Emerging COVID-19 variants and their impact on SARS-CoV-2 diagnosis, therapeutics and vaccines

Comprehensive analysis of clinical indications and viral strain variants among patients infected with SARS-CoV-2 in Inner Mongolia, China

Since the first appearance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2019, the virus is still evolving and mutating until now. In this study, we collected 6 throat swabs from patients who diagnosed with COVID-19 in Inner Mongolia, China, to understand the entry of multiple SARS-CoV-2 variants into Inner Mongolia and analyze the relationships between variants and clinical features observed in infected patients. In addition, we performed a combined analysis of clinical parameters associated with SARS-CoV-2 variants of interest, pedigree analysis, and detection of single-nucleotide polymorphisms. Our results showed that the clinical symptoms were generally mild although some patients demonstrated some degree of liver function abnormalities, and the SARS-CoV-2 strain was related to the Delta variant (B.1.617.2), AY.122 lineage. The epidemiological investigations and clinical manifestations confirmed that the variant exhibits strong transmission, a high viral load, and moderate clinical symptoms. SARS-CoV-2 has undergone extensive mutations in various hosts and countries. Timely monitoring of virus mutation can help to monitor the spread of infection and characterize the diversity of genomic variants, thus limiting future waves of SARS-CoV-2 infection.

The Potential of Nanobodies for COVID-19 Diagnostics and Therapeutics

The infectious severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the causative agent for coronavirus disease 2019 (COVID-19). Globally, there have been millions of infections and fatalities. Unfortunately, the virus has been persistent and a contributing factor is the emergence of several variants. The urgency to combat COVID-19 led to the identification/development of various diagnosis (polymerase chain reaction and antigen tests) and treatment (repurposed drugs, convalescent plasma, antibodies and vaccines) options. These treatments may treat mild symptoms and decrease the risk of life-threatening disease. Although these options have been fairly beneficial, there are some challenges and limitations, such as cost of tests/drugs, specificity, large treatment dosages, intravenous administration, need for trained personal, lengthy production time, high manufacturing costs, and limited availability. Therefore, the development of more efficient COVID-19 diagnostic and therapeutic options are vital. Nanobodies (Nbs) are novel monomeric antigen-binding fragments derived from camelid antibodies. Advantages of Nbs include low immunogenicity, high specificity, stability and affinity. These characteristics allow for rapid Nb generation, inexpensive large-scale production, effective storage, and transportation, which is essential during pandemics. Additionally, the potential aerosolization and inhalation delivery of Nbs allows for targeted treatment delivery as well as patient self-administration. Therefore, Nbs are a viable option to target SARS-CoV-2 and overcome COVID-19. In this review we discuss (1) COVID-19; (2) SARS-CoV-2; (3) the present conventional COVID-19 diagnostics and therapeutics, including their challenges and limitations; (4) advantages of Nbs; and (5) the numerous Nbs generated against SARS-CoV-2 as well as their diagnostic and therapeutic potential.

Report of consensus panel 5 from the 11th international workshop on Waldenstrom's macroglobulinemia on COVID-19 prophylaxis and management

Consensus Panel 5 (CP5) of the 11th International Workshop on Waldenstrom's Macroglobulinemia (IWWM-11; held in October 2022) was tasked with reviewing the current data on the coronavirus disease-2019 (COVID-19) prophylaxis and management in patients with Waldenstrom's Macroglobulinemia (WM). The key recommendations from IWWM-11 CP5 included the following: Booster vaccines for SARS-CoV-2 should be recommended to all patients with WM. Variant-specific booster vaccines, such as the bivalent vaccine for the ancestral Wuhan strain and the Omicron BA.4.5 strain, are important as novel mutants emerge and become dominant in the community. A temporary interruption in Bruton's Tyrosine Kinase-inhibitor (BTKi) or chemoimmunotherapy before vaccination might be considered. Patients under treatment with rituximab or BTK-inhibitors have lower antibody responses against SARS-CoV-2; thus, they should continue to follow preventive measures, including mask wearing and avoiding crowded places. Patients with WM are candidates for preexposure prophylaxis, if available and relevant to the dominant SARS-CoV-2 strains in a specific area. Oral antivirals should be offered to all symptomatic WM patients with mild to moderate COVID-19 regardless of vaccination, disease status or treatment, as soon as possible after the positive test and within 5 days of COVID-19-related symptom onset. Coadministration of ibrutinib or venetoclax with ritonavir should be avoided. In these patients, remdesivir offers an effective alternative. Patients with asymptomatic or oligosymptomatic COVID-19 should not interrupt treatment with a BTK inhibitor. Infection prophylaxis is essential in patients with WM and include general preventive measures, prophylaxis with antivirals and vaccination against common pathogens including SARS-CoV-2, influenza, and S. pneumoniae.

Public Attitudes Towards COVID-19, Antibiotic Resistance, Preventive Measures: A Multi Center Cross-Sectional Study in the Arab Countries

BACKGROUND AND AIM

COVID-19 has shown how crucial awareness of the need to protect public health is to global security. Antibiotic resistance due to antibiotic misuse is seen as a worldwide health issue. Antibiotic use was significant during the COVID-19 epidemic, according to several nations. This research aims to investigate public attitudes on COVID-19, antibiotic resistance, and preventive measures during the COVID-19 pandemic in the Middle East.

METHODS

An online quantitative cross-sectional study in 17 Arabic nations was carried out between January 3 and March 4, 2022, using a structured questionnaire to evaluate participants' knowledge of COVID-19, their attitudes toward the new standard during the pandemic, and their use of antibiotics, and their resistance to them. The research was available to all Arabic people over 18 nations in the middle east. A convenient snowball sampling technique was used. SPSS version 20.0 was used to analyze the data. To analyze the results, binominal logistic regression was utilized. Statistical significance was defined as a p value of 0.05.

RESULTS

Of the 6145 responders, 24.1% believed COVID-19 might spread to asymptomatic people, whereas 13.6% thought using antibiotics would accelerate recovery from any illness. Moreover, half of the respondents said antibiotics only work against bacteria (64.6%). 70.8% of participants adopted the necessary safety measures. More than a third of respondents strongly supported placing foreign immigrants in quarantine (33%). However, more than 50% of those surveyed (52.5%) firmly supported using face masks in all public settings. Individuals with a medical education background had 2.6 times more appropriate understanding of antibiotic resistance than others. Furthermore, participants in the 30-49 age range had a better handle on the use of antibiotics and antibiotic resistance than other respondents by 1.1 times.

CONCLUSION

Arab Health authorities should reconsider this health issue as soon about the inadequate level of awareness toward antibiotic use, resistance, and preventative practices during COVID-19. Many suggested strategies, especially solving the irregular antibiotic prescriptions during a COVID19 pandemic, should be implemented to increase public awareness of COVID19.

SARS-CoV-2 versus Influenza A Virus: Characteristics and Co-Treatments

For three years, the novel coronavirus disease 2019 (COVID-19) pandemic, caused by infection of the SARS-CoV-2 virus, has completely changed our lifestyles and prepared us to live with this novel pneumonia for years to come. Given that pre-existing flu is caused by the influenza A virus, we have begun unprecedently co-coping with two different respiratory diseases at the same time. Hence, we draw a comparison between SARS-CoV-2 and influenza A virus based on the general characteristics, especially the main variants’ history and the distribution of the two viruses. SARS-CoV-2 appeared to mutate more frequently and independently of locations than the influenza A virus. Furthermore, we reviewed present clinical trials on combined management against COVID-19 and influenza in order to explore better solutions against both at the same time.

Investigating the Use of SARS-CoV-2 (COVID-19) Odor Expression as a Non-Invasive Diagnostic Tool-Pilot Study

Since the beginning of the COVID-19 pandemic, there has been enormous interest in the development of measures that would allow for the swift detection of the disease. The rapid screening and preliminary diagnosis of SARS-CoV-2 infection allow for the instant identification of possibly infected individuals and the subsequent mitigation of the disease spread. Herein, the detection of SARS-CoV-2-infected individuals was explored using noninvasive sampling and low-preparatory-work analytical instrumentation. Hand odor samples were obtained from SARS-CoV-2-positive and -negative individuals. The volatile organic compounds (VOCs) were extracted from the collected hand odor samples using solid phase microextraction (SPME) and analyzed using gas chromatography coupled with mass spectrometry (GC-MS). Sparse partial least squares discriminant analysis (sPLS-DA) was used to develop predictive models using the suspected variant sample subsets. The developed sPLS-DA models performed moderately (75.8% (±0.4) accuracy, 81.8% sensitivity, 69.7% specificity) at distinguishing between SARS-CoV-2-positive and negative -individuals based on the VOC signatures alone. Potential markers for distinguishing between infection statuses were preliminarily acquired using this multivariate data analysis. This work highlights the potential of using odor signatures as a diagnostic tool and sets the groundwork for the optimization of other rapid screening sensors such as e-noses or detection canines.

COVID-19-Associated Paediatric Inflammatory Multisystem Syndrome (PIMS-TS) in Intensive Care: A Retrospective Cohort Trial (PIMS-TS INT)

Paediatric inflammatory multisystem syndrome temporally associated with COVID-19 (PIMS-TS) is a new disease in children and adolescents that occurs after often asymptomatic or mild COVID-19. It can be manifested by different clinical symptomatology and varying severity of disease based on multisystemic inflammation. The aim of this retrospective cohort trial was to describe the initial clinical presentation, diagnostics, therapy and clinical outcome of paediatric patients with a diagnosis of PIMS-TS admitted to one of the 3 PICUs. All paediatric patients who were admitted to the hospital with a diagnosis of paediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 (PIMS-TS) during the study period were enrolled in the study. A total of 180 patients were analysed. The most common symptoms upon admission were fever (81.6%, n = 147), rash (70.6%, n = 127), conjunctivitis (68.9%, n = 124) and abdominal pain (51.1%, n = 92). Acute respiratory failure occurred in 21.1% of patients (n = 38). Vasopressor support was used in 20.6% (n = 37) of cases. Overall, 96.7% of patients (n = 174) initially tested positive for SARS-CoV-2 IgG antibodies. Almost all patients received antibiotics during in-hospital stays. No patient died during the hospital stay or after 28 days of follow-up. Initial clinical presentation and organ system involvement of PIMS-TS including laboratory manifestations and treatment were identified in this trial. Early identification of PIMS-TS manifestation is essential for early treatment and proper management of patients.

Tailored Multiplex Real-Time RT-PCR with Species-Specific Internal Positive Controls for Detecting SARS-CoV-2 in Canine and Feline Clinical Samples

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections have been frequently reported in companion dogs and cats worldwide during the ongoing coronavirus disease. However, RT-qPCR methods developed for humans have been used for the diagnosis of SARS-CoV-2 infections in suspected companion dogs and cats owing to the lack of the companion animal-tailored methods. Therefore, we developed a multiplex RT-qPCR (mRT-qPCR) using newly designed primers and probes targeting RdRp and N genes of all currently circulating SARS-CoV-2 variants as well as the canine or feline 16S rRNA gene as an endogenous internal positive control (EIPC) for reliable diagnosis of SARS-CoV-2 infection from suspected dogs and cats. The developed mRT-qPCR assay specifically detected the target genes of SARS-CoV-2 but no other canine or feline pathogens. Furthermore, canine and feline EIPCs were stably amplified by mRT-qPCR in samples containing canine- or feline-origin cellular materials. This assay has high repeatability and reproducibility, with an optimal limit of detection (<10 RNA copies per reaction) and coefficients of variation (<1.0%). The detection rate of SARS-CoV-2 of the developed mRT-qPCR was 6.6% for canine and feline nasopharyngeal samples, which was consistent with that of a commercial mRT-qPCR kit for humans. Collectively, the newly developed mRT-qPCR with canine and feline EIPC can efficiently diagnose and evaluate the viral load in field specimens and will be a valuable tool for etiological diagnosis, epidemiological study, and controlling SARS-CoV-2 infections in canine and feline populations.

Atypical presentation of COVID-19 in older patients is associated with frailty but not with adverse outcomes

PURPOSE

Older patients with COVID-19 can present with atypical complaints, such as falls or delirium. In other diseases, such an atypical presentation is associated with worse clinical outcomes. However, it is not known whether this extends to COVID-19. We aimed to study the association between atypical presentation of COVID-19, frailty and adverse outcomes, as well as the incidence of atypical presentation.

METHODS

We conducted a retrospective observational multi-center cohort study in eight hospitals in the Netherlands. We included patients aged ≥ 70 years hospitalized with COVID-19 between February 2020 until May 2020. Atypical presentation of COVID-19 was defined as presentation without fever, cough and/or dyspnea. We collected data concerning symptoms on admission, demographics and frailty parameters [e.g., Charlson Comorbidity Index (CCI) and Clinical Frailty Scale (CFS)]. Outcome data included Intensive Care Unit (ICU) admission, discharge destination and 30-day mortality.

RESULTS

We included 780 patients, 9.5% (n = 74) of those patients had an atypical presentation. Patients with an atypical presentation were older (80 years, IQR 76-86 years; versus 79 years, IQR 74-84, p = 0.044) and were more often classified as severely frail (CFS 6-9) compared to patients with a typical presentation (47.6% vs 28.7%, p = 0.004). Overall, there was no significant difference in 30-day mortality between the two groups in univariate analysis (32.4% vs 41.5%; p = 0.173) or in multivariate analysis [OR 0.59 (95% CI 0.34-1.0); p = 0.058].

CONCLUSIONS

In this study, patients with an atypical presentation of COVID-19 were more frail compared to patients with a typical presentation. Contrary to our expectations, an atypical presentation was not associated with worse outcomes.

Genomic surveillance and sequencing of SARS-CoV-2 across South America

After 2 years of the COVID-19 pandemic, the protocols used to control infection lack attention and analysis. We present data about deposits of complete genomic sequences of SARS-CoV-2 in the Global Initiative on Sharing All Influenza Data (GISAID) database made between January 2021 and May 31, 2022. We build the distribution profile of SARS-CoV-2 variants across South America, highlighting the contribution and influence of each variant over time. Monitoring the genomic sequences in GISAID illustrates negligence in the follow up of infected patients in South America and also the discrepancies between the number of complete genomes deposited throughout the pandemic by developed and developing countries. While Europe and North America account for more than 9 million of the genomes deposited in GISAID, Africa and South America deposited less than 400 000 genome sequences. Genomic surveillance is important for detecting early warning signs of new circulating viruses, assisting in the discovery of new variants and controlling pandemics.

Omicron Variant of SARS-CoV-2: An Indian Perspective of Vaccination and Management

Omicron variants have highly influenced the entire globe. It has a high rate of transmissibility, which makes its management tedious. There are various subtypes of omicron, namely BA.1, BA.2, BA.3, BA.4, and BA.5. Currently, one omicron subvariant BF.7 is also immersed in some parts of India. Further studies are required for a better understanding of the new immersing SARS-CoV-2 subvariant of the omicron. They differ in the mutation of the spike proteins, which alters their attachment to the host receptor and hence modifies their virulence and adaptability. Delta variants have a great disastrous influence on the entire world, especially in India. While overcoming it, another mutant catches the pace. The Indian population is highly affected by omicron variants. It alters the entire management and diagnosis system against COVID-19. It demanded forcemeat in the health care system, both qualitatively and quantitively, to cope with the omicron wave. The alteration in spike protein, which is the major target of vaccines, leads to varied immunization against the subvariants. The efficacy of vaccines against the new variant was questioned. Every vaccine had a different shielding effect on the new variant. The hesitancy of vaccination was a prevalent factor in India that might have contributed to its outbreak. The prevalence of omicron, monkeypox, and tomato flu shared some similarities and distinct features when compared to their influence on the Indian population. This review emphasizes the changes omicron brings with it and how the Indian health care system outrage this dangerous variant.

Persistence of spike-specific immune responses in BNT162b2-vaccinated donors and generation of rapid ex-vivo T cells expansion protocol for adoptive immunotherapy: A pilot study

Introduction

The BNT162b2 mRNA-based vaccine has shown high efficacy in preventing COVID-19 infection but there are limited data on the types and persistence of the humoral and T cell responses to such a vaccine.

Methods

Here, we dissect the vaccine-induced humoral and cellular responses in a cohort of six healthy recipients of two doses of this vaccine.

Results and discussion

Overall, there was heterogeneity in the spike-specific humoral and cellular responses among vaccinated individuals. Interestingly, we demonstrated that anti-spike antibody levels detected by a novel simple automated assay (Jess) were strongly correlated (r=0.863, P<0.0001) with neutralizing activity; thus, providing a potential surrogate for neutralizing cell-based assays. The spike-specific T cell response was measured with a newly modified T-spot assay in which the high-homology peptide-sequences cross-reactive with other coronaviruses were removed. This response was induced in 4/6 participants after the first dose, and all six participants after the second dose, and remained detectable in 4/6 participants five months post-vaccination. We have also shown for the first time, that BNT162b2 vaccine enhanced T cell responses also against known human common viruses. In addition, we demonstrated the efficacy of a rapid ex-vivo T cell expansion protocol for spike-specific T cell expansion to be potentially used for adoptive-cell therapy in severe COVID-19, immunocompromised individuals, and other high-risk groups. There was a 9 to 13.7-fold increase in the number of expanded T cells with a significant increase of anti-spike specific response showing higher frequencies of both activation and cytotoxic markers. Interestingly, effector memory T cells were dominant in all four participants' CD8+ expanded memory T cells; CD4+ T cells were dominated by effector memory in 2/4 participants and by central memory in the remaining two participants. Moreover, we found that high frequencies of CD4+ terminally differentiated memory T cells were associated with a greater reduction of spike-specific activated CD4+ T cells. Finally, we showed that participants who had a CD4+ central memory T cell dominance expressed a high CD69 activation marker in the CD4+ activated T cells.

A fatal case of COVID-19-associated meningoencephalitis in a patient coinfected with influenza A

We report a case of COVID-19-associated meningoencephalitis with a fatal outcome in a male patient with concomitant influenza A, who had been hospitalized at the beginning of 2022, in the Northeastern region of Brazil. He died due to cardiopulmonary arrest after developing status epilepticus on the third day of hospitalization. The SARS-CoV-2 RNA was detected in cerebrospinal fluid and Influenza A was detected in the nasopharyngeal swab. Meningoencephalitis due to COVID-19 is a rare manifestation and physicians must be aware of this complication, mainly during the pandemic. In viral co-circulation situations, the possibility of respiratory coinfections should be remembered.

Characterization and application of a series of monoclonal antibodies against SARS-CoV-2 nucleocapsid protein

The ongoing coronavirus disease 2019 (COVID-19) pandemic has a significant global social and economic impact, and the emergence of new and more destructive mutant strains highlights the need for accurate virus detection. Here, 90 monoclonal antibodies (MAbs) that exclusively reacted with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid protein (NP) were generated. These MAbs did not cross-react with NPs of common human coronaviruses (HCoVs, i.e., 229E, OC43, HKU1, and NL63) and Middle East Respiratory Syndrome Coronavirus. Subsequently, overlapped peptides in individual fragments (N1-N4) of NP were synthesized. N1-3 (25-GSNQNGERSGARSKQ-39), N3-1 (217-AALALLLLDRLNQL-230), and N4-8 (393-TLLPAADLDDFSKQL-407) were identified as major epitopes using enzyme-linked immunoassay (ELISA) and recognized by 47, 1, and 18 MAbs, respectively. The 24 remaining MAbs exhibited no reactivity with all synthetic peptides. Among MAb-epitope pairs, only MAbs targeting epitope N1-3 displayed no cross-reaction with NPs of SARS-CoV-1 and other SARS-related CoVs. All Omicron variants contained a three-amino acid deletion (31ERS33) in the N1-3 region. Thus, MAbs targeting N1-3 failed to recognize these variants. Furthermore, a double-antibody sandwich ELISA for antigen detection was established using the optimal MAbs. Overall, a series of MAbs targeting SARS-CoV-2 NP was prepared, characterized with epitope mapping, and applied for the detection of SARS-CoV-2 antigens, and some novel B-cell epitopes of the viral NP were identified.

Analysing transcriptomic signatures and identifying potential genes for the protective effect of inactivated COVID-19 vaccines

Inactivated vaccines are one of the most effective strategies for controlling the coronavirus disease 2019 (COVID-19) pandemic. However, the response genes for the protective effect of inactivated vaccines are still unclear. Herein, we analysed the neutralization antibody responses elicited by vaccine serum and carried out transcriptome sequencing of RNAs isolated from the PBMCs of 29 medical staff receiving two doses of the CoronaVac vaccine. The results showed that SARS-CoV-2 neutralization antibody titers varied considerably among individuals, and revealed that many innate immune pathways were activated after vaccination. Furthermore, the blue module revealed that NRAS, YWHAB, SMARCA5, PPP1CC and CDC5L may be correlated with the protective effect of the inactivated vaccine. Additionally, MAPK1, CDC42, PPP2CA, EP300, YWHAZ and NRAS were demonstrated as the hub genes having a significant association with vaccines. These findings provide a basis for understanding the molecular mechanism of the host immune response induced by inactivated vaccines.

How information processing and risk/benefit perception affect COVID-19 vaccination intention of users in online health communities

Objective

To investigate the relationship among information processing, risk/benefit perception and the COVID-19 vaccination intention of OHCs users with the heuristic-systematic model (HSM).

Methods

This study conducted a cross-sectional questionnaire via an online survey among Chinese adults. A structural equation model (SEM) was used to examine the research hypotheses.

Results

Systematic information processing positively influenced benefit perception, and heuristic information processing positively influenced risk perception. Benefit perception had a significant positive effect on users' vaccination intention. Risk perception had a negative impact on vaccination intention. Findings revealed that differences in information processing methods affect users' perceptions of risk and benefit, which decide their vaccination intention.

Conclusion

Online health communities can provide more systematic cues and users should process information systematically to increase their perceived benefits, consequently increase their willingness to receive COVID-19 vaccine.

Durability of humoral and cell-mediated immune response after SARS-CoV-2 mRNA vaccine administration

Vaccination against the SARS-Cov-2 virus is an effective way to protect against the disease and the severe course of COVID-19. Forty-nine fully vaccinated with mRNA vaccines (BNT162b2 or mRNA-1273) SARS-CoV-2 infection-naïve volunteers aged 33-89 were enrolled in the study. Evaluation of the cellular and humoral immune response was performed within 1 to 3 months (T1) and 6-9 months (T2) after the second injection, and within 2-3 months (T3) after a booster dose. Additionally, a comparative analysis of the specific immune status was made between two age groups-below 60 (n = 22) and over 60 (n = 27) years. SARS-CoV-2-specific T-cell response was evaluated by IFN-γ-producing spot forming cells (SFCs) using a standardized ELISPOT assay. Virus neutralizing antibodies (VNA) against SARS-CoV-2 were measured by a blocking ELISA test and spike protein specific IgG (S-IgG) and IgA (S-IgA) antibodies-by semiquantitative ELISA. IFN-γ-producing SFCs, S-IgG, S-IgA and VNA significantly decreased 6-9 months after the second dose. After the third injection S-IgG and S-IgA markedly increased compared to T2 and reached the levels at T1. Of note, the highest values of VNA were observed at T3. No differences in the tested immune parameters were found between the two age groups. Data obtained showed that for a long period-6-9 months after a full course of immunization with mRNA vaccine, immune reactivity is present, but both cellular and humoral immune responses gradually decrease. The administration of a third dose mainly restores the specific humoral immune response against the SARS-CoV-2 virus.

SARS-CoV-2 emerging Omicron subvariants with a special focus on BF.7 and XBB.1.5 recently posing fears of rising cases amid ongoing COVID-19 pandemic

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron versions have been the sole one circulating for quite some time. Subvariants BA.1, BA.2, BA.3, BA.4, and BA.5 of the Omicron emerged over time and through mutation, with BA.1 responsible for the most severe global pandemic between December 2021 and January 2022. Other Omicron subvariants such as BQ.1, BQ.1.1, BA.4.6, BF.7, BA.2.75.2, XBB.1 appeared recently and could cause a new wave of increased cases amid the ongoing COVID-19 pandemic. There is evidence that certain Omicron subvariants have increased transmissibility, extra spike mutations, and ability to overcome protective effects of COVID-19 neutralizing antibodies through immunological evasion. In recent months, the Omicron BF.7 subvariant has been in the news due to its spread in China and a small number of other countries, raising concerns about a possible rebound in COVID-19 cases. More recently, the Omicron XBB.1.5 subvariant has captured international attention due to an increase in cases in the United States. As a highly transmissible sublineage of Omicron BA.5, as well as having a shorter incubation time and the potential to reinfect or infect immune population, BF.7 has stronger infection ability. It appears that the regional immunological landscape is affected by the amount and timing of previous Omicron waves, as well as the COVID-19 vaccination coverage, which in turn determines whether the increased immune escape of BF.7 and XBB.1.5 subvariants is sufficient to drive new infection waves. Expanding our understanding of the transmission and efficacy of vaccines, immunotherapeutics, and antiviral drugs against newly emerging Omicron subvariants and lineages, as well as bolstering genomic facilities for tracking their spread and maintaining a constant vigilance, and shedding more light on their evolution and mutational events, would help in the development of effective mitigation strategies. Importantly, reducing the occurrence of mutations and recombination in the virus can be aided by bolstering One health approach and emphasizing its significance in combating zoonosis and reversal zoonosis linked with COVID-19. This article provides a brief overview on Omicron variant, its recently emerging lineages and subvairants with a special focus on BF.7 and XBB.1.5 as much more infectious and highly transmissible variations that may once again threaten a sharp increase in COVID-19 cases globally amid the currently ongoing pandemic, along with presenting salient mitigation measures.

RNA Interference Approach Is a Good Strategy against SARS-CoV-2

COVID-19, caused by SARS-CoV-2, created a devastating outbreak worldwide and consequently became a global health concern. However, no verifiable, specifically targeted treatment has been devised for COVID-19. Several emerging vaccines have been used, but protection has not been satisfactory. The complex genetic composition and high mutation frequency of SARS-CoV-2 have caused an uncertain vaccine response. Small interfering RNA (siRNA)-based therapy is an efficient strategy to control various infectious diseases employing post-transcriptional gene silencing through the silencing of target complementary mRNA. Here, we designed two highly effective shRNAs targeting the conserved region of RNA-dependent RNA polymerase (RdRP) and spike proteins capable of significant SARS-CoV-2 replication suppression. The efficacy of this approach suggested that the rapid development of an shRNA-based therapeutic strategy might prove to be highly effective in treating COVID-19. However, it needs further clinical trials.

The Gut Microbiome of Children during the COVID-19 Pandemic

The gut microbiome has been shown to play a critical role in maintaining a healthy state. Dysbiosis of the gut microbiome is involved in modulating disease severity and potentially contributes to long-term outcomes in adults with COVID-19. Due to children having a significantly lower risk of severe illness and limited sample availability, much less is known about the role of the gut microbiome in children with COVID-19. It is well recognized that the developing gut microbiome of children differs from that of adults, but it is unclear if this difference contributes to the different clinical presentations and complications. In this review, we discuss the current knowledge of the gut microbiome in children with COVID-19, with gut microbiome dysbiosis being found in pediatric COVID-19 but specific taxa change often differing from those described in adults. Additionally, we discuss possible mechanisms of how the gut microbiome may mediate the presentation and complications of COVID-19 in children and the potential role for microbial therapeutics.

Exploring Highly Conserved Regions of SARS-CoV-2 Spike S2 Subunit as Targets for Fusion Inhibition Using Chimeric Proteins

Since the beginning of the COVID-19 pandemic, considerable efforts have been made to develop protective vaccines against SARS-CoV-2 infection. However, immunity tends to decline within a few months, and new virus variants are emerging with increased transmissibility and capacity to evade natural or vaccine-acquired immunity. Therefore, new robust strategies are needed to combat SARS-CoV-2 infection. The viral spike composed of S1 and S2 subunits mediates viral attachment and membrane fusion to infect the host cell. In this process, interaction between the highly conserved heptad repeat 1 and 2 regions (HR1 and HR2) of S2 is crucial and for this reason; these regions are promising targets to fight SARS-CoV-2. Here, we describe the design and characterization of chimeric proteins that structurally imitate the S2 HR1 region in a trimeric coiled-coil conformation. We biophysically characterized the proteins and determined their capacity to bind the HR2 region, as well as their inhibitory activity of SARS-CoV-2 infection in vitro. HR1 mimetic proteins showed conformational heterogeneity and a propensity to form oligomers. Moreover, their structure is composed of subdomains with varied stability. Interestingly, the full HR1 proteins showed high affinity for HR2-derived peptides and SARS-CoV-2 inhibitory activity, whereas smaller proteins mimicking HR1 subdomains had a decreased affinity for their complementary HR2 region and did not inhibit the virus. The results provide insight into effective strategies to create mimetic proteins with broad inhibitory activity and therapeutic potential against SARS-CoV-2.

Smart Nanostructured Materials for SARS-CoV-2 and Variants Prevention, Biosensing and Vaccination

The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has raised great concerns about human health globally. At the current stage, prevention and vaccination are still the most efficient ways to slow down the pandemic and to treat SARS-CoV-2 in various aspects. In this review, we summarize current progress and research activities in developing smart nanostructured materials for COVID-19 prevention, sensing, and vaccination. A few established concepts to prevent the spreading of SARS-CoV-2 and the variants of concerns (VOCs) are firstly reviewed, which emphasizes the importance of smart nanostructures in cutting the virus spreading chains. In the second part, we focus our discussion on the development of stimuli-responsive nanostructures for high-performance biosensing and detection of SARS-CoV-2 and VOCs. The use of nanostructures in developing effective and reliable vaccines for SARS-CoV-2 and VOCs will be introduced in the following section. In the conclusion, we summarize the current research focus on smart nanostructured materials for SARS-CoV-2 treatment. Some existing challenges are also provided, which need continuous efforts in creating smart nanostructured materials for coronavirus biosensing, treatment, and vaccination.

Divergent Antibody Repertoires Found for Omicron versus Wuhan SARS-CoV-2 Strains Using Ig-MS

SARS-CoV-2 Omicron (B.1.1.529) and its subvariants are currently the most common variants of concern worldwide, featuring numerous mutations in the spike protein and elsewhere that collectively make Omicron variants more transmissible and more resistant to antibody-mediated neutralization provided by vaccination, previous infections, and monoclonal antibody therapies than their predecessors. We recently reported the creation and characterization of Ig-MS, a new mass spectrometry-based serology platform that can define the repertoire of antibodies against an antigen of interest at single proteoform resolution. Here, we applied Ig-MS to investigate the evolution of plasma antibody repertoires against the receptor-binding domain (RBD) of SARS-CoV-2 in response to the booster shot and natural viral infection. We also assessed the capacity for antibody repertoires generated in response to vaccination and/or infection with the Omicron variant to bind to both Wuhan- and Omicron-RBDs. Our results show that (1) the booster increases antibody titers against both Wuhan- and Omicron- RBDs and elicits an Omicron-specific response and (2) vaccination and infection act synergistically in generating anti-RBD antibody repertoires able to bind both Wuhan- and Omicron-RBDs with variant-specific antibodies.

Molecular docking and molecular dynamics study Lianhua Qingwen granules (LHQW) treats COVID-19 by inhibiting inflammatory response and regulating cell survival

Purpose

2019 Coronavirus disease (COVID-19) is endangering health of populations worldwide. Latest research has proved that Lianhua Qingwen granules (LHQW) can reduce tissue damage caused by inflammatory reactions and relieve patients' clinical symptoms. However, the mechanism of LHQW treats COVID-19 is currently lacking. Therefore, we employed computer simulations to investigate the mechanism of LHQW treats COVID-19 by modulating inflammatory response.

Methods

We employed bioinformatics to screen active ingredients in LHQW and intersection gene targets. PPI, GO and KEGG was used to analyze relationship of intersection gene targets. Molecular dynamics simulations validated the binding stability of active ingredients and target proteins. Binding free energy, radius of gyration and the solvent accessible surface area were analyzed by supercomputer platform.

Results

COVID-19 had 4628 gene targets, LHQW had 1409 gene targets, intersection gene targets were 415. Bioinformatics analysis showed that intersection targets were closely related to inflammation and immunomodulatory. Molecular docking suggested that active ingredients (including: licopyranocoumarin, Glycyrol and 3-3-Oxopropanoic acid) in LHQW played a role in treating COVID-19 by acting on CSF2, CXCL8, CCR5, NLRP3, IFNG and TNF. Molecular dynamics was used to prove the binding stability of active ingredients and protein targets.

Conclusion

The mechanism of active ingredients in LHQW treats COVID-19 was investigated by computer simulations. We found that active ingredients in LHQW not only reduce cell damage and tissue destruction by inhibiting the inflammatory response through CSF2, CXCL8, CCR5 and IFNG, but also regulate cell survival and growth through NLRP3 and TNF thereby reducing apoptosis.

COVID-19 vaccine response and safety in patients with cancer: An overview of systematic reviews

Background

To date, the COVID-19 pandemic does not appear to be overcome with new variants continuously emerging. The vaccination against COVID-19 has been the trend, but there are multiple systematic reviews on COVID-19 vaccines in patients with cancer, resulting in redundant and sub-optimal systematic reviews. There are still some doubts about efficacy and safety of the COVID-19 vaccine in cancer patients.

Purpose

To identify, summarize and synthesize the available evidence of systematic reviews on response and COVID-19 vaccine safety in patients with cancer.

Methods

Multiple databases were searched from their inception to May 1, 2022 to fetch the relevant articles. Study quality was assessed by AMSTAR2. The protocol of this study was registered on PROSPERO (CRD42022327931).

Results

A total of 18 articles were finally included. The seroconversion rates after first dose were ranged from 37.30-54.20% in all cancers, 49.60-62.00% in solid cancers and 33.30-56.00% in hematological malignancies. The seroconversion rates after second dose were ranged from 65.30-87.70% in all cancers, 91.60-96.00% in solid cancers and 58.00-72.60% in hematological malignancies. Cancer types and types of therapy could influence vaccine response. COVID-19 vaccines were safe and well-tolerated.

Conclusions

This study suggests COVID-19 vaccine response is significantly lower in cancer patients. Number of received doses, cancer types and treatment strategies could influence response of COVID-19 vaccine in cancer patients. COVID-19 vaccines are safe and well-tolerated. Considering the emergence of several new variants of SARS-CoV-2 with potential influence on ongoing vaccination programs, there is a need for booster doses to increase the effectiveness of COVID-19 vaccines.

Systematic review registration

https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42022327931, identifier CRD42022327931.

A potent, broadly protective vaccine against SARS-CoV-2 variants of concern

Since the first outbreak in December 2019, SARS-CoV-2 has been constantly evolving and five variants have been classified as Variant of Concern (VOC) by the World Health Organization (WHO). These VOCs were found to enhance transmission and/or decrease neutralization capabilities of monoclonal antibodies and vaccine-induced antibodies. Here, we successfully designed and produced a recombinant COVID-19 vaccine in CHO cells at a high yield. The vaccine antigen contains four hot spot substitutions, K417N, E484K, N501Y and D614G, based on a prefusion-stabilized spike trimer of SARS-CoV-2 (S-6P) and formulated with an Alum/CpG 7909 dual adjuvant system. Results of immunogenicity studies showed that the variant vaccine elicited robust cross-neutralizing antibody responses against SARS-CoV-2 prototype (Wuhan) strain and all 5 VOCs. It further, stimulated a TH1 (T Helper type 1) cytokine profile and substantial CD4+ T cell responses in BALB/c mice and rhesus macaques were recorded. Protective efficacy of the vaccine candidate was evaluated in hamster and rhesus macaque models of SARS-CoV-2. In Golden Syrian hamsters challenged with Beta or Delta strains, the vaccine candidate reduced the viral loads in nasal turbinates and lung tissues, accompanied by significant weight gain and relieved inflammation in the lungs. In rhesus macaque challenged with prototype SARS-CoV-2, the vaccine candidate decreased viral shedding in throat, anal, blood swabs over time, reduced viral loads of bronchus and lung tissue, and effectively relieved the lung pathological inflammatory response. Together, our data demonstrated the broadly neutralizing activity and efficacy of the variant vaccine against both prototype and current VOCs of SARS-CoV-2, justifying further clinical development.

Review of preclinical data of PF-07304814 and its active metabolite derivatives against SARS-CoV-2 infection

Main protease (M^pro) is a superior target for anti-SARS-COV-2 drugs. PF-07304814 is a phosphate ester prodrug of PF-00835231 that is rapidly metabolized into the active metabolite PF-00835231 by alkaline phosphatase (ALP) and then suppresses SARS-CoV-2 replication by inhibiting M^pro. PF-07304814 increased the bioavailability of PF-00835231 by enhancing plasma protein binding (PPB). P-glycoprotein (P-gp) inhibitors and cytochrome P450 3A (CYP3A) inhibitors increased the efficacy of PF-00835231 by suppressing its efflux from target cells and metabolism, respectively. The life cycle of SARS-CoV-2 is approximately 4 h. The mechanisms and efficacy outcomes of PF-00835231 occur simultaneously. PF-00835231 can inhibit not only cell infection (such as Vero E6, 293T, Huh-7.5, HeLa^{+angiotensin-converting enzyme 2 (ACE2)}, A549^+ACE2, and MRC-5) but also the human respiratory epithelial organ model and animal model infection. PF-07304814 exhibits a short terminal elimination half-life and is cleared primarily through renal elimination. There were no significant adverse effects of PF-07304814 administration in rats. Therefore, PF-07304814 exhibits good tolerability, pharmacology, pharmacodynamics, pharmacokinetics, and safety in preclinical trials. However, the Phase 1 data of PF-07304814 were not released. The Phase 2/3 trial of PF-07304814 was also suspended. Interestingly, the antiviral activities of PF-00835231 derivatives (compounds 5–22) are higher than, similar to, or slightly weaker than those of PF-00835231. In particular, compound 22 exhibited the highest potency and had good safety and stability. However, the low solubility of compound 22 limits its clinical application. Prodrugs, nanotechnology and salt form drugs may solve this problem. In this review, we focus on the preclinical data of PF-07304814 and its active metabolite derivatives to hopefully provide knowledge for researchers to study SARS-CoV-2 infection.

Urine Metabolites Enable Fast Detection of COVID-19 Using Mass Spectrometry

The COVID-19 pandemic boosted the development of diagnostic tests to meet patient needs and provide accurate, sensitive, and fast disease detection. Despite rapid advancements, limitations related to turnaround time, varying performance metrics due to different sampling sites, illness duration, co-infections, and the need for particular reagents still exist. As an alternative diagnostic test, we present urine analysis through flow-injection-tandem mass spectrometry (FIA-MS/MS) as a powerful approach for COVID-19 diagnosis, targeting the detection of amino acids and acylcarnitines. We adapted a method that is widely used for newborn screening tests on dried blood for urine samples in order to detect metabolites related to COVID-19 infection. We analyzed samples from 246 volunteers with diagnostic confirmation via PCR. Urine samples were self-collected, diluted, and analyzed with a run time of 4 min. A Lasso statistical classifier was built using 75/25% data for training/validation sets and achieved high diagnostic performances: 97/90% sensitivity, 95/100% specificity, and 95/97.2% accuracy. Additionally, we predicted on two withheld sets composed of suspected hospitalized/symptomatic COVID-19-PCR negative patients and patients out of the optimal time-frame collection for PCR diagnosis, with promising results. Altogether, we show that the benchmarked FIA-MS/MS method is promising for COVID-19 screening and diagnosis, and is also potentially useful after the peak viral load has passed.

Relevant SARS-CoV-2 viremia is associated with COVID-19 severity: Prospective cohort study and validation cohort

Early kinetics of SARS-CoV-2 viral load (VL) in plasma determined by quantitative reverse-transcription polymerase chain reaction (RT-PCR) was evaluated as a predictor of poor clinical outcome in a prospective study and assessed in a retrospective validation cohort. Prospective observational single-center study including consecutive adult patients hospitalized with COVID-19 between November 2020 and January 2021. Serial plasma samples were obtained until discharge. Quantitative RT-PCR was performed to assess SARS-CoV-2 VL. The main outcomes were in-hospital mortality, admission to the Intensive Care Unit (ICU), and their combination (Poor Outcome). Relevant viremia (RV), established in the prospective study, was assessed in a retrospective cohort including hospitalized COVID-19 patients from April 2021 to May 2022, in which plasma samples were collected according to clinical criteria. Prospective cohort: 57 patients were included. RV was defined as at least a twofold increase in VL within ≤2 days or a VL > 300 copies/ml, in the first week. Patients with RV (N = 14; 24.6%) were more likely to die than those without RV (35.7% vs. 0%), needed ICU admission (57% vs. 0%) or had Poor Outcome (71.4% vs. 0%), (p < 0.001 for the three variables). Retrospective cohort: 326 patients were included, 18.7% presented RV. Patients with RV compared with patients without RV had higher rates of ICU-admission (odds ratio [OR]: 5.6 [95% confidence interval [CI]: 2.1-15.1); p = 0.001), mortality (OR: 13.5 [95% CI: 6.3-28.7]; p < 0.0001) and Poor Outcome (OR: 11.2 [95% CI: 5.8-22]; p < 0.0001). Relevant SARS-CoV-2 viremia in the first week of hospitalization was associated with higher in-hospital mortality, ICU admission, and Poor Outcome. Findings observed in the prospective cohort were confirmed in a larger validation cohort.

Extensive neutralization against SARS-CoV-2 variants elicited by Omicron-specific subunit vaccine as a heterologous booster

To overcome the increased risk of SARS-CoV-2 reinfection or post-vaccination infection caused by the Omicron variant, Omicron-specific vaccines were considered a potential strategy. We reported the increased magnitude and breadth of antibody response against VOCs elicited by post-vaccination Delta and Omicron infection, compared to WT infection without vaccination. Then, in mouse models, three doses of Omicron-RBD immunization elicited comparable neutralizing antibody (NAb) titers with three doses of WT-RBD immunization, but the neutralizing activity was not cross-active. By contrast, a heterologous Omicron-RBD booster following two doses of WT-RBD immunization increased the NAb titers against Omicron by 9-folds than the homologous WT-RBD booster. Moreover, it retains neutralization against both WT and current VOCs. Results suggest that Omicron-specific subunit booster shows its advantages in the immune protection from both WT and current VOCs and that SARS-CoV-2 vaccines including two or more virus lineages might improve the NAb response.

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Post-vaccination SARS-CoV-2 infection can elicit higher and boarder immune response

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A heterologous booster with the Omicron-RBD protein elicits a 9-fold increased NAb

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Heterologous boosting with Omicron enhance the potency and breadth of immune response

Therapeutic and palliative role of a Unani herbal decoction in COVID-19 and similar respiratory viral illnesses: Phytochemical & pharmacological perspective

ETHNOPHARMACOLOGICAL RELEVANCE

Outbreaks of respiratory viral infections like Severe Acute Respiratory Syndrome, Middle-East Respiratory Syndrome, and Coronavirus Disease-2019 have been a regular occurrence in the past 100 years. A significant proportion of the morbidity and mortality in influenza is attributed to the co-morbidities and complications induced by the disease, involving the vital organs and physiological functions. In this context, traditional medicines offer effective protective, palliative, and therapeutic benefits, as observed in several studies on various types of influenza, including COVID-19. The Unani herbal decoction comprising of 'Unnāb (Ziziphus jujuba Mill. fruit), Sapistān (Cordia dichotoma G. Forst. fruit), and Behīdāna (Cydonia oblonga Mill. seed) was originally prescribed by Hakim Ajmal Khan (1868-1927 AD) for various respiratory ailments as a bronchodilator, anti-inflammatory, and for clearing the respiratory tract. During COVID-19, the decoction was prescribed by the Ministry of Ayurveda, Yoga, Unani, Siddha, and Homeopathy (AYUSH), Government of India, for mild patients in home isolation, and also as a self-care drink for healthy people. Preliminary studies are of the view that the decoction could reduce COVID-19 incidence and prevent severe disease in the population where it was administered.

AIMS OF THE STUDY

We intend to review the pharmacological activity of the Unani decoction ingredients, i.e., Z. jujuba, C. dichotoma, and C. oblonga, in context with respiratory viral infections and their co-morbidities, to develop an understanding of its action mechanism.

METHODOLOGY

We reviewed Unani classical textbooks for information on the therapeutic activity of the decoction ingredients. Scientific studies published in English from the year 2000 onwards on leading scientific websites (PubMed, MEDLINE, Scopus, and Springer) were searched for information regarding the efficacy of the drugs in influenza and its common complications. Non-English language articles, or those published prior to 2000, and those which included plant parts other than those traditionally included in the decoction were excluded.

OBSERVATIONS

A wide range of therapeutic and palliative effects have been observed in the three herbs included in the Unani decoction, including anti-viral, anti-bacterial, immuno-modulatory, anti-inflammatory, hepato-, and nephroprotective, anti-atherosclerotic, anti-tussive, broncho-dilatory, and regulation of gut microbiota. Together, these effects can help to mitigate and prevent most of the complications caused as a result of respiratory viral infections.

CONCLUSION

The combined effects of ingredients in this Unani herbal decoction can potentially help to mitigate most of the pathological changes and complications caused by influenza viruses. With further clinical research, the decoction may be potentially utilized as a prophylactic and therapeutic against viral influenza.

An Exploration of Nanoparticle-Based Diagnostic Approaches for Coronaviruses: SARS-CoV-2, SARS-CoV and MERS-CoV

The wildfire-like spread of COVID-19, caused by severe acute respiratory syndrome-associated coronavirus-2, has resulted in a pandemic that has put unprecedented stress on the world's healthcare systems and caused varying severities of socio-economic damage. As there are no specific treatments to combat the virus, current approaches to overcome the crisis have mainly revolved around vaccination efforts, preventing human-to-human transmission through enforcement of lockdowns and repurposing of drugs. To efficiently facilitate the measures implemented by governments, rapid and accurate diagnosis of the disease is vital. Reverse-transcription polymerase chain reaction and computed tomography have been the standard procedures to diagnose and evaluate COVID-19. However, disadvantages, including the necessity of specialized equipment and trained personnel, the high financial cost of operation and the emergence of false negatives, have hindered their application in high-demand and resource-limited sites. Nanoparticle-based methods of diagnosis have been previously reported to provide precise results within short periods of time. Such methods have been studied in previous outbreaks of coronaviruses, including severe acute respiratory syndrome-associated coronavirus and middle east respiratory syndrome coronavirus. Given the need for rapid diagnostic techniques, this review discusses nanoparticle use in detecting the aforementioned coronaviruses and the recent severe acute respiratory syndrome-associated coronavirus-2 to highlight approaches that could potentially be used during the COVID-19 pandemic.

Tissue resident memory T cells- A new benchmark for the induction of vaccine-induced mucosal immunity

Historically, the gold-standard benchmark for vaccine immunogenicity has been the induction of neutralizing antibodies detectable in the serum of peripheral blood. However, in recent years there has been a new appreciation for the mucosa as an important site for vaccine induced immunity. As a point of first contact, the mucosal tissue represents a major site of immune based detection and restriction of pathogen entry and dissemination. Tissue resident memory T cells (Trm) are one of the critical cell types involved in this early detection and restriction of mucosal pathogens. Following tissue-specific infection or vaccination, Trm lodge themselves within tissues and can perform rapid sensing and alarm functions to control local re-infections, in an effort that has been defined as important for restriction of a number of respiratory pathogens including influenza and respiratory syncytial virus. Despite this characterized importance, only minor attention has been paid to the importance of Trm as a benchmark for vaccine immunogenicity. The purpose of this review is to highlight the functions of Trm with particular emphasis on respiratory infections, and to suggest the inclusion of Trm elicitation as a benchmark for vaccine immunogenicity in animal models, and where possible, human samples.

COVID-19, obesity, and immune response 2 years after the pandemic: A timeline of scientific advances

In the 2 years since the COVID-19 pandemic was officially declared, science has made considerable strides in understanding the disease's pathophysiology, pharmacological treatments, immune response, and vaccination, but there is still much room for further advances, especially in comprehending its relationship with obesity. Science has not yet described the mechanisms that explain how obesity is directly associated with a poor prognosis. This paper gathers all published studies over the past 2 years that have described immune response, obesity, and COVID-19, a historical and chronological record for researchers and the general public alike. In summary, these studies describe how the cytokine/adipokine levels and inflammatory markers, such as the C-reactive protein, are associated with a higher body mass index in COVID-19-positive patients, suggesting that the inflammatory background and immune dysregulation in individuals with obesity may be expressed in the results and that adiposity may influence the immune response. The timeline presented here is a compilation of the results of 2 years of scientific inquiry, describing how the science has progressed, the principal findings, and the challenges ahead regarding SARS-CoV-2, COVID-19, and emerging variants, especially in patients with obesity.

Computed Tomographic Imaging Features of COVID-19 Pneumonia Caused by the Delta (B.1.617.2) and Omicron (B.1.1.529) Variant in a German Nested Cohort Pilot Study Group

Background: The aim of this study was to evaluate CT (computed tomography) imaging differences for the Delta and the Omicron variant in COVID-19 infection. Methods: The study population was derived from a retrospective study cohort investigating chest CT imaging patterns in vaccinated and nonvaccinated COVID-19 patients. CT imaging patterns of COVID-19 infection were evaluated by qualitative and semiquantitative scoring systems, as well as imaging pattern analysis. Results: A total of 60 patients (70.00% male, 62.53 ± 17.3 years, Delta: 43 patients, Omicron: 17 patients) were included. Qualitative scoring systems showed a significant correlation with virus variants; “typical appearance” and “very high” degrees of suspicion were detected more often in patients with Delta (RSNA: p = 0.003; CO-RADS: p = 0.002; COV-RADS: p = 0.001). Semiquantitative assessment of lung changes revealed a significant association with virus variants in univariate (Delta: 6.3 ± 3.5; Omicron: 3.12 ± 3.2; p = 0.002) and multivariate analysis. The vacuolar sign was significantly associated with the Delta variant (OR: 14.74, 95% CI: [2.32; 2094.7], p = 0.017). Conclusion: The Delta variant had significantly more extensive lung involvement and showed changes classified as “typical” more often than the Omicron variant, while the Omicron variant was more likely associated with CT findings such as “absence of pulmonary changes”. A significant correlation between the Delta variant and the vacuolar sign was observed.

Humoral response and neutralising capacity at 6 months post-vaccination against COVID-19 among institutionalised older adults in Argentina

The COVID-19 pandemic has particularly affected older adults residing in nursing homes, resulting in high rates of hospitalisation and death. Here, we evaluated the longitudinal humoral response and neutralising capacity in plasma samples of volunteers vaccinated with different platforms (Sputnik V, BBIBP-CorV, and AZD1222). A cohort of 851 participants, mean age 83 (60-103 years), from the province of Buenos Aires, Argentina were included. Sequential plasma samples were taken at different time points after vaccination. After completing the vaccination schedule, infection-naïve volunteers who received either Sputnik V or AZD1222 exhibited significantly higher specific anti-Spike IgG titers than those who received BBIBP-CorV. Strong correlation between anti-Spike IgG titers and neutralising activity levels was evidenced at all times studied (rho=0.7 a 0.9). Previous exposure to SARS-CoV-2 and age <80 years were both associated with higher specific antibody levels. No differences in neutralising capacity were observed for the infection-naïve participants in either gender or age group. Similar to anti-Spike IgG titers, neutralising capacity decreased 3 to 9-fold at 6 months after initial vaccination for all platforms. Neutralising capacity against Omicron was between 10-58 fold lower compared to ancestral B.1 for all vaccine platforms at 21 days post dose 2 and 180 days post dose 1. This work provides evidence about the humoral response and neutralising capacity elicited by vaccination of a vulnerable elderly population. This data could be useful for pandemic management in defining public health policies, highlighting the need to apply reinforcements after a complete vaccination schedule.

The impact of CoronaVac on the neutralization breadth and magnitude of the antibody response to SARS-CoV-2 viruses

Although immune response enhancement has been reported after primary and booster vaccines of CoronaVac, neutralization breadth of SARS-CoV-2 variants is still unclear. In the present study, we examined the neutralization magnitude and breadth of SARS-CoV-2 variants including Beta (B.1.351), Delta (B.1.617.2) and Omicron (B.1.1.529) in 33 convalescent COVID-19 patients and a cohort of 55 medical staff receiving primary CoronaVac vaccines and an additional homologous booster dose. Results showed that, as compared with the two-dose primary vaccination, the homologous booster dose achieved 2.24-, 3.98-, 4.58- and 2.90-fold increase in neutralization titer against wild-type, Beta, Delta, and Omicron, respectively. After booster dose, neutralization titer reduction for variants was less than that after the primary vaccine or that for convalescents. The proportion of recipients able to neutralize 2 or more variants increased from 36.36% post the primary vaccination to 87.27% after the booster. Significant increase in neutralization breadth of 1.24 (95% confidence interval (CI), 0.89–1.59) variants was associated with a log₁₀ increase in neutralization titer against the wild-type. In addition, anti-RBD IgG level was identified as an excellent surrogate for positive neutralization of SARS-CoV-2 and neutralization breadth of variants. These findings highlight the value of an additional homologous CoronaVac dose in broadening the cross-neutralization against SARS-CoV-2 variants, and are critical for informing the booster dose vaccination efforts.

The Impact of Elexacaftor/Ivacaftor/Tezacaftor on Cystic Fibrosis Patients Who Acquire COVID-19 Infection

The combination of medication containing elexacaftor, ivacaftor, and tezacaftor (EIT) has dramatically impacted the treatment and prognosis for patients with cystic fibrosis (CF). Lung function, weight, and self-reported quality of life have improved for many of these patients, but little is known about whether this treatment will have a beneficial effect in preventing morbidity and/or mortality from respiratory infections such as COVID-19. EIT received Food and Drug Administration (FDA) approval shortly before the first cases of COVID-19 appeared in the United States. We performed an analysis using the TriNetX (Cambridge, MA, USA) research database to determine if patients being treated with EIT who became infected with COVID-19 experienced significantly different outcomes compared to patients who were not receiving it.

The Atmospheric Environment Effects of the COVID-19 Pandemic: A Metrological Study

Since the COVID-19 outbreak, the scientific community has been trying to clarify various problems, such as the mechanism of virus transmission, environmental impact, and socio-economic impact. The spread of COVID-19 in the atmospheric environment is variable and uncertain, potentially resulting in differences in air pollution. Many scholars are striving to explore the relationship between air quality, meteorological indicators, and COVID-19 to understand the interaction between COVID-19 and the atmospheric environment. In this study, we try to summarize COVID-19 studies related to the atmospheric environment by reviewing publications since January 2020. We used metrological methods to analyze many publications in Web of Science Core Collection. To clarify the current situation, hotspots, and development trends in the field. According to the study, COVID-19 research based on the atmospheric environment has attracted global attention. COVID-19 and air quality, meteorological factors affecting the spread of COVID-19, air pollution, and human health are the main topics. Environmental variables have a certain impact on the spread of SARS-CoV-2, and the prevalence of COVID-19 has improved the atmospheric environment to some extent. The findings of this study will aid scholars to understand the current situation in this field and provide guidance for future research.

Microbiological and Clinical Findings of SARS-CoV-2 Infection after 2 Years of Pandemic: From Lung to Gut Microbiota

Early recognition and prompt management are crucial for improving survival in COVID-19 patients, and after 2 years of the pandemic, many efforts have been made to obtain an early diagnosis. A key factor is the use of fast microbiological techniques, considering also that COVID-19 patients may show no peculiar signs and symptoms that may differentiate COVID-19 from other infective or non-infective diseases. These techniques were developed to promptly identify SARS-CoV-2 infection and to prevent viral spread and transmission. However, recent data about clinical, radiological and laboratory features of COVID-19 at time of hospitalization could help physicians in early suspicion of SARS-CoV-2 infection and distinguishing it from other etiologies. The knowledge of clinical features and microbiological techniques will be crucial in the next years when the endemic circulation of SARS-CoV-2 will be probably associated with clusters of infection. In this review we provide a state of the art about new advances in microbiological and clinical findings of SARS-CoV-2 infection in hospitalized patients with a focus on pulmonary and extrapulmonary characteristics, including the role of gut microbiota.

Exploring the mechanism of action of licorice in the treatment of COVID-19 through bioinformatics analysis and molecular dynamics simulation

Purpose: The rapid worldwide spread of Corona Virus Disease 2019 (COVID-19) has become not only a global challenge, but also a lack of effective clinical treatments. Studies have shown that licorice can significantly improve clinical symptoms such as fever, dry cough and shortness of breath in COVID-19 patients with no significant adverse effects. However, there is still a lack of in-depth analysis of the specific active ingredients of licorice in the treatment of COVID-19 and its mechanism of action. Therefore, we used molecular docking and molecular dynamics to explore the mechanism of action of licorice in the treatment of COVID-19.

Methods: We used bioinformatics to screen active pharmaceutical ingredients and potential targets, the disease-core gene target-drug network was established and molecular docking was used for verification. Molecular dynamics simulations were carried out to verify that active ingredients were stably combined with protein targets. The supercomputer platform was used to measure and analyze stability of protein targets at the residue level, solvent accessible surface area, number of hydrogen bonds, radius of gyration and binding free energy.

Results: Licorice had 255 gene targets, COVID-19 had 4,628 gene targets, the intersection gene targets were 101. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene ontology (GO) analysis showed that licorice played an important role mainly through the signaling pathways of inflammatory factors and oxidative stress. Molecular docking showed that Glycyrol, Phaseol and Glyasperin F in licorice may playe a role in treating COVID-19 by acting on STAT3, IL2RA, MMP1, and CXCL8. Molecular dynamics were used to demonstrate and analyze the binding stability of active ingredients to protein targets.

Conclusion: This study found that Phaseol in licorice may reduce inflammatory cell activation and inflammatory response by inhibiting the activation of CXCL8 and IL2RA; Glycyrol may regulate cell proliferation and survival by acting on STAT3. Glyasperin F may regulate cell growth by inhibiting the activation of MMP1, thus reducing tissue damage and cell death caused by excessive inflammatory response and promoting the growth of new tissues. Therefore, licorice is proposed as an effective candidate for the treatment of COVID-19 through STAT3, IL2RA, MMP1, and CXCL8.

Rapid and qualitative identification of SARS-CoV-2 mutations associated with variants of concern using a multiplex RT-PCR assay coupled with melting analysis

OBJECTIVES

Considering the spread of new genetic variants and their impact on public health, it is important to have assays that are able to rapidly detect SARS-CoV-2 variants.

METHODS

We retrospectively examined 118 positive nasopharyngeal swabs, first characterized by the Sanger sequencing, using the Simplexa® SARS-CoV-2 Variants Direct assay, with the aim of evaluating the performance of the assay to detect N501Y, G496S, Q498R, Y505H, E484K, E484Q, E484A, and L452R mutations.

RESULTS

A total of 111/118 nasopharyngeal swabs were in complete agreement with the Sanger sequencing, whereas the remaining seven samples were not amplified due to the low viral load. The evaluation of the ability of the assay to detect the E484Q mutation was performed using a viral isolate of the SARS-CoV-2 Kappa variant, showing concordance in 15/15 samples. Simplexa® SARS-CoV-2 Variant Direct assay was able to detect mutation pattern of Alpha, Beta, Gamma, Delta, and Omicron variants with 100% specificity and 94% sensitivity, whereas 100% sensitivity and specificity for the Kappa variant was observed.

CONCLUSION

The assay can be useful to obtain faster results, contributing to a prompt surveillance of SARS-CoV-2 variants; however, it requires to be confirmed by the Sanger method, especially in the case of pattern of mutations that are different from those expected and also requires updates as new variants emerge.

Protective Duration of ChAdOx1 and BNT162b2 Vaccines Against SARS-CoV-2 Infection

Background and Objective

A limited number of studies have addressed the protective duration of coronavirus disease 2019 (COVID-19) vaccines following primary and booster doses in Saudi Arabia. Therefore, this study aimed to evaluate the protective duration of primary and booster doses of BNT162b2 and ChAdOx1 COVID-19 vaccine batches in Saudi Arabia.

Methods

A cross-sectional study was conducted from 1 January to 31 December, 2021. The study included 53,354 people infected with severe acute respiratory syndrome coronavirus-2 2 weeks or more after receiving at least a primary vaccination of either the ChAdOx1 or BNT162b2 vaccine.

Results

The total median protective duration of both primary COVID-19 vaccinations was 134 days. Heterologous primary vaccination (ChAdOx1 followed by BNT162b2) showed a significantly higher median protective duration of 142 days. The results show that the total median protective duration of the first booster doses of COVID-19 vaccines was 57 days. ChAdOx1 batch code C1 was found to have the most extended protective duration of 173 days (range 163–192 days).

Conclusions

The current study revealed that the median protective duration of ChAdOx1 and BNT162b2 COVID-19 primary vaccination regimens administered in Saudi Arabia in 2021 was 134 days and that heterologous primary vaccination (ChAdOx1→BNT162b2) exhibited a significantly higher protective duration than other vaccination regimens.

The history, mechanism, and perspectives of nirmatrelvir (PF-07321332): an orally bioavailable main protease inhibitor used in combination with ritonavir to reduce COVID-19-related hospitalizations

The rapid development of effective vaccines to combat the SARS-CoV-2 virus has been an effective counter measure to decrease hospitalization and the mortality rate in many countries. However, with the risk of mutated strains decreasing the efficacy of the vaccine, there has been an increasing demand for antivirals to treat COVID-19. While antivirals, such as remdesivir, have had some success treating COVID-19 patients in hospital settings, there is a need for orally bioavailable, cost-effective antivirals that can be administered in outpatient settings to minimize COVID-19-related hospitalizations and death. Nirmatrelvir (PF-07321332) is an orally bioavailable M^pro (also called 3CL^pro) inhibitor developed by Pfizer. It is administered in combination with ritonavir, a potent CYP3A4 inhibitor that decreases the metabolism of nirmatrelvir. This review seeks to outline the history of the rational design, the target selectivity, synthesis, drug resistance, and future perspectives of nirmatrelvir.

Cerebral microvascular complications associated with SARS-CoV-2 infection: How did it occur and how should it be treated?

Cerebral microvascular disease has been reported as a central feature of the neurological disorders in patients with SARS-CoV-2 infection that may be associated with an increased risk of ischemic stroke. The main pathomechanism in the development of cerebrovascular injury due to SARS-CoV-2 infection can be a consequence of endothelial cell dysfunction as a structural part of the blood-brain barrier (BBB), which may be accompanied by increased inflammatory response and thrombocytopenia along with blood coagulation disorders. In this review, we described the properties of the BBB, the neurotropism behavior of SARS-CoV-2, and the possible mechanisms of damage to the CNS microvascular upon SARS-CoV-2 infection.

Dynamicity and persistence of severe acute respiratory syndrome coronavirus-2 antibody response after double dose and the third dose with BBV-152 and AZD1222 vaccines: A prospective, longitudinal cohort study

Introduction

Vaccines are available worldwide to combat coronavirus disease-19 (COVID-19). However, the long-term kinetics of the vaccine-induced antibodies against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) have not been sufficiently evaluated. This study was performed to investigate the persistence and dynamicity of BBV-152 (Covaxin)- and AZD1222 (Covishield)-induced immunoglobulin-G (IgG) antibodies over the year and neutralizing antibodies’ status after 1-month of booster dose.

Materials and methods

This 52-week longitudinal cohort study documented antibody persistence and neutralizing antibodies status among 304 healthcare workers (HCWs) from six hospitals and research facilities in Odisha, enrolled during January 2021 and continued till March 2022. IgG antibodies against spike receptor-binding domain (RBD) of SARS-CoV-2 were quantified in an automated chemiluminescence immune assay-based (CLIA) platform and a surrogate virus neutralization test (sVNT) was performed by enzyme-linked immunosorbent assay (ELISA).

Results

Among these 304 HCWs vaccinated with double doses, 154 HCWs (50.66%) were Covaxin recipients and the remaining 150 (49.34%) were Covishield recipients. During the follow-ups for seven times, a total of 114 participants were identified as vaccine breakthrough cases. In 190 non-infected HCWs, the median antibody titer was significantly waned from DD2 to DD10, both for Covaxin (231.8 vs. 42.7 AU/ml) and Covishield (1,884.6 vs. 369.2 AU/ml). No statistically significant differences in antibody titers were observed based on age, gender, comorbidities, and blood groups. The median inhibition activity of sVNT increased from 23.8 to 91.3% for Covaxin booster recipients and from 41.2 to 96.0% for Covishield booster recipients. Among 146 booster dose recipients, 48 were breakthrough cases after booster and all were contracted by the omicron variant.

Conclusion

This year-long follow-up study found a 7- and 5-fold antibody waning in Covaxin and Covishield recipients, respectively, without any breakthrough infection history. However, individuals with booster breakthrough had mild symptoms and did not require hospital admission. The data also indicate the possible escape of omicron variants despite the presence of vaccine-induced neutralizing antibodies.

Visual Detection of COVID-19 from Materials Aspect

ABSTRACT

In the recent COVID-19 pandemic, World Health Organization emphasized that early detection is an effective strategy to reduce the spread of SARS-CoV-2 viruses. Several diagnostic methods, such as reverse transcription-polymerase chain reaction (RT-PCR) and lateral flow immunoassay (LFIA), have been applied based on the mechanism of specific recognition and binding of the probes to viruses or viral antigens. Although the remarkable progress, these methods still suffer from inadequate cellular materials or errors in the detection and sampling procedure of nasopharyngeal/oropharyngeal swab collection. Therefore, developing accurate, ultrafast, and visualized detection calls for more advanced materials and technology urgently to fight against the epidemic. In this review, we first summarize the current methodologies for SARS-CoV-2 diagnosis. Then, recent representative examples are introduced based on various output signals (e.g., colorimetric, fluorometric, electronic, acoustic). Finally, we discuss the limitations of the methods and provide our perspectives on priorities for future test development.

Structural Evolution of Delta (B.1.617.2) and Omicron (BA.1) Spike Glycoproteins

The vast amount of epidemiologic and genomic data that were gathered as a global response to the COVID-19 pandemic that was caused by SARS-CoV-2 offer a unique opportunity to shed light on the structural evolution of coronaviruses and in particular on the spike (S) glycoprotein, which mediates virus entry into the host cell by binding to the human ACE2 receptor. Herein, we carry out an investigation into the dynamic properties of the S glycoprotein, focusing on the much more transmissible Delta and Omicron variants. Notwithstanding the great number of mutations that have accumulated, particularly in the Omicron S glycoprotein, our data clearly showed the conservation of some structural and dynamic elements, such as the global motion of the receptor binding domain (RBD). However, our studies also revealed structural and dynamic alterations that were concentrated in the aa 627–635 region, on a small region of the receptor binding motif (aa 483–485), and the so-called “fusion-peptide proximal region”. In particular, these last two S regions are known to be involved in the human receptor ACE2 recognition and membrane fusion. Our structural evidence, therefore, is likely involved in the observed different transmissibility of these S mutants. Finally, we highlighted the role of glycans in the increased RBD flexibility of the monomer in the up conformation of Omicron.