Publications by authors named "Josh Quick"
Long-term severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in immunodeficient patients are an important source of variation for the virus but are understudied. Many case studies have been published which describe one or a small number of long-term infected individuals but no study has combined these sequences into a cohesive dataset. This work aims to rectify this and study the genomics of this patient group through a combination of literature searches as well as identifying new case series directly from the COVID-19 Genomics UK (COG-UK) dataset.
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- - This study analyzes 203 whole genome sequences of SARS-CoV-2 from Rwanda between May 2020 and February 2021, revealing a shift towards the A.23.1 sub-lineage, which is now the dominant strain.
- - The research also identified the first cases of the concerning B.1.1.7 and B.1.351 variants among travelers arriving at Kigali International Airport.
- - It emphasizes the significant role of neighboring countries in introducing new cases to Rwanda and calls for ongoing genomic surveillance and regional cooperation to effectively tackle COVID-19.
The response to the coronavirus disease 2019 (COVID-19) pandemic has been hampered by lack of an effective severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antiviral therapy. Here we report the use of remdesivir in a patient with COVID-19 and the prototypic genetic antibody deficiency X-linked agammaglobulinaemia (XLA). Despite evidence of complement activation and a robust T cell response, the patient developed persistent SARS-CoV-2 pneumonitis, without progressing to multi-organ involvement.
View Article and Find Full Text PDFAfter two decades of improvements, the current human reference genome (GRCh38) is the most accurate and complete vertebrate genome ever produced. However, no single chromosome has been finished end to end, and hundreds of unresolved gaps persist. Here we present a human genome assembly that surpasses the continuity of GRCh38, along with a gapless, telomere-to-telomere assembly of a human chromosome.
View Article and Find Full Text PDFCoronavirus disease 2019 (COVID-19) is caused by SARS-CoV-2 infection and was first reported in central China in December 2019. Extensive molecular surveillance in Guangdong, China's most populous province, during early 2020 resulted in 1,388 reported RNA-positive cases from 1.6 million tests.
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- Chikungunya virus (CHIKV) has spread across 51 countries in the Americas since its first detection in the Caribbean in 2013, with a notable outbreak in the Brazilian Amazon region, particularly in Boa Vista, Roraima state, from 2014 to 2018.
- Researchers identified 20 new genomes of the CHIKV-East-Central-South-America (ECSA) lineage, indicating that a major outbreak was likely caused by this lineage introduced from northeast Brazil, despite the earlier presence of the Asian genotype.
- The study suggests a significant infection rate in Roraima's population and emphasizes the importance of combining genomic sequencing and digital data to enhance public health surveillance and response to CHIKV
We report the sequencing and assembly of a reference genome for the human GM12878 Utah/Ceph cell line using the MinION (Oxford Nanopore Technologies) nanopore sequencer. 91.2 Gb of sequence data, representing ∼30× theoretical coverage, were produced.
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