An update on COVID-19: SARS-CoV-2 variants, antiviral drugs, and vaccines.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly contagious and pathogenic virus that first appeared in late December 2019. This SARS-CoV-2 causes an infection of an acute respiratory disease called "coronavirus infectious disease-2019 (COVID-19). The World Health Organization (WHO) declared this SARS-CoV-2 outbreak a great pandemic on March 11, 2020. As of January 31, 2023, SARS-CoV-2 recorded more than 67 million cases and over 6 million deaths. Recently, novel mutated variants of SARS-CoV are also creating a serious health concern worldwide, and the future novel variant is still mysterious. As infection cases of SARS-CoV-2 are increasing daily, scientists are trying to combat the disease using numerous antiviral drugs and vaccines against SARS-CoV-2. To our knowledge, this is the first comprehensive review that summarized the dynamic nature of SARS-CoV-2 transmission, SARS-CoV-2 variants (a variant of concern and variant of interest), antiviral drugs and vaccines utilized against SARS-CoV-2 at a glance. Hopefully, this review will enable the researcher to gain knowledge on SARS-CoV-2 variants and vaccines, which will also pave the way to identify efficient novel vaccines against forthcoming SARS-CoV-2 strains.

The Influence of Sex, Gender, and Age on COVID-19 Data in the Piedmont Region (Northwest Italy): The Virus Prefers Men.

Several important sex and gender differences in the clinical manifestation of diseases have been known for a long time but are still underestimated. The infectious Coronavirus 2019 disease pandemic has provided evidence of the importance of a sex and gender-based approach; it mainly affected men with worse symptomatology due to a different immune system, which is stronger in women, and to the Angiotensin-converting enzyme 2 and Transmembrane protease serine 2 roles which are differently expressed among the sexes. Additionally, women are more inclined to maintain social distance and smoke less. Analysis of data on the infectious Coronavirus 2019 disease testing from people admitted to the Amedeo di Savoia Hospital, a regional referral center for infectious diseases, has been applied to the whole of 2020 data (254,640 records). A high percentage of data in the dataset was not suitable due to a lack of information or entering errors. Among the suitable samples, records have been analyzed for positive/negative outcomes, matching records for unique subjects (N = 123,542), to evaluate individual recurrence of testing. Data are presented in age and sex-disaggregated ways. Analyses of the suitable sample also concerned the relation between testing and hospital admission motivation and symptoms. Our analysis indicated that a sex and gender-based approach is mandatory for patients and the National Health System's sustainability.

The role of respiratory microbiota in the protection against viral diseases: respiratory commensal bacteria as next-generation probiotics for COVID-19.

On March 11, 2020, the World Health Organization declared a pandemic of coronavirus infectious disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and imposed the biggest public health challenge for our civilization, with unforeseen impacts in the subsequent years. Similar to other respiratory infections, COVID-19 is associated with significant changes in the composition of the upper respiratory tract microbiome. Studies have pointed to a significant reduction of diversity and richness of the respiratory microbiota in COVID-19 patients. Furthermore, it has been suggested that Prevotella, Staphylococcus, and Streptococcus are associated with severe COVID-19 cases, while Dolosigranulum and Corynebacterium are significantly more abundant in asymptomatic subjects or with mild disease. These results have stimulated the search for new microorganisms from the respiratory microbiota with probiotic properties that could alleviate symptoms and even help in the fight against COVID-19. To date, the potential positive effects of probiotics in the context of SARS-CoV-2 infection and COVID-19 pandemics have been extrapolated from studies carried out with other viral pathogens, such as influenza virus and respiratory syncytial virus. However, scientific evidence has started to emerge demonstrating the capacity of immunomodulatory bacteria to beneficially influence the resistance against SARS-CoV-2 infection. Here we review the scientific knowledge regarding the role of the respiratory microbiota in viral infections in general and in the infection caused by SARS-CoV-2 in particular. In addition, the scientific work that supports the use of immunomodulatory probiotic microorganisms as beneficial tools to reduce the severity of respiratory viral infections is also reviewed. In particular, our recent studies that evaluated the role of immunomodulatory Dolosigranulum pigrum strains in the context of SARS-CoV-2 infection are highlighted.

The Predictive Value of Cell Blood Count Parameters to Diagnose Pulmonary Embolism in Patients with SARS-CoV-2 Infection: A Case Control Study.

Introduction: Acute pulmonary embolism (aPE) is frequently associated with coronavirus infectious disease-2019 (COVID-19) with an incidence of more than 16%. Among the new promising biomarkers of aPE, neutrophil-to-lymphocyte ratio (NLR) and platelet-to-lymphocyte ratio (PLR) showed correlations with aPE prognosis. The aim of this study was to conduct an exploratory analysis to check the possible role of cell blood count (CBC) parameters as diagnostic and prognostic biomarkers of aPE in COVID-19 patients. Materials and Methods: A case control study was conducted. Two populations were compared: (i) patients hospitalised from 31 January 2020 to 30 June 2021 with severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) infection and aPE confirmed at angio computed tomography (aCT) or pulmonary scintigraphy (COVID-19 aPE group); (ii) patients hospitalised from 31 January 2017 to 30 June 2021 without SARS-CoV-2 infection whose suspicion of aPE was excluded by aCT or pulmonary scintigraphy (no-aPE group). Results: Overall, 184 patients were included in the study, 83 in COVID-19 aPE group and 101 in no-aPE group. At the univariate analysis, COVID-19 patients with aPE had higher NLR, PLR, neutrophil and lymphocyte counts than patients without aPE (p < 0.05). No significant difference was found in mean platelet volume and platelet counts. No difference in mortality rate was detected. At the multivariate analysis, neutrophil and lymphocyte counts were both associated with diagnostic of aPE while no CBC parameters were associated with mortality at day#7. Conclusions: Neutrophiland lymphocyte counts could be predictors of the early detection of aPE in COVID-19 patients. The value of CBC indices as biomarkers of aPE in daily clinical practice needs to be investigated in further studies.

Ventilator-Associated Pneumonia in COVID-19 Patients: A Retrospective Cohort Study.

INTRODUCTION: Aim of this study is to analyse the characteristics of ventilator-associated pneumonia (VAP) inpatients infected by severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2). MATERIALS AND METHODS: A retrospective study was conducted, including coronavirus infectious disease 2019 (COVID-19) patients who developed VAP from March to May 2020 (VAP COVID-19). They were compared to non-COVID-19 patients who developed VAP from January 2011 to December 2019 (VAP NO COVID-19) and COVID-19 patients who did not develop VAP (NO VAP COVID-19). RESULTS: Overall, 42 patients were included in the VAP COVID-19group, 37 in the NO VAP COVID-19 group, and 188 in the VAP NO COVID-19 group. VAP COVID-19 had significantly higher rates of shock (71% vs. 48%, p = 0.009), death in ICU (52% vs. 30%, p = 0.011), VAP recurrence (28% vs. 4%, p < 0.0001), positive blood culture (26% vs. 13%, p = 0.038), and polymicrobial culture (28% vs. 13%, p = 0.011) than VAP NO COVID-19. At the multivariate analysis, death in patients with VAP was associated with shock (p = 0.032) and SARS-CoV-2 (p = 0.008) infection. CONCLUSIONS: VAP in COVID-19 patients is associated with shock, bloodstream, and polymicrobial infections.

Diagnostic performance of an automated chemiluminescence immunoassay for SARS-CoV-2 IgG and IgM antibodies detection: A real life experience.

BACKGROUND: Recently many serological assays for detection of antibodies to SARS-COV-2 virus were introduced on the market. Aim of this study was to assess the diagnostic performance of an automated CLIA for quantitative detection of anti-SARS-CoV-2 IgM and IgG antibodies. METHODS: A total of 354 sera, 89 from consecutive patients diagnosed with COVID-19 (43 mild, 32 severe and 13 critical) and 265 from asymptomatic and negative on rRT-PCR testing healthcare workers, were evaluated for IgM and IgG anti-SARS-CoV-2 antibodies with MAGLUMI immunoassay. RESULTS: The overall sensitivity and specificity were 86.5% (95%CI: 77.6-92.8) and 98.5% (95%CI:96.2-99.6), respectively. PPV, PPN, LR+, LR- and OR were 95.1 (95%CI: 87.8-98.6), 95.6 (95%CI: 92.4-97.7), 57.3 (95%CI: 21.6-152.1), 7.3 (95%CI: 4.31-12.4) and 418.6 (95%CI: 131.2-1335.2), respectively. The levels of SARS-CoV-2 IgM and IgG antibodies were 1.22 â€‹± â€‹1.2 AU/mL and 15.86 â€‹± â€‹24.83 AU/mL, 2.86 â€‹± â€‹2.4 AU/mL and 69.3 â€‹± â€‹55.5 AU/mL, 2.47 â€‹± â€‹1.33 AU/mL and 83.9 â€‹± â€‹83.9 AU/mL in mild, severe and critical COVID-19 groups, respectively. A significant difference in antibody levels between mild and severe/critical subjects has been shown. CONCLUSIONS: The CLIA assay showed good diagnostic performance and a significant association between antibody levels and severity of the disease was found.

How Do We Manage Hematopoietic Cell Transplant during the SARS-CoV-2 Pandemic?

Patients receiving a hematopoietic cell transplant are thought to be at increased risk of infection with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and coronavirus infectious disease 2019. Transplant activities at our center continue, and notably, no patient has been infected with SARS-CoV-2. Indeed, social distancing, masking, and education for patients and donors are major pillars of prevention. We recommend potential transplant recipients and donors to be tested for SARS-CoV-2 with qRT-PCR, serum antibody detection, and a lung CT scan pretransplant. If possible, stem cells from HLA-matched unrelated donors by local processing laboratories should be cryopreserved and shipped before initiating pretransplant conditioning. An alternative HLA-haplotype-matched related donor should be identified and evaluated as a backup. The interval immediately after discharge is the time of greatest risk for SARS-CoV-2 infection because of travel and exposure to infected persons. We recommend self-isolation and minimal contact with family members. Nonessential clinic visits should be deferred or substituted with telemedicine consultations if possible. These recommendations are based on our experience at a major transplant center in China. Although some recommendations are evidence based, other recommendations are not and warrant validation in controlled trials.

Detection of SARS-CoV-2 in wastewater in Japan during a COVID-19 outbreak.

The presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in wastewater samples has been documented in several countries. Wastewater-based epidemiology (WBE) is potentially effective for early warning of a COVID-19 outbreak. In this study, presence of SARS-CoV-2 RNA in wastewater samples was investigated and was compared with the number of the confirmed COVID-19 cases in the study area during COVID-19 outbreak in Japan. In total, 45 influent wastewater samples were collected from five wastewater treatment plants in Ishikawa and Toyama prefectures in Japan. During the study period, the numbers of confirmed COVID-19 cases in these prefectures increased from 0.3 and 0 to >20 per 100,000 people. SARS-CoV-2 ribonucleic acid (RNA) in the samples was detected using several PCR-based assays. Of the 45 samples, 21 were positive for SARS-CoV-2 according to at least one of the three quantitative RT-PCR assays. The detection frequency increased when the number of total confirmed SARS-CoV-2 cases in 100,000 people exceeded 10 in each prefecture; however, SARS-CoV-2 could also be detected at a low frequency even when the number was below 1.0. SARS-CoV-2 in wastewater could be detected in the early stage of the epidemic, even if the number of confirmed cases potentially underestimates the actual numbers of cases. This suggests that WBE approach can potentially act as an early warning of COVID-19 outbreaks in Japan.

The missing pieces in the jigsaw and need for cohesive research amidst coronavirus infectious disease 2019 global response.

Identifying the research needs and gaps amidst this COVID-19 travelling across the countries is absolutely important for finely improving on the way we think and act. The natural history of the disease as well as viral shedding in different stages of clinical illness needs to be known which helps in triaging the patients in hospital settings. Animal and environmental interface need to be studied for defining the high-risk situations. Transmission dynamics in community or hospital and defining the laboratory criteria for the case confirmation will be most crucial. Gene sequencing and validation and, suitable use of molecular based tests such as real-time polymerase chain reaction (qRT-PCR) should be clearly evaluated for diagnosis and/ or surveillance. The movement control strategy must be defined to prevent secondary transmission in healthcare as well as in community settings. Repurposing of drug molecules is an elegant strategy to develop therapeutics in the case of pandemics quickly. Unproven practices and treatment protocols should invite critical scrutiny on the basis of ethics. Socioeconomic status of the community is also an important determinant for the compliance and sustainable public health measures.

Infusion of HLA-matched and static magnetic field-exposed allogenic lymphocytes treating lymphocytopenia and cytokine storm syndrome: A treatment proposal for COVID-19 patients.

Among haematological parameters of patients seriously ill with the coronavirus infectious disease 2019 (COVID-19), leucocytosis, lymphocytopenia, and the abnormal release of circulating cytokines, termed cytokine storm syndrome (CSS, also known as cytokine release syndrome or CRS), were found associated with disease severity. In particular, according to the serum cytokine profiling, pro-inflammatory interleukin 6 (IL-6) and anti-inflammatory interleukin 10 (IL-10) were observed to be considerably higher in patients experiencing respiratory distress, septic shock and/or multi-organ failure, namely "critical cases" requiring intensive care unit (ICU) admission, very often resulting in death. Interestingly, the production of these cytokines from human lymphocytes was found to be modulated by exposure of 24 h to a 554.2-553.8 mT inhomogeneous static magnetic field (SMF), which elicits IL-10 and suppresses IL-6. Thus, herein, with the aim of restoring lymphocyte count and physiological serum levels of IL-6 and IL-10, the infusion of human leukocyte antigen (HLA)-matched and SMF-exposed allogenic lymphocytes is proposed for the first time as an easy and affordable treatment option for COVID-19 patients. Even if the count of lymphocytes in COVID-19 patients is very low, SMF exposure may be a valuable tool for reprogramming autologous lymphocytes towards physiological conditions. Furthermore, the same procedure could be extended to include the whole autologous or allogenic white blood cells (WBCs). Time-varying/pulsed magnetic fields exerting comparable cell effects could also be employed.

Time to Treat: Applying Lessons Learned from Other Viral Syndromes to SARS-CoV-2.

In many different infectious syndromes, most notably several viral conditions, time to therapy initiation from symptom onset has been identified as a critical component contributing to the success of therapy. Regarding COVID-19, several therapeutic antivirals, both repurposed and novel, have been evaluated for overall safety and efficacy. As the literature related to these therapies has expanded recently, a wide array of trial designs, time to therapy initiation thresholds, and clinical outcomes in regard to time to initiation have been reported. We describe the potential effects of time to therapy initiation on outcomes in patients with COVID-19 and detail the existing data surrounding this topic in relation to remdesivir, convalescent plasma, lopinavir/ritonavir, and hydroxychloroquine.

Proteomics Insights Into the Molecular Basis of SARS-CoV-2 Infection: What We Can Learn From the Human Olfactory Axis.

Like other RNA viruses, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replicates in host cells, continuously modulating the molecular environment. It encodes 28 multifunctional proteins that induce an imbalance in the metabolic and proteostatic homeostasis in infected cells. Recently, proteomic approaches have allowed the evaluation of the impact of SARS-CoV-2 infection in human cells. Here, we discuss the current use of proteomics in three major application areas: (i) virus-protein interactomics, (ii) differential proteotyping to map the virus-induced changes in different cell types, and (iii) diagnostic methods for coronavirus infectious disease 2019 (COVID-19). Since the nasal cavity is one of the entry sites for SARS-CoV-2, we will also discuss the potential application of olfactory proteomics to provide novel insights into the olfactory dysfunction triggered by SARS-CoV-2 in patients with COVID-19.

Haemoglobin A1c is a predictor of COVID-19 severity in patients with diabetes.

AIM: Poor outcomes of coronavirus disease 2019 (COVID-19) have been linked to diabetes, but its relation to pre-infection glycaemic control is still unclear. MATERIALS AND METHODS: To address this question, we report here the association between pre-infection Haemoglobin A1c (HbA1c) levels and COVID-19 severity as assessed by need for hospitalization in a cohort of 2068 patients with diabetes tested for COVID-19 in Leumit Health Services (LHSs), Israel, between 1 February and 30 April 2020. Using the LHS-integrated electronic medical records system, we were able to collect a large amount of clinical information including age, sex, socio-economic status, weight, height, body mass index, HbA1c, prior diagnosis of ischaemic heart disease, depression/anxiety, schizophrenia, dementia, hypertension, cerebrovascular accident, congestive heart failure, smoking, and chronic lung disease. RESULTS: Of the patients included in the cohort, 183 (8.85%) were diagnosed with COVID-19 and 46 were admitted to hospital. More hospitalized patients were female, came from higher socio-economic background and had a higher baseline HbA1c. A prior diagnosis of cerebrovascular accident and chronic lung disease conferred an increased risk of hospitalization but not obesity or smoking status. In a multivariate analysis, controlling for multiple prior clinical conditions, the only parameter associated with a significantly increased risk for hospitalization was HbA1c ≥ 9%. CONCLUSION: Using pre-infection glycaemic control data, we identify HbA1c as a clear predictor of COVID-19 severity. Pre-infection risk stratification is crucial to successfully manage this disease, efficiently allocate resources, and minimize the economic and social burden associated with an undiscriminating approach.

Expert Opinions on the Current Therapeutic Management of Inflammatory Bowel Disease during the COVID-19 Pandemic: Japan IBD COVID-19 Taskforce, Intractable Diseases, the Health and Labor Sciences Research.

BACKGROUND: The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has emerged as a dramatic challenge for all healthcare systems worldwide. This outbreak immediately affected gastroenterologists as well as global physicians worldwide because COVID-19 can be associated with not only triggering respiratory inflammation but also gastrointestinal (GI) inflammation based on the mechanism by which SARS-CoV-2 enters cells via its receptor the angiotensin-converting enzyme 2, which is expressed on GI cells. However, the comorbidity spectrum of digestive system in patients with COVID-19 remains unknown. Because the inflammatory bowel disease (IBD) management involves treating uncontrolled inflammation with immune-based therapies, physicians, and patients have great concern about whether IBD patients are more susceptible to SARS-CoV-2 infection and have worsened disease courses. SUMMARY: It is necessary to precisely ascertain the risk of SARS-CoV-2 infection and the COVID-19 severity in IBD patients and to acknowledge the IBD management during the COVID-19 pandemic with clinically reliable information from COVID-19 cohorts and IBD experts' opinions. In this review, we highlight clinical questions regarding IBD management during the COVID-19 pandemic and make comments corresponding to each question based on recent publications. Key Messages: We propose that there is (1) no evidence that IBD itself increases the risk of SARS-CoV-2 infection, (2) to basically prioritize the control of disease activity of IBD, (3) no need for physicians to suddenly discontinue immunomodulatory or biologic therapy in patients with quiescent IBD, and (4) a need for careful observation of elderly (>60 years old) and IBD patients receiving corticosteroid treatment during the COVID-19 pandemic.

Evaluation of Four Commercial Kits for SARS-CoV-2 Real-Time Reverse-Transcription Polymerase Chain Reaction Approved by Emergency-Use-Authorization in Korea.

SARS-CoV-2 real-time reverse-transcription PCR (rRT-PCR) is the most effective testing system currently available to counter COVID-19 epidemics when potent treatments and vaccines are unavailable. Therefore, four SARS-CoV-2 rRT-PCR kits have been approved by the emergency-use-authorization (EUA) without clinical validation in Korea until March 15, 2020. This study evaluated the analytical and clinical performance of these kits. Allplex 2019-nCoV Real-time PCR (Seegene, Seoul, Korea), PowerChek 2019-nCoV (KogeneBiotech, Seoul), Real-Q 2019-nCoV Real-Time Detection (BioSewoom, Seoul), and StandardM nCoV Detection (SD BIOSENSOR, Osong, Korea) were evaluated. The limit of detection (LODs) of Allplex, PowerChek, and Real-Q was determined by testing the transcribed RNA of SARS-CoV-2 E and the RNA of SARS-CoV Frankfurt1. A total of 27 consecutive samples comprising 13 sputum, 12 nasopharyngeal swab (NPS), 1 urine and 1 stool sample were collected from 2 COVID-19 patients for sensitivity analysis. Precision was assessed via daily tests of positive and negative controls in each kit for 5 d. Reproducibility was examined by repeating 21 samples and 10-fold dilutions of 14 samples in pairs using Allplex. Specificity was evaluated with 24 other respiratory virus-positive samples. LOD of Allplex, PowerChek, and Real-Q were 153.9, 84.1, and 80.6 copies/mL, respectively. The degrees of association between Cts and log viral concentrations by Allplex and PowerChek was expressed as y = -3.319 log (x) + 42.039 (R = 0.96) and y = -3.392 log(x) + 43.113 (R = 0.98), respectively. One or more of the 4 kits detected 20 out of 27 clinical samples positive. Of the 20 positive samples, the detection rates of positives for Allplex, PowerChek, Real-Q, and StandardM were 90.0, 82.3, 75.0, and 100.0%, respectively, but those of PowerChek and Real-Q would be 100% if out-of-cutoff Cts were counted as positives. Precision was 100%. Interpretation of Allplex results was reproducible when Ct of E ≤33. All 4 kits showed no cross-reactivity with other respiratory viruses. Performance of the 4 kits indicated the suitability of these for diagnosis and follow-up testing of COVID-19. Laboratory doctors who initially implement these EUA kits must be able to interpret quality control parameters.

The neurological significance of COVID-19: Lesson learn from the pandemic.

Coronavirus Infectious Disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; previously known as 2019 novel coronavirus) is an emerging and rapidly evolving health issue that has been widespread globally and become a pandemic. The typical symptoms of COVID-19 are: a cough, shortness of breath and a fever; from the initial estimates, about 15% of COVID-19 patients present with severe respiratory symptoms and requires hospitalization and intensive care. Recent accumulated evidences showed that the neurological insults also occurred in patients with COVID-19, ranging from mild headache to severe neurological symptoms. In this review, we summarize the COVID-19 and neurological significance of COVID-19.

Anti COVID-19 Drugs: Need for More Clinical Evidence and Global Action.

The World Health Organization (WHO) called the outbreak of coronavirus infectious disease-2019 (COVID-19) a "Public Health Emergency of International Concern" (PHEIC). According to the WHO, Centers for Disease Control and Prevention (CDC), and the US Food and Drug Administration (FDA), currently there are no medicines or vaccines that have been claimed to be useful in the prevention or treatment of COVID-19. Several existing antiviral drugs, previously developed or used as treatments for severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), human immunodeficiency virus (HIV), and malaria, are being investigated as COVID-19 treatments and some of them are being used in clinical trials. According to the CDC and Chinese treatment guidelines for COVID-19, chloroquine, hydroxychloroquine, lopinavir/ritonavir, and one of the investigational agents (remdesivir) are recommended in critically ill older patients. The use of other potential drugs reported in different studies may be considered if treatment with first-line drugs is ineffective. There are currently no complete data available from large randomized clinical trials (RCTs) to provide clinical guidance on the use, dosing, or duration to validate the effective role, safety profile, and adverse effects of all of the trial drugs for prophylaxis or treatment of COVID-19. Until now, it is still unclear which drug can successfully fight against the disease. Therefore, for the better safety of patients with COVID-19, further clinical trials and large randomized controlled studies are needed to validate the effective role, safety profile, and adverse effects of all the potential drugs. Such a measure requires action at the global level.