The clinical characteristics of pediatric patients infected by SARS-CoV-2 Omicron variant and whole viral genome sequencing analysis.

Pediatric population was generally less affected clinically by SARS-CoV-2 infection. Few pediatric cases of COVID-19 have been reported compared to those reported in infected adults. However, a rapid increase in the hospitalization rate of SARS-CoV-2 infected pediatric patients was observed during Omicron variant dominated COVID-19 outbreak. In this study, we analyzed the B.1.1.529 (Omicron) genome sequences collected from pediatric patients by whole viral genome amplicon sequencing using Illumina next generation sequencing platform, followed by phylogenetic analysis. The demographic, epidemiologic and clinical data of these pediatric patients are also reported in this study. Fever, cough, running nose, sore throat and vomiting were the more commonly reported symptoms in children infected by Omicron variant. A novel frameshift mutation was found in the ORF1b region (NSP12) of the genome of Omicron variant. Seven mutations were identified in the target regions of the WHO listed SARS-CoV-2 primers and probes. On protein level, eighty-three amino acid substitutions and fifteen amino acid deletions were identified. Our results indicate that asymptomatic infection and transmission among children infected by Omicron subvariants BA.2.2 and BA.2.10.1 are not common. Omicron may have different pathogenesis in pediatric population.

Targeted Sequencing Approach and Its Clinical Applications for the Molecular Diagnosis of Human Diseases.

The outbreak of COVID-19 has positively impacted the NGS market recently. Targeted sequencing (TS) has become an important routine technique in both clinical and research settings, with advantages including high confidence and accuracy, a reasonable turnaround time, relatively low cost, and fewer data burdens with the level of bioinformatics or computational demand. Since there are no clear consensus guidelines on the wide range of next-generation sequencing (NGS) platforms and techniques, there is a vital need for researchers and clinicians to develop efficient approaches, especially for the molecular diagnosis of diseases in the emergency of the disease and the global pandemic outbreak of COVID-19. In this review, we aim to summarize different methods of TS, demonstrate parameters for TS assay designs, illustrate different TS panels, discuss their limitations, and present the challenges of TS concerning their clinical application for the molecular diagnosis of human diseases.

An update on COVID-19 pandemic: the epidemiology, pathogenesis, prevention and treatment strategies.

INTRODUCTION: To date, the transmission of Coronavirus Disease-2019 (COVID-19) is still uncontrollable with the fact that the numbers of confirmed and death cases are still increasing. Up to 1st October 2020, 33,842,281 confirmed cases and 1,010,634 confirmed deaths have been reported to the World Health Organization from 216 different countries, areas and territories. Despite the urgent demand for effective treatment strategies, there is still no specific antiviral treatment for COVID-19 and the treatment guidelines for COVID-19 vary between countries. AREA COVERED: In this article, we summarized the current knowledge on COVID-19 and the pandemic worldwide. Moreover, the epidemiology, pathogenesis, prevention and different treatment options will be discussed so that we shall prepare ourselves better to fight with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). EXPERT OPINION: The situation of the COVID-19 pandemic is still unpredictable. There is no effective vaccine or specific anti-viral drug to treat serve COVID-19 patients. Combination therapies have shown promising clinical improvement. Repurposing FDA-approved drugs might be one of possible treatment options. Without specific treatment and vaccines for COVID-19, the most effective way to prevent from being infected is to generate an ecosystem with effective protection, precautions and preventive measures.

The diagnostic methods in the COVID-19 pandemic, today and in the future.

INTRODUCTION: The emergence of anovel coronavirus identified in patients with unknown cause of acute respiratory disease in Wuhan, China at the end of 2019 has caused aglobal outbreak. The causative coronavirus was later named as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the disease caused by SARS-CoV-2 was named as Coronavirus Disease-2019 (COVID-19). As of 10 August 2020, more than 19,718,030 confirmed cases and 728,013 deaths have been reported. COVID-19 is spread via respiratory droplets which are inhaled into the lungs. AREAS COVERED: In this article, we summarized the knowledge about the causative pathogen of COVID-19 and various diagnostic methods in this pandemic for better understanding of the limitations and the nuances of virus testing for COVID-19. EXPERT OPINION: In this pandemic, rapid and accurate identification of COVID-19 patients are critical to break the chain of infection in the community. RT-PCR provides a rapid and reliable identification of SARS-CoV-2 infection. In the future, molecular diagnostics will still be the gold standard and next-generation sequencing can help us to understand more on the pathogenesis and detect novel mutations. It is believed that more sophisticated detection methods will be introduced to detect SARS-CoV-2 as earliest as possible.