Emergence of SARS-CoV-2 New Variants and Their Clinical Significance

Political polarization and health

In addition to social determinants of health, such as economic resources, education, access to care and various environmental factors, there is growing evidence that political polarization poses a substantial risk to individual and collective well-being. Here we review the impact of political polarization on public health. We describe the different forms of polarization and how they are connected to health outcomes, highlighting the COVID-19 pandemic as a case study of the health risks of polarization. We then offer strategies for mitigating potential harms associated with polarization, with an emphasis on building social trust. Finally, we propose future research directions on this topic, underscore the need for more work in a global context and encourage greater collaboration between social scientists and medical scientists. We conclude that polarization is a serious-if largely overlooked-determinant of health, whose impacts must be more thoroughly understood and mitigated.

Investigating the FLiRT variants of COVID-19: Is it an emerging concern?

The ongoing COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to multiple waves of infections globally. As the virus continues to evolve, new variants have emerged, some with concerning changes in transmissibility and virulence. Among these variants, the "FLiRT Variants" have recently gained attention due to their potential to alter the dynamics of transmission and disease severity. According to the Infectious Disease Society of America, the nickname 'FLiRT' is based on the technical names for their mutations. The FLiRT variants, particularly KP.2, seem to exhibit heightened transmissibility in comparison to earlier Omicron sub-variants. Additionally, they demonstrate a capacity to evade immunity conferred by prior infection and vaccines, although the full extent of this evasion is still being investigated. In this article, we review the characteristics of the FLiRT variants, including their genetic mutations, epidemiological features, potential impact on public health measures, and implications for vaccine efficacy. We also discuss strategies for surveillance, prevention, and mitigation efforts to control the spread of this variant and mitigate its impact on global health.

Can periodontitis affect the COVID-19 severity, symptoms, hospital stay, and mortality? A case-control study

Background/purpose

Poor oral hygiene and periodontal disease have been identified as potential risk factors for the coronavirus disease 2019 (COVID-19). The present study aimed to determine the association between periodontitis and COVID-19 severity, nature of symptoms, mortality, and hospital stay.

Methods

In total, 163 COVID-19-positive patients (men: 93; women: 70) were categorized into two groups: the control group, consisting of 120 patients with asymptomatic or mild symptoms, and the case group, consisting of 43 patients with moderate-to-severe symptoms. The severity of periodontal disease, oral hygiene status (OHI), pocket depth (PD), bleeding on probing (BOP), number of decayed/missing/filled teeth, mortality, duration of stay in the hospital, oxygen requirement, and nature of COVID-19 symptoms were assessed in both groups. The association between periodontitis and COVID-19 was analyzed with other confounding factors such as age, sex, comorbidities, oral hygiene, and smoking status.

Results

The presence of periodontitis increases the severity of COVID-19 by 3.7 times (p = 0.002). A statistically significant difference was noted for symptoms such as dizziness (p = 0.036), running nose/cold (p = 0.009), and headache (p = 0.005) in the presence of periodontitis. The risk estimate for death associated with periodontitis was 1.03. Additionally, the average duration of stay was longer for individuals with periodontitis than for those in the control group.

Conclusion

There is a positive association between periodontal disease and COVID-19. Periodontitis increases the severity of COVID-19 and alters the symptoms. Hence, periodontal disease management should be an integral part of managing patients with coronavirus infection.

An ISG15-Based High-Throughput Screening Assay for Identification and Characterization of SARS-CoV-2 Inhibitors Targeting Papain-like Protease

Emergence of newer variants of SARS-CoV-2 underscores the need for effective antivirals to complement the vaccination program in managing COVID-19. The multi-functional papain-like protease (PLpro) of SARS-CoV-2 is an essential viral protein that not only regulates the viral replication but also modulates the host immune system, making it a promising therapeutic target. To this end, we developed an in vitro interferon stimulating gene 15 (ISG15)-based Förster resonance energy transfer (FRET) assay and screened the National Cancer Institute (NCI) Diversity Set VI compound library, which comprises 1584 small molecules. Subsequently, we assessed the PLpro enzymatic activity in the presence of screened molecules. We identified three potential PLpro inhibitors, namely, NSC338106, 651084, and 679525, with IC50 values in the range from 3.3 to 6.0 µM. These molecules demonstrated in vitro inhibition of the enzyme activity and exhibited antiviral activity against SARS-CoV-2, with EC50 values ranging from 0.4 to 4.6 µM. The molecular docking of all three small molecules to PLpro suggested their specificity towards the enzyme's active site. Overall, our study contributes promising prospects for further developing potential antivirals to combat SARS-CoV-2 infection.

Inhibitory effect of food-functioned phytochemicals on dysregulated inflammatory pathways triggered by SARS-CoV-2: a mechanistic review

Inflammatory cascades of the dysregulated inflammatory pathways in COVID-19 can cause excessive production of pro-inflammatory cytokines and chemokines leading to cytokine storm syndrome (CSS). The molecular cascades involved in the pathways may be targeted for discovery of new anti-inflammatory agents. Many plant extracts have been used clinically in the management of COVID-19, however, their immunosuppressive activities were mainly investigated based on in silico activity. Dietary flavonoids of the extracts such as quercetin, luteolin, kaempferol, naringenin, isorhamnetin, baicalein, wogonin, and rutin were commonly identified as responsible for their inhibitory effects. The present review critically analyzes the anti-inflammatory effects and mechanisms of phytochemicals, including dietary compounds against cytokine storm (CS) and hyperinflammation via inhibition of the altered inflammatory pathways triggered by SARS-CoV-2, published since the emergence of COVID-19 in December 2019. Only a few phytochemicals, mainly dietary compounds such as nanocurcumin, melatonin, quercetin, 6-shagoal, kaempferol, resveratrol, andrographolide, and colchicine have been investigated either in in silico or preliminary clinical studies to evaluate their anti-inflammatory effects against COVID-19. Sufficient pre-clinical studies on safety and efficacy of anti-inflammatory effects of the phytochemicals must be performed prior to proper clinical studies to develop them into therapeutic adjuvants in the prevention and treatmemt of COVID-19 symptoms.

Natural products from Streptomyces spp. as potential inhibitors of the major factors (holoRdRp and nsp13) for SARS-CoV-2 replication: an in silico approach

The COVID-19 pandemic caused unprecedented damage to humanity, and while vaccines have been developed, they are not fully effective against the SARS-CoV-2 virus. Limited targeted drugs, such as Remdesivir and Paxlovid, are available against the virus. Hence, there is an urgent need to explore and develop new drugs to combat COVID-19. This study focuses on exploring microbial natural products from soil-isolated bacteria Streptomyces sp. strain 196 and RI.24 as a potential source of new targeted drugs against SARS-CoV-2. Molecular docking studies were performed on holoRdRp and nsp13, two key factors responsible for virus replication factor. Our in silico studies, K-252-C aglycone indolocarbazole alkaloid (K252C) and daunorubicin were found to have better binding affinities than the respective control drugs, with K252C exhibiting binding energy of - 9.1 kcal/mol with holoRdRp and - 9.2 kcal/mol with nsp13, and daunorubicin showing binding energy at - 8.1 kcal/mol with holoRdRp and - 9.3 kcal/mol with nsp13. ADMET analysis, MD simulation, and MM/GBSA studies indicated that K252C and daunorubicin have the potential to be developed as targeted drugs against SARS-CoV-2. The study concludes that K252C and daunorubicin are potential lead compounds that might suppress the inhibition of SARS-CoV-2 replication among the tested microbial compounds and could be developed as targeted drugs against COVID-19. In the future, further in vitro studies are required to validate these findings.

Role of SARS-COV-2 and ACE2 in the pathophysiology of peripheral vascular diseases

The occurrence of a novel coronavirus known as severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), created a serious challenge worldwide. SARS-CoV-2 has high infectivity, the ability to be transmitted even during the asymptomatic phase, and relatively low virulence, which has resulted in rapid transmission. SARS-CoV-2 can invade epithelial cells, hence, many patients infected with SARS-CoV-2 have suffered from vascular diseases (VDs) in addition to pulmonary manifestations. Accordingly, SARS-CoV-2 may can worsen the clinical condition of the patients with pre-existing VDs. Endothelial cells express angiotensin-converting enzyme 2 (ACE2). ACE2 is a biological enzyme that converts angiotensin (Ang)- 2 to Ang-(1-7). SARS-CoV-2 uses ACE2 as a cell receptor for viral entry. Thus, the SARS-CoV-2 virus promotes downregulation of ACE2, Ang-(1-7), and anti-inflammatory cytokines, as well as, an increase in Ang-2, resulting in pro-inflammatory cytokines. SARS-CoV-2 infection can cause hypertension, and endothelial damage, which can lead to intravascular thrombosis. In this review, we have concentrated on the effect of SARS-CoV-2 in peripheral vascular diseases (PVDs) and ACE2 as an enzyme in Renin-angiotensin aldosterone system (RAAS). A comprehensive search was performed on PubMed, Google Scholar, Scopus, using related keywords. Articles focusing on ("SARS-CoV-2", OR "COVID-19"), AND ("Vascular disease", OR "Peripheral vascular disease", OR interested disease name) with regard to MeSH terms, were selected. According to the studies, it is supposed that vascular diseases may increase susceptibility to severe SARS-CoV-2 infection due to increased thrombotic burden and endothelial dysfunction. Understanding SARS-CoV-2 infection mechanism and vascular system pathogenesis is crucial for effective management and treatment in pre-existing vascular diseases.

Acupressure in the treatment of patients with mild infection of COVID-19 omicron variant: A prospectively observational study

During the coronavirus disease 2019 epidemic, acupressure has been widely used as a complementary treatment for coronavirus disease 2019 in China, but its safety and effectiveness have not been determined until now. This was a prospectively observational study containing 400 cases of mild infection of Omicron who were admitted to Chongming Flower Expo Makeshift Hospital from April 1, 2022 to May 1, 2022. Patients were assigned to receive basic treatment or a combination with acupressure treatment (5 minutes per acupoint, at least twice daily), from admission to discharge. The conversion time of viral RNA assay, the recovery time of symptoms and the clinical cure rate at day 7 were compared in 2 groups. All cases were included in the final analysis. The time to conversion of viral RNA assay (6 vs 7 days, P < .001) and time to symptom recovery (2 vs 4 days, P < .001) were markedly shortened in the acupressure treatment group compared to controls. The time to recovery from individual symptoms of coughing, a sore throat, a fever, fatigue, poor appetite, and insomnia were shorter in the treatment group compared to the control (all P < .05), but there was no statistical difference in reducing the recovery time from headache, muscle ache, anxiety, loss of taste between 2 groups (all P > .05). In addition, acupressure therapy also revealed a higher clinical cure rate at day 7 than basic treatment alone (91% vs 65%, P < .001) and reported no serious adverse events. This study provided evidence for acupressure therapy in treatment of Omicron infection concerning the viral load disappearance and the clinical symptoms improvements. Findings were expected to help guide efforts to position acupressure therapy as a therapeutic option for patients with Omicron variant.

Mutational Analysis of Circulating Omicron SARS-CoV-2 Lineages in the Al-Baha Region of Saudi Arabia

Purpose

Omicron (B.1.1.529) is one of the highly mutated variants of concern of SARS-CoV-2. Lineages of Omicron bear a remarkable degree of mutations leading to enhanced pathogenicity and upward transmission trajectory. Mutating Omicron lineages may trigger a fresh COVID-19 wave at any time in any region. We aimed at the whole-genome sequencing of SARS-CoV-2 to determine variants/subvariants and significant mutations which can foster virus evolution, monitoring of disease spread, and outbreak management.

Methods

We used Illumina-NovaSeq 6000 for SARS-CoV-2 genome sequencing, MEGA 10.2 and nextstrain tools for phylogeny; CD-HIT program (version 4.8.1) and MUSCLE program for clustering and alignment. At the same time, UCSF Chimera was employed for protein visualization.

Results

Predominant Omicron pango lineages in Al-Baha were BA.5.2/B22 (n=4, 57%), and other lineages were BA.2.12/21L (n=1, 14.28%), BV.1/22B (n=1, 14.28%) and BA.5.2.18/22B (n=1, 14.28%). 22B nextstrain clade was predominant, while only one lineage showed 21L. BA.5.2/22B, BA.5.2/22B harbored a maximum of n=24 mutations in the spike region. Twelve crucial RBD mutations: D405N, R408S, K417N, N440K, L452R, S477N, T478K, E484A, F486V, Q498R, N501Y, and Y505H were identified except the lineage BA.5.2/22B in which F486V mutation was not observed. Critical deletions S106 in membrane protein NSP6, E31in nucleocapsid, and L24 in spike region were observed in all the lineages. Furthermore, we identified common mutations of Omicron variants of SARS-CoV-2 in therapeutic hot spot spike region: T19I, D405N, R408S, K417N, N440K, L452R, S477N, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, A653V, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K, D1146D, L452R, F486V, N679K and D796Y. The effect of RBD-targeted mutations on neutralizing (NAbs) binding was considerable.

Conclusion

The outcome of this first report on SARS-CoV-2 variants identification and mutation in the Al-Baha region could be used to lay down the policies to manage and impede the regional outbreak of COVID-19 effectively.

Preclinical evaluation of PHH-1V vaccine candidate against SARS-CoV-2 in non-human primates

SARS-CoV-2 emerged in December 2019 and quickly spread worldwide, continuously striking with an unpredictable evolution. Despite the success in vaccine production and mass vaccination programs, the situation is not still completely controlled, and therefore accessible second-generation vaccines are required to mitigate the pandemic. We previously developed an adjuvanted vaccine candidate coded PHH-1V, based on a heterodimer fusion protein comprising the RBD domain of two SARS-CoV-2 variants. Here, we report data on the efficacy, safety, and immunogenicity of PHH-1V in cynomolgus macaques. PHH-1V prime-boost vaccination induces high levels of RBD-specific IgG binding and neutralizing antibodies against several SARS-CoV-2 variants, as well as a balanced Th1/Th2 cellular immune response. Remarkably, PHH-1V vaccination prevents SARS-CoV-2 replication in the lower respiratory tract and significantly reduces viral load in the upper respiratory tract after an experimental infection. These results highlight the potential use of the PHH-1V vaccine in humans, currently undergoing Phase III clinical trials.

Real-World Effectiveness of Four Types of COVID-19 Vaccines

BACKGROUND

There is a scarcity of evidence regarding the real-world effectiveness of coronavirus disease 2019 (COVID-19) vaccines. This was the first study to evaluate the effectiveness of four types of vaccines against asymptomatic and symptomatic infection, and COVID-19 outcomes among the general population.

METHODS

This was a matched comparison group quasi-experimental study conducted in Jordan between 1 January and 29 August 2021. In the first part of the study, 1200 fully vaccinated individuals were matched with 1200 unvaccinated control participants. In order to measure vaccine effectiveness, the infection rates of both vaccinated and unvaccinated groups were calculated. The second part of the study included measuring specific anti-SARS CoV-2 immune cells and antibodies.

RESULTS

BNT162b2 (Pfizer, New York, NY, USA) showed a significantly higher effectiveness against asymptomatic COVID-19 infection (91.7%) and hospitalization (99.5%) than BBIBP-CorV (Sinopharm, Beijing, China) (88.4% and 98.7%, respectively) and ChAdOx1 nCoV-19 (AstraZeneca, Cambridge, UK) (84.3%, and 98.9%, respectively). The effectiveness rates of the Sputnik V (Gamaleya Research Institute, Moscow, Russia) vaccine against asymptomatic, symptomatic, and hospitalization were 100%, 100%, and 66.7%, respectively. The highest median anti-spike (S) IgG values were seen in individuals who received BNT162b2 (2.9 AU/mL) and ChAdOx1 nCoV-19 (2.8 AU/mL) vaccines. The levels of anti-S IgG were significantly decreased after 7 months of vaccination with BNT162b2 and BBIBP-CorV. There were significant decreases in the median number of neutralizing antibodies one month and seven months after receiving BNT162b2 (from 88.5 to 75.2 4 Bioequivalent Allergen Unit per milliliter/mL), BBIBP-CorV (from 69.5 to 51.5 BAU/mL), and ChAdOx1 nCoV-19 (from 69.2 to 58.BAU/mL) vaccines. The highest percentage of T cells specific to COVID-19 vaccine was found in individuals who received BNT162b2 (88.5%).

CONCLUSION

All four vaccines evaluated in this study showed effectiveness against asymptomatic COVID-19 infection, symptomatic infection, hospitalization, and death. Furthermore, BNT162b2, BBIBP-CorV, and ChAdOx1 nCoV-19 induced high levels of immunology markers within one month of vaccination.

SARS-CoV-2 Omicron variant causes brain infection with lymphoid depletion in a mouse COVID-19 model

BACKGROUND

The Omicron variant has become the most prevalent SARS-CoV-2 variant. Omicron is known to induce milder lesions compared to the original Wuhan strain. Fatal infection of the Wuhan strain into the brain has been well documented in COVID-19 mouse models and human COVID-19 cases, but apparent infections into the brain by Omicron have not been reported in human adult cases or animal models. In this study, we investigated whether Omicron could spread to the brain using K18-hACE2 mice susceptible to SARS-CoV-2 infection.

RESULTS

K18-hACE2 mice were intranasally infected with 1 × 10⁵ PFU of the original Wuhan strain and the Omicron variant of SARS-CoV-2. A follow-up was conducted 7 days post infection. All Wuhan-infected mice showed > 20% body weight loss, defined as the lethal condition, whereas two out of five Omicron-infected mice (40%) lost > 20% body weight. Histopathological analysis based on H&E staining revealed inflammatory responses in the brains of these two Omicron-infected mice. Immunostaining analysis of viral nucleocapsid protein revealed severe infection of neuron cells in the brains of these two Omicron-infected mice. Lymphoid depletion and apoptosis were observed in the spleen of Omicron-infected mice with brain infection.

CONCLUSION

Lethal conditions, such as severe body weight loss and encephalopathy, can occur in Omicron-infected K18-hACE2 mice. Our study reports, for the first time, that Omicron can induce brain infection with lymphoid depletion in the mouse COVID-19 model.

Evidence of Copper Nanoparticles and Poly I:C Modulating Cas9 Interaction and Cleavage of COR (Conserved Omicron RNA)

Conserved omicron RNA (COR) is a 40 base long 99.9% conserved sequence in SARS-CoV-2 Omicron variant, predicted to form a stable stem loop, the targeted cleavage of which can be an ideal next step in controlling the spread of variants. The Cas9 enzyme has been traditionally utilized for gene editing and DNA cleavage. Previously Cas9 has been shown to be capable of RNA editing under certain conditions. Here we investigated the ability of Cas9 to bind to single-stranded conserved omicron RNA (COR) and examined the effect of copper nanoparticles (Cu NPs) and/or polyinosinic-polycytidilic acid (poly I:C) on the RNA cleavage ability of Cas9. The interaction of the Cas9 enzyme and COR with Cu NPs was shown by dynamic light scattering (DLS) and zeta potential measurements and was confirmed by two-dimensional fluorescence difference spectroscopy (2-D FDS). The interaction with and enhanced cleavage of COR by Cas9 in the presence of Cu NPs and poly I:C was shown by agarose gel electrophoresis. These data suggest that Cas9-mediated RNA cleavage may be potentiated at the nanoscale level in the presence of nanoparticles and a secondary RNA component. Further explorations in vitro and in vivo may contribute to the development of a better cellular delivery platform for Cas9.

Hesitancy about SARS-CoV-2 rapid antigen testing in China: a nationwide cross-sectional study

BACKGROUND

SARS-CoV-2 rapid antigen testing (RAT) could be a useful supplementary test to diagnose larger numbers of acute asymptomatic infection and alleviate the limitations of polymerase chain reaction (PCR) test. However, hesitancy about SARS-CoV-2 RAT may compromise its implementation.

OBJECTIVE

We aimed to understand the prevalence and correlates of hesitancy about RAT among adults uninfected with SARS-CoV-2 in mainland China.

METHODS

A nationwide cross-sectional survey on hesitancy about SARS-CoV-2 RAT was conducted among adults uninfected with SARS-CoV-2 in mainland China between 29 April and 10 May 2022. Participants completed an online questionnaire that covered the following COVID-19 related questions: sociodemographic characteristics, experiences of COVID-19 restrictions and knowledge of COVID-19, and attitude towards COVID-19 and its screening. This study was a secondary analysis of data from the survey. We compared the characteristics of participants by levels of hesitancy about SARS-CoV-2 RAT. Thereafter, logistic regression with the sparse group minimax concave penalty was used to identify correlates of hesitancy about RAT.

RESULTS

We recruited 8856 individuals with diverse demographic, socioeconomic and geographic characteristics in China. 5388 participants (valid response rate 60.84%, 52% men, median age 32 years) were included the analysis. 12.75% (687) expressed hesitancy about RAT. Notably, those who were from the central region (adjusted odds ratio [aOR]: 1.815, 95% confidence interval [CI]: 1.441-2.278), and received COVID-19 information from traditional media (1.544, 1.279-1.863) were significantly more likely to report hesitancy about RAT. However, those who were women (0.720, 0.599-0.864), older (0.982, 0.969-0.995), had postgraduate education (0.612, 0.435-0.858), had children (< 6 years old) and elders (> 60 years old) in family (0.685, 0.510-0.911), had better knowledge about COVID-19 (0.942, 0.916-0.970), and had mental health disorders (0.795, 0.646-0.975) were less likely to report hesitancy about RAT.

CONCLUSIONS

Hesitancy about SARS-CoV-2 RAT was low among individuals who were not yet infected with SARS-CoV-2. Efforts should be made to improve the awareness and acceptance of RAT among men, younger adults, individuals with lower education or salary, families without children and elders, individuals who access COVID-19 information via traditional media. In the midst of a reopening world, our study could inform the development of contextualized mass screening strategies, the scale-up of RAT in particular, which remains an indispensable option in emergency preparedness.

Rapid and Visual Detection of SARS-CoV-2 RNA Based on Reverse Transcription-Recombinase Polymerase Amplification with Closed Vertical Flow Visualization Strip Assay

Coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was initially identified in 2019, after which it spread rapidly throughout the world. With the progression of the epidemic, new variants of SARS-CoV-2 with faster transmission speeds and higher infectivity have constantly emerged. The proportions of people asymptomatically infected or reinfected after vaccination have increased correspondingly, making the prevention and control of COVID-19 extremely difficult. There is therefore an urgent need for rapid, convenient, and inexpensive detection methods. In this paper, we established a nucleic acid visualization assay targeting the SARS-CoV-2 nucleoprotein (N) gene by combining reverse transcription-recombinase polymerase amplification with closed vertical flow visualization strip (RT-RPA-VF). This method had high sensitivity, comparable to that of reverse transcription-quantitative PCR (RT-qPCR), and the concordance between RT-RPA-VF and RT-qPCR methods was 100%. This detection method is highly specific and is not compatible with bat coronavirus HKU4, human coronaviruses 229E, OC43, and HKU1-CoV, Middle East respiratory syndrome coronavirus (MERS-CoV), or other respiratory pathogens. However, multiple SARS-CoV-2 variants are detectable within 25 min at 42°C using this visual method, including RNA transcripts of the Wuhan-Hu-1 strain at levels as low as 1 copy/μL, the Delta strain at 1 copy/μL, and the Omicron strain at 0.77 copies/μL. The RT-RPA-VF method is a simple operation for the rapid diagnosis of COVID-19 that is safe and free from aerosol contamination and could be an affordable and attractive choice for governments seeking to promote their emergency preparedness and better their responses to the continuing COVID-19 epidemic. In addition, this method also has great potential for early monitoring and warning of the epidemic situation at on-site-nursing points. IMPORTANCE The global COVID-19 epidemic, ongoing since the initial outbreak in 2019, has caused panic and huge economic losses worldwide. Due to the continuous emergence of new variants, COVID-19 has been responsible for a higher proportion of asymptomatic patients than the previously identified SARS and MERS, which makes early diagnosis and prevention more difficult. In this manuscript, we describe a rapid, sensitive, and specific detection tool, RT-RPA-VF. This tool provides a new alternative for the detection of SARS-CoV-2 variants in a range as low as 1 to 0.77 copies/μL RNA transcripts. RT-RPA-VF has great potential to ease the pressure of medical diagnosis and the accurate identification of patients with suspected COVID-19 at point-of-care.

Association between immunity and viral shedding duration in non-severe SARS-CoV-2 Omicron variant-infected patients

Background

Coronavirus disease 2019 (COVID-19) is a respiratory-related disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). More than 200 countries worldwide are affected by this disease. The Omicron variant of SARS-CoV-2 is the major epidemic variant worldwide and is characterized by higher infectivity. However, the immunity and risk factors for prolonged viral elimination in patients with non-severe SARS-CoV-2 Omicron variant infections are unclear. Therefore, this study aimed to examine the relationship between immunity and duration of viral elimination in non-severe SARS-CoV-2 Omicron variant-infected patients in Shanghai.

Methods

In total, 108 non-severe SARS-CoV-2 Omicron variant-infected patients from Shanghai New International Expo Center Fangcang Shelter Hospital were recruited in this study. They were further allocated to the early elimination (EE) and prolonged elimination (PE) groups according to SARS-CoV-2 nucleic acid positivity duration.

Results

Compared to patients with EE, those with PE had increased serum concentrations of interleukin (IL)-5, IL-6, and IL-8; higher neutrophil count and neutrophil-to-lymphocyte ratio (NLR); lower lymphocyte, eosinophil, and red blood cell counts; and lower concentrations of hemoglobin and albumin (ALB). In lymphocyte subpopulation analysis, lower numbers of CD3⁺ T cells, CD4⁺ T cells, CD8⁺ T cells, and NK cells and a higher CD4/CD8 ratio were observed in patients with PE. In addition, correlation analysis results revealed that cycle threshold values of SARS-CoV-2 Omicron variant ORF1ab and N were negatively correlated with IL-6 and IL-8 levels and positively correlated with eosinophil count in patients with COVID-19. Finally, multivariate regression analysis showed that ALB, CD4/CD8 ratio, NLR, and eosinophil count were predictors of the SARS-CoV-2 Omicron variant elimination.

Conclusion

In this study, we identified that the ALB, CD4/CD8 ratio, NLR, and eosinophil count were risk factors for prolonged viral elimination in non-severe SARS-CoV-2 Omicron variant-infected patients. These factors might be efficient indicators in the diagnosis, evaluation, and prognosis monitoring of the disease.

Multiplex protein profiling of bronchial aspirates reveals disease-, mortality- and respiratory sequelae-associated signatures in critically ill patients with ARDS secondary to SARS-CoV-2 infection

Introduction

Bronchial aspirates (BAS) obtained during invasive mechanical ventilation (IMV) constitutes a useful tool for molecular phenotyping and decision making.

Aim

To identify the proteomic determinants associated with disease pathogenesis, all-cause mortality and respiratory sequelae in BAS samples from critically ill patients with SARS-CoV-2-induced ARDS.

Methods

Multicenter study including 74 critically ill patients with COVID-19 and non-COVID-19 ARDS. BAS were obtained by bronchoaspiration after IMV initiation. Three hundred sixty-four proteins were quantified using proximity extension assay (PEA) technology. Random forest models were used to assess predictor importance.

Results

After adjusting for confounding factors, CST5, NADK, SRPK2 and TGF-α were differentially detected in COVID-19 and non-COVID-19 patients. In random forest models for COVID-19, CST5, DPP7, NADK, KYAT1 and TYMP showed the highest variable importance. In COVID-19 patients, reduced levels of ENTPD2 and PTN were observed in nonsurvivors of ICU stay, even after adjustment. AGR2, NQO2, IL-1α, OSM and TRAIL showed the strongest associations with in-ICU mortality and were used to construct a protein-based prediction model. Kaplan-Meier curves revealed a clear separation in mortality risk between subgroups of PTN, ENTPD2 and the prediction model. Cox regression models supported these findings. In survivors, the levels of FCRL1, NTF4 and THOP1 in BAS samples obtained during the ICU stay correlated with lung function (i.e., D_LCO levels) 3 months after hospital discharge. Similarly, Flt3L and THOP1 levels were correlated with radiological features (i.e., TSS). These proteins are expressed in immune and nonimmune lung cells. Poor host response to viral infectivity and an inappropriate reparative mechanism seem to be linked with the pathogenesis of the disease and fatal outcomes, respectively.

Conclusion

BAS proteomics identified novel factors associated with the pathology of SARS-CoV-2-induced ARDS and its adverse outcomes. BAS-based protein testing emerges as a novel tool for risk assessment in the ICU.

Treating patients infected with the SARS-CoV-2 Omicron variant with a traditional Chinese medicine, Shufeng Jiedu capsule

Patients infected with the Omicron variant of SARS-CoV-2 mainly develop mild COVID-19, manifesting as upper respiratory symptoms, fatigue, and fever. Shufeng Jiedu capsule (SFJDC), a traditional Chinese medicine indicated for treatment of upper respiratory infections in China, was tested for its efficacy and safety in treatment of an Omicron infection at a mobile cabin hospital in response to an outbreak of COVID-19 in Shanghai, China in April 2022. In this open-label, randomized controlled trial, patients in the control group received best supportive care, while those in the test group received additional SFJDC therapy for 7 days. SFJDC markedly alleviated patients' symptoms including a sore throat, coughing, fatigue, and a fever after 7 days of treatment. The virus negative time was significantly shorter in the SFJDC treatment group, but there were no obvious differences in the virus negative rate between the two groups at the end of the 7-day follow-up. These results suggest that patients with the Omicron infection may benefit from SFJDC treatment. Double-blind, randomized controlled trials are warranted to comprehensively evaluate the efficacy and safety of SFJDC in a large cohort study in the future.