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| http://dx.doi.org/10.1128/jcm.00025-22 | DOI Listing |
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[Clinical Impact of Current Variants in COVID-19 Patients: Clinical Characteristics in Variant EG.5].
Mikrobiyol Bul
October 2024
University of Health Sciences, Ankara Bilkent City Health Application and Research Center, Clinic of Medical Microbiology, Ankara, Türkiye.
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) virus has mutated at a high rate since the beginning of the pandemic, leading to the formation of different variants. Alpha, Beta, Gamma, Delta and Omicron have emerged as concerning variants identified by the World Health Organization (WHO). The Omicron variant and its sublineages became dominant worldwide in 2022.
View Article and Find Full Text PDFUse of strips of rapid diagnostic tests as a source of ribonucleic acid for genomic surveillance of viruses: an example of SARS-CoV-2.
Virol J
August 2024
Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de Conakry, Conakry, Guinea.
Background: This study aimed to demonstrate that the genomic material of SARS-CoV-2 can be isolated from strips of COVID-19 rapid diagnostic test cassettes.
Method: It was a prospective cross-sectional study involving patients admitted to treatment centers and sampling sites in the city of Conakry, Guinea. A total of 121 patients were double sampled, and 9 more patients were tested only for RDT.
Unveiling the emergence of SARS-CoV-2 JN.1 sub-variant: Insights from the first cases at Charles Nicolle Hospital, Tunisia.
Acta Microbiol Immunol Hung
July 2024
1University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09, Tunis 1007, Tunisia.
The JN.1 sub-variant is a new variant of the SARS-CoV-2 Omicron strain, derived from the BA.2.
View Article and Find Full Text PDFEvaluation of Illumina® COVIDSeq™ as a tool for Omicron SARS-CoV-2 characterisation.
J Virol Methods
December 2023
The Queensland Paediatric Infectious Diseases (QPID) Sakzewski Laboratory, Queensland Children's Hospital, Brisbane, Queensland, Australia; The University of Queensland Centre for Clinical Research (UQCCR), Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia; Infectious Diseases Laboratory, Pathology Queensland, Brisbane, Queensland, Australia.
The continued emergence and transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants requires ongoing genetic surveillance to support public health responses. The expansion of reliable next generation sequence (NGS) platforms has enabled the rapid characterisation of the constant emergence of new SARS-CoV-2 variants using nasopharyngeal swab specimens. Several studies have assessed the ability of COVIDSeq to type earlier SARS-CoV-2 strains (pre-Delta) rapidly and successfully, however, there is limited data showing suitability against Omicron variants.
View Article and Find Full Text PDFIntensity of sample processing methods impacts wastewater SARS-CoV-2 whole genome amplicon sequencing outcomes.
Sci Total Environ
June 2023
Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA. Electronic address:
Wastewater SARS-CoV-2 surveillance has been deployed since the beginning of the COVID-19 pandemic to monitor the dynamics in virus burden in local communities. Genomic surveillance of SARS-CoV-2 in wastewater, particularly efforts aimed at whole genome sequencing for variant tracking and identification, are still challenging due to low target concentration, complex microbial and chemical background, and lack of robust nucleic acid recovery experimental procedures. The intrinsic sample limitations are inherent to wastewater and are thus unavoidable.
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