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.

The clinical application of metagenomic next-generation sequencing for detecting pathogens in bronchoalveolar lavage fluid: case reports and literature review.

INTRODUCTION: Clinical metagenomic next-generation sequencing (mNGS) allows a comprehensive genetic analysis of microbial materials. Different from other traditional target-driven molecular diagnostic tests, such as PCR, mNGS is a hypothesis-free diagnostic approach that allows a comprehensive genetic analysis of the clinical specimens that cover nearly any common, rare, and new pathogens ranging broadly from viruses, bacteria, fungi to parasites. AREAS COVERED: In this article, we discussed the clinical application of the mNGS using two clinical cases as examples and described the use of mNGS to assist the diagnosis of parasitic pulmonary infection. The advantages and challenges in implementing mNGS in clinical microbiology are also discussed. EXPERT OPINION: mNGS is a promising technology that allows quick diagnosis of infectious diseases. Currently, a plethora of sequencing and analysis methods exists for mNGS, each with individual merits and pitfalls. While standards and best practices were proposed by various metagenomics working groups, they are yet to be widely adopted in the community. The development of a consensus set of guidelines is necessary to guide the usage of this new technology and the interpretation of NGS results before clinical adoption of mNGS testing.

Whole genome amplicon sequencing and phylogenetic analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from lineage B.1.36.27 isolated in Hong Kong.

BACKGROUND: The import of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage B.1.36.27 has sparked the fourth wave of COVID-19 outbreak in Hong Kong. This strain has been circulating in Hong Kong since September 2020 but rarely found in other countries (<1%). RESEARCH DESIGN AND METHODS: A total of 14 SARS-CoV-2 genome sequences collected from patients in Hong Kong between July 2020 and March 2021 were determined by whole viral genome sequencing using Illumina next-generation sequencing platform, followed by phylogenetic analysis. RESULTS: Of the 14 SARS-CoV-2 genome sequences analyzed, 9 strains belonged to the PANGO lineage B.1.36.27, GISAID clade GH, and Nextclade clade 20A. Compared to the reference genome, 31 nucleotide differences and 11 amino acid differences were identified in the genome of the SARS-CoV-2 from PANGO lineage B.1.36.27. CONCLUSIONS: We reported the nucleotides and amino acids mutations identified in the SARS-CoV-2 from PANGO lineage B.1.36.27. Our viral genome sequences enriched the understanding of SARS-CoV-2 mutational landscape and improved the repertoire of known SARS-CoV-2 variants for tracking and tracing. From this study, we found no evidence to show that SARS-CoV-2 from lineage B.1.36.27 can compromise existing vaccines and antibody therapies.

Performance comparison of the Cobas® Liat® and Cepheid® GeneXpert® systems on SARS-CoV-2 detection in nasopharyngeal swab and posterior oropharyngeal saliva.

Background: Nucleic acid amplification tests (NAATs) based methods such as real-time reverse transcription polymerase-chain reaction (real-time RT-PCR) are the gold standard for diagnosis of current infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The cobas® Liat® and cepheid® GeneXpert® systems are two rapid real-time RT-PCR platforms offering rapid, specimen-to-answer detection of SARS-CoV-2.Research design and methods: In this study, we compared the performance of these two systems on SARS-CoV-2 detection in 9 nasopharyngeal swab (NPS) and 70 posterior oropharyngeal saliva specimens collected from 79 patients suspected of SARS-CoV-2 infection between August 2020 and March 2021.Results: The Positive Percent Agreement (PPA), Negative Percent Agreement (NPA) and overall Percent Agreement (OPA) between cepheid® Xpress SARS-CoV-2 assay and cobas® Liat® SARS-CoV-2 & Influenza A/B assay were found to be 100%. We demonstrated an excellent overall test concordance of the Liat® SARS-CoV-2 & Influenza A/B assay and Xpress SARS-CoV-2 assay. The small sample size of SARS-CoV-2 positive and weak-positive specimens is the inherent limitation of this study.Conclusions: The performance of the cobas® Liat® SARS-CoV-2 & Influenza A/B assay is equivalent to the cepheid® Xpress SARS-CoV-2 assay for SARS-CoV-2 detection using NPS and posterior oropharyngeal saliva.