Virological, epidemiological features and prevention of SARS-CoV-2 Omicron (B.1.1.529) variant: a review

The emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant Omicron (B.1.1.529) has been a cause for serious concern worldwide due to its high rate of transmission and number of mutations. During genomic studies in South Africa and Botswana in November 2021, a new variant of SARS-CoV-2 was identified associated with a rapid resurgence of infections in Gauteng Province, South Africa. Omicron variant was identified as a type of concern by the World Health Organization after sequence uploads of the first genome. It was subsequently identified in 87 countries within three weeks. The Omicron variant is a very exceptional virus carrying more than 30 mutations in the spike glycoprotein that are predicted to affect antibody neutralization and spike function. Omicron is highly contagious and spreads faster than previous variants, but may cause less severe symptoms than previous variants. Omicron variant can evade the immune system. It can also evade the vaccine responses developed against COVID-19. Rapid and careful preventive steps, including vaccination, will always be a key for suppression of the Omicron variant. This review summarizes the highly mutated regions, core infectiousness, vaccine elimination, and antibody resistance of the Omicron variant of SARSCoV-2.

Comparison of immunogenicity for Sinovac-CoronaVac vaccine vs. natural infection during cancer treatment.

OBJECTIVE: Efficacy of the COVID-19 vaccines in cancer patients, especially during their active treatment, are lacking. Most of the studies in the literature compared the immunity in cancer patients with a cross-sectional cohort or retrospectively. Our study investigated Sinovac-CoronaVac COVID-19 vaccine immunogenicity and compared it with natural COVID-19 disease in cancer patients during their cancer therapy. PATIENTS AND METHODS: A total of 111 patients with cancer and who are on active treatment were included in the study. This is a single-center study and was designed prospectively. Two group of patients were included in the study, natural disease and vaccinated group. RESULTS: A total of 111 patients were included in the study, 34 of whom had natural COVID-19 disease. Antibody levels following the first dose vaccine were 0.4 (0-1.9) U/ml while after the second dose of vaccine were 2.6 (1.0-7.25) U/ml. Immunogenicity levels were 82.4% in the natural disease group and 75.8% in the vaccinated group after the second shot of the vaccine. Immunogenicity rate was significantly higher in non-chemotherapy (receiving immunotehrapy/targeted therapy or biologic agent) group compared to chemotherapy drug (92.9% vs. 63.3%, p=0.004). There was a difference between the antibody levels following the first and second vaccination [median (IQR): 0.3 (0-1.0) and 3.3 (2.0-6.7), p=0.001, respectively]. CONCLUSIONS: The present study revealed that the Sinovac-CoronaVac vaccine showed an acceptable immunogenicity following two shots in cancer patients who were receiving active systemic therapy. On the other hand, natural disease immunogenicity was higher than vaccinated group.

Surveillance of SARS CoV-2 and other respiratory viruses in 2020-2021 winter season

Aim: The global COVID-19 pandemic and new variants continue to seriously threaten society. In this study;It was aimed to investigate surveillance of SARS CoV-2 and other respiratory viruses in respiratory tract samples in the winter season of 2020-2021 in Sakarya province. Material and Method: The study was carried out at Sakarya Training and Research Hospital between 2020-2021. e study was carried out with respiratory tract samples (Nasopharyngeal swab) stored in the laboratory. Clinical samples included in study were stored in a Bio-SpeedyRvNATRtransfer tube (Bioeksen,Turkey) and no extraction was performed in accordance with manufacturer's instructions. All analyzes were recorded on BIO-RAD CFX-96C1000 Touch Real-time system device using Diagnovital influenza A/B, SARS CoV-2, RSV multiplex Real Time PCR amplification kit. Results: Of the 200 patients diagnosed with URTI/LRTI, 54.5% were male and 45.5% female. e most common clinical symptoms;sore throat 74%, cough 73.5%, fatigue 71%, fever 57%, runny nose 56%, headache 48.5%, sneezing 41.5%, loss of smell / taste 39.5%, diarrhea 36%, dyspnea was 31.5% and myalgia was 23.5%. PCR positivity rates of samples were analyzed as 28.5% for SARS COV-2 and 1.5% for RSV, respectively. PCR positivity for influenza A/B was not defined in the study. Considering the statistical significance between PCR results and COVID-19 symptoms in patients;symptoms of dyspnea (n=63), fever(n= 62) and sneezing(n=56), respectively, were statistically significant(p<0.05). Conclusion: Due to the circumstances, only three main viral agents could be investigated in the study. RSV was frequently identified as an important factor in pediatric patients, whereas influenza-which may be related to social and individual measures (mask,distance,hygiene)- was not detected in any sample. More comprehensive scientific studies are needed to support the data.

Acute Serious Hepatitis of Unknown Cause in Children

On April 5, 2022, an increase in cases of acute hepatitis of unknown etiology was reported in previously healthy children under the age of 10 in the United Kingdom. Since there is no link between these patients, called acute non-HepA-E hepatitis, and viral hepatitis agents (hepatitis A, B, C, D, and E), the possible etiology, and pathogenesis of this emergency is being investigated. One of the alarming features of this epidemic is the high requirement for liver transplantation in a fraction of the cases. In cases other than hepatitis A, B, C, D, and E, a case definition is made by looking at a series of clinical pictures, including serum transaminase levels and age. As of August 26, 2022, 513 cases of acute hepatitis have been reported in Europe and 1,010 globally. Adenovirus was detected in 75% of cases tested in the UK, but data for other countries are still lacking. The role of other etiologic agents is still under investigation. The exact disease pathogenesis has not yet clear. Evidence of human-to-human transmission of the disease remains unclear. Epidemiological studies are critical in clarifying the uncertainties regarding the existence of links between the cases reported to date. Continuing the national and international surveillance activities of the countries in an organized manner is the most basic issue required for the elimination of the epidemic. Copyright © 2022 Tehran University of Medical Sciences.

Overview of sequence analysis methods in COVID-19 infections

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) was identified as the agent of COVID-19, and genomic data was first shared by China on January 10, 2020. Since then, tremendous effort has been devoted to sequencing the viral genome from samples collected around the world. In the recent past, next-generation sequencing (NGS) strategies have been used successfully to trace the origins, understand the evolution of infectious agents, to investigate the chains of the spread of epidemics, to facilitate the development of effective and rapid molecular diagnostic tests, and to contribute to the research of treatments and vaccines. Recent advances in technology and science have allowed the genomes of SARS-CoV-2, the agent of COVID-19, to be sequenced within hours or days after a case is identified. In this way, for the first time, the public health and epidemic size of a pandemic can be monitored in real-time. The early sharing of SARS-CoV-2 genome sequences has allowed the rapid development of molecular diagnostic tests, contributing to global preparedness and the design of countermeasures. Rapid, large-scale sequencing of the virus genome is essential in understanding the dynamics of viral outbreaks and assessing the effectiveness of control measures. SARS-CoV-2 gene sequencing can be used in many different areas, including improved diagnosis, development of countermeasures, and investigation of disease epidemiology. The development of effective and rapid sequencing methods to fully identify the genomic sequence of the etiologic agent of COVID-19 has been fundamental to the design of diagnostic molecular tests and the determination of effective measures and strategies to reduce the spread of the pandemic. Different approaches and sequencing methods can be applied to SARS-CoV-2 genomes, as evidenced by the number of sequences available. However, each technology and sequencing approach has its advantages and limitations. In this review, current platforms and methodological approaches for sequencing SARS-CoV-2 genomes will be discussed.

Oral symptoms in COVID-19 disease

SARS Cov-2 virus has spread rapidly all over the world, and since March 2020, it has been declared a worldwide pandemic by the World Health Organization (WHO). The general symptoms of COVID-19 are fever, fatigue, cough, myalgia, dyspnea, headache, sore throat and pneumonia. The most common oral symptom in COVID-19 is taste disorders, which is seen in 45% of patents. In addition, various oral mucosal lesions such as herpetiform and aphthous-like lesions, candidiasis and Kawasak-like lesions can be observed in patents. The purpose of this revew study is to examine the mouth findings seen in COVID-19 disease.

Update on the First Year of COVID-19

The current outbreak of the Coronavirus, severe acute respiratory syndrome Coronavirus-2, which originated in the Wuhan province of the People's Republic of China became a pandemic. Although the clinical findings of the infection vary in adults, the most common symptoms are fever, dry cough, and shortness of breath. The diagnosis of the Coronavirus disease-2019 (COVID-19) is made by clinical symptoms, laboratory tests, and radiological methods. Many drugs such as antivirals, antibiotics, and corticosteroids are used in the treatment of COVID-19. For the successful control of the pandemic, prevention strategies are the key. There is strong consensus that, in addition to wearing masks, hand hygiene, and social distancing, an effective COVID-19 vaccine is probably the most effective approach to sustainably control the pandemic. In this article, current information about the pathogenesis, epidemiology, risk groups, diagnosis, treatment, prevention strategies, and vaccination of the disease in the first year of the COVID-19 pandemic are discussed.

Saliva in the diagnosis of COVID-19

The use of saliva samples for the diagnosis of severe acute respiratory syndrome-Coronavirus-2 (SARS-CoV-2) provides several advantages over the use of nasopharyngeal (NP) swabs, such as comfort, ease of self-collection, less use of personal protective equipment, and protection of healthcare personnel from transmission. This review included current studies using saliva samples for the detection of SARS-CoV-2, comparing its sensitivity, cycle threshold, and specificity with those of NP swab. In the literature, the sensitivity rates of saliva samples in the diagnosis of SARS-CoV-2 ranged from 70% to 98%. Despite different opinions, we concluded that saliva is a reliable sample for the detection of SARS-CoV-2. However, studies with large samples and comparing different diagnostic methods are needed to reach precise and reliable results and include saliva collection in diagnostic guidelines.

COVID-19 prevalence and oncologic outcomes of asymptomatic patients with active cancer who received chemotherapy

Introduction: The outbreak of the new coronavirus disease 2019 (COVID-19) has become the most significant global health threat in the World. We do not have well-established guidelines for cancer patients. We aimed to clarify chemotherapy's oncologic outcomes in patients with active cancer and asymptomatic COVDI 19 disease. Material and methods: This study is single-center research and designed prospectively. Only patients who were receiving intravenous systemic chemotherapy were selected and tested for COVID19 Results: During the peak period of the COVID-19 pandemic for Turkey, we started the study and analyzed 198 patients. Eighty (40%) patients were male, and 118 (60%) patients were female. Following the analysis, there was no nasal and pharyngeal swab specimen PCR positive patient, but 7 (3.5%) of 199 patients had blood antibody test positive and received their regular chemotehrapies. No patient died during the 90 days follow up. Conclusions: Even though we cannot generalize, emergent chemotherapies can administered to the COVID-19 patients if the patient did not have any symptoms for COVID-19. © 2021 A. CARBONE Editore. All rights reserved.