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

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.

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.

Graphical Abstract

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.

Recent Progress in the Discovery and Development of Monoclonal Antibodies against Viral Infections

Monoclonal antibodies (mAbs), the new revolutionary class of medications, are fast becoming tools against various diseases thanks to a unique structure and function that allow them to bind highly specific targets or receptors. These specialized proteins can be produced in large quantities via the hybridoma technique introduced in 1975 or by means of modern technologies. Additional methods have been developed to generate mAbs with new biological properties such as humanized, chimeric, or murine. The inclusion of mAbs in therapeutic regimens is a major medical advance and will hopefully lead to significant improvements in infectious disease management. Since the first therapeutic mAb, muromonab-CD3, was approved by the U.S. Food and Drug Administration (FDA) in 1986, the list of approved mAbs and their clinical indications and applications have been proliferating. New technologies have been developed to modify the structure of mAbs, thereby increasing efficacy and improving delivery routes. Gene delivery technologies, such as non-viral synthetic plasmid DNA and messenger RNA vectors (DMabs or mRNA-encoded mAbs), built to express tailored mAb genes, might help overcome some of the challenges of mAb therapy, including production restrictions, cold-chain storage, transportation requirements, and expensive manufacturing and distribution processes. This paper reviews some of the recent developments in mAb discovery against viral infections and illustrates how mAbs can help to combat viral diseases and outbreaks.

Alveolar macrophages: Achilles' heel of SARS-CoV-2 infection

The coronavirus disease 2019 (COVID-19) pandemic has caused more than 6.3 million deaths to date. Despite great efforts to curb the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), vaccines and neutralizing antibodies are in the gloom due to persistent viral mutations and antiviral compounds face challenges of specificity and safety. In addition, vaccines are unable to treat already-infected individuals, and antiviral drugs cannot be used prophylactically. Therefore, exploration of unconventional strategies to curb the current pandemic is highly urgent. Alveolar macrophages (AMs) residing on the surface of alveoli are the first immune cells that dispose of alveoli-invading viruses. Our findings demonstrate that M1 AMs have an acidic endosomal pH, thus favoring SARS-CoV-2 to leave endosomes and release into the cytosol where the virus initiates replication; in contrast, M2 AMs have an increased endosomal pH, which dampens the viral escape and facilitates delivery of the virus for lysosomal degradation. In this review, we propose that AMs are the Achilles’ heel of SARS-CoV-2 infection and that modulation of the endosomal pH of AMs has the potential to eliminate invaded SARS-CoV-2; the same strategy might also be suitable for other lethal respiratory viruses.

Neutralization Activity against SARS-CoV-2 Variants after Booster Vaccination in Populations without COVID-19: A Meta-Analysis

A number of SARS-CoV-2 variants that have evolved to have significant immune escape have emerged worldwide since the COVID-19 outbreak. The efficacy of prime vaccination is waning with the evolution of SARS-CoV-2, and the necessity of booster doses is more and more prominent. Therefore, this study aimed to compare the neutralization activity against the wild type and variants (Beta, Delta, and Omicron) in different prime-boost vaccination regimens. Electronic databases including PubMed, the Cochrane Library, Embase, medRxiv, Wanfang and CNKI were used to retrieve original studies. A total of 16 studies, 9 prime-boost vaccination regimes, and 3134 subjects were included in the meta-analysis and random effect models were used to estimate pooled neutralization titers. The neutralization activity against SARS-CoV-2 showed a significant decline with the evolution of the virus, especially in the populations primed with inactivated vaccines. For homologous immunization, only the populations boosted with mRNA vaccines consistently had a significant rise in neutralization titers (Beta: MD = 0.97; Delta: MD = 1.33; Omicron: MD = 0.74). While the heterologous immunization was more effective, the increment of neutralization titers against wild type, Beta, Delta and Omicron was 1.65 (95% CI: 1.32-1.96), 1.03 (95% CI: 0.53-1.54), 1.46 (95% CI: 1.07-1.85) and 1.15 (95% CI: 0.68-1.61), respectively. With the evolution of SARS-CoV-2, the effectiveness of prime immunization is waning. Although the administration of the booster dose could ameliorate the neutralization titers, homologous immunization regimens were gradually losing their effectiveness. Therefore, a heterologous booster dose is required, especially in populations primed with inactivated vaccines.

Repurposing the Antiplatelet Agent Ticlopidine to Counteract the Acute Phase of ER Stress Condition: An Opportunity for Fighting Coronavirus Infections and Cancer

Different pathological conditions, including viral infections and cancer, can have a massive impact on the endoplasmic reticulum (ER), causing severe damage to the cell and exacerbating the disease. In particular, coronavirus infections, including SARS coronavirus-2 (SARS-CoV-2), responsible for COVID-19, cause ER stress as a consequence of the enormous amounts of viral glycoproteins synthesized, the perturbation of ER homeostasis and the modification of ER membranes. Therefore, ER has a central role in the viral life cycle, thus representing one of the Achilles’ heels on which to focus therapeutic intervention. On the other hand, prolonged ER stress has been demonstrated to promote many pro-tumoral attributes in cancer cells, having a key role in tumor growth, metastasis and response to therapies. In this report, adopting a repurposing approach of approved drugs, we identified the antiplatelet agent ticlopidine as an interferent of the unfolded protein response (UPR) via sigma receptors (SRs) modulation. The promising results obtained suggest the potential use of ticlopidine to counteract ER stress induced by viral infections, such as COVID-19, and cancer.

Antiviral efficacy of selective estrogen receptor modulators against SARS-CoV-2 infection in vitro and in vivo reveals bazedoxifene acetate as an entry inhibitor

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the seventh member of the coronavirus family that can infect humans. Recently, more contagious and pathogenic variants of SARS-CoV-2 have been continuously emerging. Clinical candidates with high efficacy and ready availability are still in urgent need. To identify potent anti-SARS-CoV-2 repurposing drugs, we evaluated the antiviral efficacy of 18 selective estrogen receptor modulators (SERMs) against SARS-CoV-2 infection. Six SERMs exhibited excellent anti-SARS-CoV-2 effects in Vero E6 cells and three human cell lines. Clomifene citrate, tamoxifen, toremifene citrate, and bazedoxifene acetate reduced the weight loss of hamsters challenged with SARS-CoV-2, and reduced hamster pulmonary viral load and IL-6 expression when assayed at 4 days post-infection. In particular, bazedoxifene acetate was identified to act on the penetration stage of the post-attachment step via altering cholesterol distribution and endosome acidification. And, bazedoxifene acetate inhibited pseudoviruses infection of original SARS-CoV-2, Delta variant, Omicron variant and SARS-CoV. These results offer critical information supporting bazedoxifene acetate as a promising agent against coronaviruses. This article is protected by copyright. All rights reserved.

COVID-19: the possibility, ways, mechanisms, and interruptions of mother-to-child transmission

Background

In December 2019, novel coronavirus pneumonia was detected in Wuhan, Hubei Province, China, and as the epidemic spread, such cases emerged worldwide. Recently, the World Health Organization (WHO) named a new mutant Omicron (B.1.1.529), which disrupts the binding of most antibodies to the S protein and has a greater ability to break through the vaccine, posing a serious risk to population safety. Positive pregnant women give birth to positive newborns despite appropriate isolation measures taken by medical staff, suggesting that we may have vertical transmission of the novel coronavirus. This article analyzes and studies the possible vertical transmission path of the new coronavirus in the perinatal period of pregnant women and the antibody-dependent enhancement (ADE), and puts forward effective preventive measures for positive pregnant women to provide further reference for clinical work.

Methods

We searched multiple databases, including PubMed, CNKI, Google Scholar, WHO COVID-19 database, and CDC database. Search terms included COVID-19, SARS-CoV-2, vertical transmission, Omicron, Vaginal, Breast Feeding, Vaccine, Neonatal, Severe acute respiratory syndrome coronavirus, Pregnancy, and Semen.

Selection criteria

The following criteria were also met: (1) positive maternal novel coronavirus nucleic acid test; (2) reporting of neonatal outcome; (3) language in Chinese or English; (4) study date or location indicated; (5) no suspected or confirmed duplicated reports.

Results

There is evidence of vertical transmission, and the risk of possible vertical transmission is 5.7% (75/1314). The article listed four possible vertical transmission routes, namely placental transmission, vaginal upstream transmission, breastfeeding transmission and monocyte, and macrophage transmission route, with placental transmission being the most probable. Meanwhile, SARS-CoV-2 may also enter the placenta to infect the fetus through antibody-dependent enhanced substitution mechanism. We recommend three methods for early surveillance of vertical transmission, namely nucleic acid testing, antibody screening, and antigen testing, and analyze their advantages and disadvantages. Finally, the article provides recommendations in four areas: labor management, neonatal management, nosocomial infection prevention and control, and vaccination. As well as suggesting effective preventive measures for positive pregnant women and analyzing the advantages and disadvantages of vaccination, it is recommended that pregnant women should be vaccinated promptly, but considering that the vaccine may cause fever, it is recommended to consider vaccination cautiously in the first trimester of pregnancy.

Conclusion

The article concludes that vertical transmission is possible, with placental transmission being the most likely, and that the risk of possible vertical transmission is 5.7% (75/1314). Good personal protection, patient isolation, ward disinfection, and vaccination are the best means of interrupting SARS-CoV-2.

Development of Flat Warts on the Cheeks after BioNTech-Pfizer BNT162b2 Vaccine: Is There a Correlation?

The SARS-CoV-2 pandemic has affected health systems across the globe, making the use of vaccines more urgent and topical than ever. Since the first months after the introduction of vaccinations, several reactions, both local and systemic, have been reported although they were mostly very mild and only rarely harbingers of more serious complications. We present a case of multiple flat warts onset over the cheeks in a patient after the second dose of mRNA BioNTech-Pfizer BNT162b2 vaccine, and we discuss the possible temporal association between the two events, also considering the patient's antibody status.

A Rapid and Consistent Method to Identify Four SARS-CoV-2 Variants during the First Half of 2021 by RT-PCR

Since 2020, the COVID-19 pandemic has spread worldwide, causing health, economic, and social distress. Containment strategies rely on rapid and consistent methodology for molecular detection and characterization. Emerging variants of concern (VOCs) are currently associated with increased infectivity and immune escape (natural defence mechanisms and vaccine). Several VOCs have been detected, including Alpha variant (B.1.1.7), Beta variant (B.1.351), Gamma variant (P.1/B.1.1.28.1) and Delta variant (B.1.617.2), first identified in the UK, South Africa, Brazil and India, respectively. Here, a rapid and low-cost technique was validated to distinguish the Alpha, Beta, Gamma, and Delta SARS-CoV-2 variants by detecting spike gene mutations using a real-time reverse transcription polymerase chain reaction methodology (RT-PCR). A total of 132 positive patients affected by coronavirus disease-19 (COVID-19) were analysed by employing RT-PCR to target single-nucleotide polymorphisms (SNPs) to screen spike protein mutations. All data were validated by the next-generation sequencing (NGS) methodology and using sequences from a public database. Among 132 COVID-19-positive samples, we were able to discriminate all of the investigated SARS-CoV-2 variants with 100% concordance when compared with the NGS method. RT-PCR -based assays for identifying circulating VOCs of SARS-CoV-2 resulted in a rapid method used to identify specific SARS-CoV-2 variants, allowing for a better survey of the spread of the virus and its transmissibility in the pandemic phase.