs. 13 [27.08]) occurred in the units that were not believed to have achieved herd immunity. The percentage of fully vaccinated individuals among the confirmed COVID-19 cases increased over time, possibly due to the prevalence of the delta variant. Nevertheless, the incidence rate remained lower in military units than in the general Korean population.

CONCLUSION

After completing mass vaccination, the incidence rates of COVID-19 infection in the military were lower than those in the national population. New cluster infections did not occur in vaccinated units, thereby suggesting that herd immunity has been achieved in these military units. Further research is needed to determine the extent to which levels of non-pharmacological intervention can be reduced in the future.

Image challenge: A diabetic man with facial swelling following recent Covid-19 infection

A 68-year-old man with diabetes presented with shortness of breath, left sided facial swelling, and nasal discharge. He had recently returned from India and PCR was positive for SARS-CoV-2 Delta variant. CT head and diffusion-weighted MRI sinuses were performed and the patient underwent endoscopic sinus surgery before being transferred to a specialist skull base centre.

Epistasis at the SARS-CoV-2 RBD Interface and the Propitiously Boring Implications for Vaccine Escape

At the time of this writing, December 2021, potential emergence of vaccine escape variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a grave global concern. The interface between the receptor-binding domain (RBD) of SARS-CoV-2 spike (S) protein and the host receptor (ACE2) overlap with the binding site of principal neutralizing antibodies (NAb), limiting the repertoire of viable mutations. Nonetheless, variants with multiple mutations in the RBD have rose to dominance. Non-additive, epistatic relationships among RBD mutations are apparent, and assessing the impact of such epistasis on the mutational landscape is crucial. Epistasis can substantially increase the risk of vaccine escape and cannot be completely characterized through the study of the wild type (WT) alone. We employed protein structure modeling using Rosetta to compare the effects of all single mutants at the RBD-NAb and RBD-ACE2 interfaces for the WT, Delta, Gamma, and Omicron variants. Overall, epistasis at the RBD interface appears to be limited and the effects of most multiple mutations are additive. Epistasis at the Delta variant interface weakly stabilizes NAb interaction relative to ACE2 interaction, whereas in the Gamma variant, epistasis more substantially destabilizes NAb interaction. Although a small, systematic trend towards NAb destabilization not observed for Delta or Gamma was detected for Omicron, and despite bearing significantly more RBD mutations, the epistatic landscape of the Omicron variant closely resembles that of Gamma. These results suggest that, although Omicron poses new risks not observed with Delta, structural constraints on the RBD hamper continued evolution towards more complete vaccine escape. The modest ensemble of mutations relative to the WT that are currently known to reduce vaccine efficacy is likely to comprise the majority of all possible escape mutations for future variants, predicting continued efficacy of the existing vaccines.

Clinical Features of Adult COVID-19 Patients without Risk Factors before and after the Nationwide SARS-CoV-2 B.1.617.2 (Delta)-variant Outbreak in Korea: Experience from Gyeongsangnam-do

BACKGROUND

Data on severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) delta variant virulence are insufficient. We retrospectively compared the clinical features of adult coronavirus disease 2019 (COVID-19) patients without risk factors for severe COVID-19 who entered residential treatment centers (RTCs) before and after the delta variant outbreak.

METHODS

We collected medical information from two RTCs in South Korea. On the basis of nationwide delta variant surveillance, we divided the patients into two groups: 1) the delta-minor group (diagnosed from December 2020-June 2021, detection rate < 10%) and 2) the delta-dominant group (diagnosed during August 2021, detection rate > 90%). After propensity-score matching, the incidences of pneumonia, hospital transfer and need for supplemental oxygen were compared between the groups. In addition, risk factors for hospital transfer were analysed.

RESULTS

A total of 1,915 patients were included. The incidence of pneumonia (14.6% vs. 9.2%, P = 0.009), all-cause hospital transfer (10.4% vs. 6.3%, P = 0.020) and COVID-19-related hospital transfer (7.5% vs. 4.8%, P = 0.081) were higher in the delta-dominant group than those in the delta-minor group. In the multivariate analysis, the delta-dominant group was an independent risk factor for all-cause (adjusted odds ratio [aOR], 1.91; 95% confidence interval [CI], 1.16-3.13; P = 0.011) and COVID-19-related hospital transfer (aOR, 1.86; 95% CI, 1.04-3.32; P = 0.036).

CONCLUSION

Hospitalization rates were increased in the adult COVID-19 patients during the delta variant nationwide outbreak. Our results showed that the delta variant may be more virulent than previous lineages.

COVID-19 Incidence and Hospitalization During the Delta Surge Were Inversely Related to Vaccination Coverage Among the Most Populous U.S. Counties

Objective

We tested whether COVID-19 incidence and hospitalization rates during the Delta surge were inversely related to vaccination coverage among the 112 most populous counties in the United States, comprising 44 percent of the country's total population.

Methods

We measured vaccination coverage as the percent of the county population fully vaccinated as of July 15, 2021. We measured COVID-19 incidence as the number of confirmed cases per 100,000 population during the 14-day period ending August 12, 2021 and hospitalization rates as the number of confirmed COVID-19 admissions per 100,000 population during the same 14-day period.

Results

In log-linear regression models, a 10-percentage-point increase in vaccination coverage was associated with a 28.3% decrease in COVID-19 incidence (95% confidence interval, 16.8 - 39.7%), a 44.9 percent decrease in the rate of COVID-19 hospitalization (95% CI, 28.8 - 61.0%), and a 16.6% decrease in COVID-19 hospitalizations per 100 cases (95% CI, 8.4 - 24.8%). Inclusion of demographic covariables, as well as county-specific diabetes prevalence, did not weaken the observed inverse relationship with vaccination coverage. A significant inverse relationship between vaccination coverage and COVID-19 deaths per 100,000 during August 20 – September 16 was also observed. The cumulative incidence of COVID-19 through June 30, 2021, a potential indicator of acquired immunity due to past infection, had no significant relation to subsequent case incidence or hospitalization rates in August.

Conclusion

Higher vaccination coverage was associated not only with significantly lower COVID-19 incidence during the Delta surge, but also significantly less severe cases of the disease.

Public Interest Summary

We tested whether COVID-19 incidence and hospitalization rates during the Delta variant-related surge were inversely related to vaccination coverage among the 112 most populous counties in the United States, together comprising 44 percent of the country's total population. A 10-percentage-point increase in vaccination coverage was associated with a 28.3% decrease in COVID-19 incidence, a 44.9 percent decrease in the rate of COVID-19 hospitalization, and a 16.6% decrease in COVID-19 hospitalizations per 100 cases. Inclusion of demographic covariables, as well as county-specific diabetes prevalence, did not weaken the observed inverse relationship with vaccination coverage. A significant inverse relationship between vaccination coverage and COVID-19 deaths per 100,000 during August 20 – September 16 was also observed. Higher vaccination coverage was associated not only with significantly lower COVID-19 incidence during the Delta surge, but also significantly less severe cases of the disease.