Next generation sequencing and bioinformatics methodologies for infectious disease research and public health: approaches, applications, and considerations for …
I Maljkovic Berry, MC Melendrez… - The Journal of …, 2020 - academic.oup.com
Next generation sequencing (NGS) combined with bioinformatics has successfully been
used in a vast array of analyses for infectious disease research of public health relevance …
used in a vast array of analyses for infectious disease research of public health relevance …
The microbial ecology of Escherichia coli in the vertebrate gut
E Foster-Nyarko, MJ Pallen - FEMS microbiology reviews, 2022 - academic.oup.com
Escherichia coli has a rich history as biology's 'rock star', driving advances across many
fields. In the wild, E. coli resides innocuously in the gut of humans and animals but is also a …
fields. In the wild, E. coli resides innocuously in the gut of humans and animals but is also a …
Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis
Viral whole-genome sequencing (WGS) provides critical insight into the transmission and
evolution of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Long-read …
evolution of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Long-read …
Patterns of within-host genetic diversity in SARS-CoV-2
Monitoring the spread of SARS-CoV-2 and reconstructing transmission chains has become
a major public health focus for many governments around the world. The modest mutation …
a major public health focus for many governments around the world. The modest mutation …
A highly virulent variant of HIV-1 circulating in the Netherlands
We discovered a highly virulent variant of subtype-B HIV-1 in the Netherlands. One hundred
nine individuals with this variant had a 0.54 to 0.74 log10 increase (ie, a~ 3.5-fold to 5.5-fold …
nine individuals with this variant had a 0.54 to 0.74 log10 increase (ie, a~ 3.5-fold to 5.5-fold …
Limited emergence of resistance to integrase strand transfer inhibitors (INSTIs) in ART-experienced participants failing dolutegravir-based antiretroviral therapy: A …
A Abdullahi, IM Kida, UA Maina… - Journal of …, 2023 - academic.oup.com
Background Due to the high prevalence of resistance to NNRTI-based ART since 2018,
consolidated recommendations from the WHO have indicated dolutegravir as the preferred …
consolidated recommendations from the WHO have indicated dolutegravir as the preferred …
Human cytomegalovirus haplotype reconstruction reveals high diversity due to superinfection and evidence of within-host recombination
J Cudini, S Roy, CJ Houldcroft… - Proceedings of the …, 2019 - National Acad Sciences
Recent sequencing efforts have led to estimates of human cytomegalovirus (HCMV)
genome-wide intrahost diversity that rival those of persistent RNA viruses [Renzette N …
genome-wide intrahost diversity that rival those of persistent RNA viruses [Renzette N …
Pneumococcal within-host diversity during colonization, transmission and treatment
Characterizing the genetic diversity of pathogens within the host promises to greatly improve
surveillance and reconstruction of transmission chains. For bacteria, it also informs our …
surveillance and reconstruction of transmission chains. For bacteria, it also informs our …
Reassessing the ethics of molecular HIV surveillance in the era of cluster detection and response: Toward HIV data justice
S Molldrem, AKJ Smith - The American Journal of Bioethics, 2020 - Taylor & Francis
Abstract In the United States, clinical HIV data reported to surveillance systems operated by
jurisdictional departments of public health are re-used for epidemiology and prevention. In …
jurisdictional departments of public health are re-used for epidemiology and prevention. In …
Superspreaders drive the largest outbreaks of hospital onset COVID-19 infections
SARS-CoV-2 is notable both for its rapid spread, and for the heterogeneity of its patterns of
transmission, with multiple published incidences of superspreading behaviour. Here, we …
transmission, with multiple published incidences of superspreading behaviour. Here, we …