Coronavirus [NEW TOPIC PAGE]

Hot Topics of the Day|PHGKB

CRISPR–Cas12-based detection of SARS-CoV-2
JP Broughton et al, Nature BIotechnology

Human leukocyte antigen susceptibility map for SARS-CoV-2
A Nguyen et al, BIORXIV, April 15, 2020

CoV Genome Tracker: tracing genomic footprints of Covid-19 pandemic
S Akhter et al, BIORXIV, April 15, 2020

CoV Genome Tracker is a web portal dedicated to trace Covid-19 outbreaks in real time using a haplotype network, an accurate and scalable representation of genomic changes in a rapidly evolving population. At a broader evolutionary time scale, a companion browser facilitates the search for molecular targets of clinical interventions.

The global population of SARS-CoV-2 is composed of six major subtypes
IJM Junior et al, BIORXIV, April 15, 2020

We propose the subdivision of the global SARS-CoV-2 population into sixteen well-defined subtypes by focusing on the widely shared polymorphisms in nonstructural (nsp3, nsp4, nsp6, nsp12, nsp13 and nsp14) cistrons, structural (spike and nucleocapsid) and accessory (ORF8) genes. Six virus subtypes were predominant in the population.

5 burning questions about tech efforts to track Covid-19 cases
C Ross, Stat News, April 15, 2020

Some of the promises of what are sometimes called proximity tracing [tools] may be a little bit over the top. It’s not yet clear whether digital surveillance methods used in several Asian countries truly helped to control the spread of infections. What we’ve seen from various countries is information that this was done, but not information that it was effective.

An army of virus tracers takes shape in Massachusetts.
E Barry, NY Times, April 16, 2020

Asian countries have invested heavily in digital contact tracing which uses technology to warn people when they have been exposed to the coronavirus. Massachusetts is using an old-fashioned means: people

Covid-19: Sequencing a pandemic
C Wigley, CEO Genomics England, video, April 2020