Micro binfie podcast

We discuss the latest developments in SARS-CoV-2 genomics over the last 2 weeks with Peter van Heusden, covering the growing list of Variants of Concern and the latest developments in Africa.

Papers & resources mentioned:

American birds (677) - https://www.medrxiv.org/content/10.1101/2021.02.12.21251658v2

https://github.com/cov-lineages/pango-designation

PHE thresholds for different variants:

https://www.gov.uk/government/publications/covid-19-variants-genomically-confirmed-case-numbers/variants-distribution-of-cases-data

A.23.1 in Uganda - https://www.medrxiv.org/content/10.1101/2021.02.08.21251393v1

B.1.525 - https://github.com/cov-lineages/pango-designation/issues/4

Zambia sequences -

https://www.cdc.gov/mmwr/volumes/70/wr/mm7008e2.htm?s_cid=mm7008e2_w

We present a rapid round up of SARS-CoV-2 questions and issues, hopefully with some answers, so that you can stay on top of the latest in SARS-CoV-2 genomics. Recorded 5 February 2021.

Topics covered:

Why missing 1 SNP can cause lineage assignment to break and how it works?

How do we describe lineages with a chain of mutation events?

Are we seeing convergent evolution?

Co-infections of different lineages discovered?

For nanopore basecalling do use HAC & should you get a GPU?

Basic logistics difficult for sequencing in many parts of world.

Can I look at recombination with ARTIC on Illumina?

How do you annotate a SARS-CoV-2 sequence?

http://cov-glue.cvr.gla.ac.uk/#/home

FASTA > nextclade

VCF > snpeff

https://github.com/cov-ert/type_variants

Spotting community spread from NextStrain?

Scientists call for fully open sharing of coronavirus genome data: https://www.nature.com/articles/d41586-021-00305-7

We discuss recent updates to the best SARS-CoV-2 resources, so that you can stay on top of the latest bioinformatics and genomics tools. Recorded 5 February 2021.

CoVariants website: http://covariants.org/

Microreact: https://microreact.org/project/cogconsortium/

Lineage reports: https://cov-lineages.org/

CLIMB ARTIC workshop online resources: https://www.climb.ac.uk/artic-and-climb-big-data-joint-workshop/

Multiplex PCR for B.1.1.7, B.1.351 and P.1: https://www.protocols.io/view/multiplexed-rt-qpcr-to-screen-for-sars-cov-2-b-1-1-brrhm536

CDC videos: https://www.cdc.gov/amd/training/covid-19-gen-epi-toolkit.html

We chat with Nabil about EnteroBase, and learn about the background to the project, the general benefits of the platforms and some of the strange quirks users might encounter. EnteroBase is an integrated software environment that supports the identification of global population structures within several bacterial genera that include pathogens.

Papers:

Mentioned PLOS genetics paper:

Alikhan et al. (2018) A genomic overview of the population structure of Salmonella. PLoS Genet 14 (4): e1007261 https://doi.org/10.1371/journal.pgen.1007261

Paper describing Enterobase and the genome fishing expeditions:

Zhou et al. (2020) The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny and Escherichia core genomic diversity. Genome Res. 30:138-152. https://doi.org/10.1101/gr.251678.119

rMLST is described in: Jolley et al. 2012 Microbiology 158:1005-15. https://doi.org/10.1099/mic.0.055459-0

Resources

Enterobase: http://enterobase.warwick.ac.uk/

PubMLST https://pubmlst.org/

About EnteroBase schemes: https://enterobase.readthedocs.io/en/latest/enterobase-tutorials/deeper-lineages.html

Software:

Enterobase toolkit and background software: https://github.com/zheminzhou/EToKi

Errata.

Jay Hinton’s Salmonella is a ST313 (D23580), not ST131 (I always mix the numbers up -- Nabil)

Joshua Quick from the University of Birmingham talks about "How to sequence SARS-CoV-2 using the ARTIC protocol".

This was part of a joint ARTICnetwork & CLIMB-BIG-DATA workshop on COVID-19 data analysis and chaired by Nick Loman.

Links:

https://twitter.com/Scalene/status/1349402397249056779

https://primalscheme.com/

https://www.protocols.io/view/ncov-2019-sequencing-protocol-v3-locost-bh42j8ye

https://github.com/artic-network/rampart

Sam Sheppard from the University of Bath presents at the ARTICnetwork & CLIMB-BIG-DATA workshop on COVID-19 data analysis, motivating why we should use genomics in an epidemic.

He gives background on typing schemes, different ways of sequencing and challenges such as how you can analyse large mounts of genomic data.

Resources:

https://sheppardlab.com/

https://www.climb.ac.uk/artic-and-climb-big-data-joint-workshop/

ARTICnetwork & CLIMB-BIG-DATA present a panel discussion on overcoming barriers to SARS-CoV-2 data analysis with Nick Loman and Will Rowe from the University of Birmingham, Áine O'Toole from the University of Edinburgh, Andrew Page from the Quadram Institute and Anna Price from MRC CLIMB and Cardiff University. This was part of a workshop on COVID-19 data analysis.

Topics covered:

Collecting sample metadata

intrapatient variability

Building bridges with policy makers to start sequencing

Data sharing

Improving bioinformatics skills

Pipeline and software validation

Bioinformatics reproducibility and quality

Papers:

The PHA4GE SARS-CoV-2 Contextual Data Specification for Open Genomic Epidemiology https://www.preprints.org/manuscript/202008.0220/v1

MAJORA: Continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance https://www.biorxiv.org/content/10.1101/2020.10.06.328328v1

Genomic sequencing of SARS-CoV-2: a guide to implementation for maximum impact on public health https://www.who.int/publications/i/item/9789240018440

Resources:

https://www.climb.ac.uk/artic-and-climb-big-data-joint-workshop/

https://github.com/SamStudio8/majora

https://soundcloud.com/microbinfie/majora

https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification

https://pha4ge.org/

Software:

https://github.com/cov-lineages/pangolin

https://github.com/artic-network/civet

https://github.com/COG-UK/grapevine

https://github.com/cov-lineages/pangoLEARN

ARTICnetwork & CLIMB-BIG-DATA present a panel discussion on SARS-CoV-2 phylogenomics with Nick Loman from the University of Birmingham, Verity Hill from the University of Edinburgh, Andrew Page from the Quadram Institute and Anna Price from MRC CLIMB and Cardiff University. This was part of a workshop on COVID-19 data analysis.

The topics covered are:

More about Polecat

Whats the difference between COG-UK Phylotypes and Pangolin lineages?

What is the difference between Civet and Llama

Can you use BLAST to find similar SARS-CoV-2 genomes?

How do you find similar sequences in the public repositories to give your samples context?

How do you manually curate the dataset for PangoLEARN?

How does Civet choose what constitutes a subtree?

Can Civet be adapted to other viruses?

Are the vaccine sequences available?

Databases that report variation

Quality of variant calls?

Groups:

https://www.climb.ac.uk/artic-and-climb-big-data-joint-workshop/

https://www.climb.ac.uk/

https://artic.network/

https://cogconsortium.uk/

Software:

https://github.com/COG-UK/polecat

https://github.com/cov-lineages/pangolin

https://github.com/cov-lineages/llama

https://github.com/artic-network/civet

https://github.com/cov-lineages/pangoLEARN

http://tree.bio.ed.ac.uk/software/figtree/

Analysis websites:

https://cov-lineages.org/

https://clades.nextstrain.org/

https://pangolin.cog-uk.io/

http://cov-glue.cvr.gla.ac.uk/

Over the last year we've learnt a lot about SARS-CoV-2 genomics. Lee extracts all the insider knowledge from our brains and we give him the honest truth to his probing questions.

We cover:

Pipelines for SARS-CoV-2

Archives & metadata

Read filtering

Assembly vs consensus

Amplicon data analysis

Controls

If things look too good

Coverage

....

Some URLs:

https://github.com/connor-lab/ncov2019-artic-nf

https://github.com/jts/ncov-tools

https://github.com/lskatz/SARS-CoV-2-trueTree

Andrew talks to Niamh Tumelty from the University of Cambridge about SARS-CoV-2 'new variants' and tries to clear up some of the confusion around all the names flying around. Hopefully this helps to give some insights into the various names you hear, but probably by the time you listen the whole thing will have changed again since this field moves so rapidly. Andrew apologises in advance for all the errors that will be found in this podcast!

If you want to read a bit more theres an interesting news item on Nature: https://www.nature.com/articles/d41586-021-00097-w