Proficiency testing for SARS-CoV-2 whole genome sequencing

Article Multidisciplinary Sciences

AusTrakka: Fast-tracking nationalized genomics surveillance in response to the COVID-19 pandemic

Tuyet Hoang et al.

Summary: The COVID-19 pandemic has driven the development of Australia's pathogen genomics platform AusTrakka, enabling rapid data sharing and real-time genomic surveillance.

NATURE COMMUNICATIONS (2022)

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Article Multidisciplinary Sciences

Clinical and whole genome characterization of SARS-CoV-2 in India

Radhakrishna Muttineni et al.

Summary: The study reported the clinical profiles of 109 patients with SARS-CoV-2 infection and the whole genome sequences of 7 virus isolates, indicating the associations between disease severity and comorbidities, blood cell counts, and biochemical indicators. The research also suggested possible transmission pathways of the virus from the Middle East and Europe.

PLOS ONE (2021)

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Article Multidisciplinary Sciences

Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan

Massab Umair et al.

Summary: This study reports the sequencing, genomic characterization, and phylogenetic analysis of five SARS-CoV-2 strains isolated from patients in Pakistan, revealing the presence of GH and S clade strains and the G614 variant. There were 29 amino acid mutations detected, including 15 missense and 4 novel mutations, with the D614G mutation in spike protein identified as a key mutation affecting virus infectivity.

PLOS ONE (2021)

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Article Medicine, General & Internal

Surveillance for SARS-CoV-2 variants of concern in the Australian context

Patiyan Andersson et al.

MEDICAL JOURNAL OF AUSTRALIA (2021)

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Article Virology

Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool

Aine O'Toole et al.

Summary: The global virus genomics community has responded unprecedentedly to the SARS-CoV-2 pandemic, leading to significant advances in 'real-time' generation and sharing of genomic data. The development of new analytical methods, such as pangolin, has been necessary to handle the rapid growth in virus genome data production. Pangolin has processed nearly two million virus genomes, aiding in SARS-CoV-2 genomic epidemiology and providing researchers with valuable information about the pandemic's transmission lineages.

VIRUS EVOLUTION (2021)

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Article Multidisciplinary Sciences

A benchmarking study of SARS-CoV-2 whole-genome sequencing protocols using COVID-19 patient samples

Tiantian Liu et al.

Summary: The research compared seven different SARS-CoV-2 WGS library protocols and found significant differences in mappability, genome coverage, sensitivity, reproducibility, and precision, with certain protocols requiring important trimming steps for accurate variant calling. The study results provide guidance for choosing appropriate WGS protocols to study SARS-CoV-2 and its evolution.

ISCIENCE (2021)

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Article Infectious Diseases