SARS-CoV-2 bioinformatics

We discuss the latest developments in SARS-CoV-2 genomics over the last 2 weeks with Mads Albertsen and the latest developments in Denmark.

Denmark covid stats: www.covid19genomics.dk/statistics

Tools and resources mentioned:  
https://outbreak.info/
https://virological.org/t/outbreak-info-sars-cov-2-mutation-situation-reports/629
https://gitlab.com/johan.bernal.morales/sarscov2

Publications mentioned:
A Comparison of Performance for Different SARS-Cov-2 Sequencing Protocols https://www.biorxiv.org/content/10.1101/2021.03.01.433428v1

Before the Surge: Molecular Evidence of SARS-CoV-2 in New York City Prior to the First Report
https://www.medrxiv.org/content/10.1101/2021.02.08.21251303v1

SARS-CoV-2 within-host diversity and transmission https://science.sciencemag.org/content/early/2021/03/09/science.abg0821

Info on masking SARSCOV2 sites: 
https://virological.org/t/issues-with-sars-cov-2-sequencing-data/473
https://github.com/W-L/ProblematicSites_SARS-CoV2/blob/master/subset_vcf/problematic_sites_sarsCov2.mask.vcf

51 SARSCOV2 Round-up 3 and updates from Denmark

Denmark is one of the leading countries in the world forSARS-CoV-2 genomic surveillance.  Prof Mads Albertsen chats to us about SARS-CoV-2 sequencing in Denmark, how it got started, logistics, tweaked protocols and things hes learnt along the way. 

Edited by Niamh Page

52 SARS-CoV-2 sequencing in Denmark with Mads Albertsen

The Canadians have taken over the podcast ! 

Join guest host Dr. Emma Griffiths, as she talks with Dr. Finlay McGuire and Dr. William Hsiao about the SARS-CoV-2 genomics epidemiology efforts in Canada. 

Cancogen website : https://www.genomecanada.ca/en/cancogen

53 SARS-CoV-2 surveillance in Canada with CANCOGEN

The Canadians have taken over the podcast - AGAIN ! 

Join guest host Dr. Emma Griffiths, as she talks with Dr. Finn McGuire and Dr. William Hsiao about the SARS-CoV-2 genomics epidemiology efforts in Canada. 

Cancogen website : https://www.genomecanada.ca/en/cancogen

54 SARS-CoV-2 In Canada and addressing data sharing and privacy

Part 2 going through a new method for identifying variants of concern using Sanger sequencing, and we’re joined by two of the authors of this method Kai Blin and Tue Jorgensen, both from the Technical University of Denmark.

The preprint:
www.medrxiv.org/content/10.1101/2….03.27.21252266v1

The protocol:
www.protocols.io/view/sanger-sequ…-2-spik-bsbdnai6

The software:
github.com/kblin/covid-spike-classification

The web app:
ssi.biolib.com/app/covid-spike-classification/run

56 SARS-CoV-2 And Sequencing Spike With Sanger Sequencing part 2

Today we’re going through a new method for identifying variants of concern using Sanger sequencing, and we’re joined by two of the authors of this method Kai Blin and Tue Jorgensen, both from the Technical University of Denmark. 

The preprint: 
https://www.medrxiv.org/content/10.1101/2021.03.27.21252266v1

The protocol: 
https://www.protocols.io/view/sanger-sequencing-of-a-part-of-the-sars-cov-2-spik-bsbdnai6

The software: 
https://github.com/kblin/covid-spike-classification

The web app: 
https://ssi.biolib.com/app/covid-spike-classification/run

55 SARS-CoV-2 And Sequencing Spike With Sanger Sequencing - Welcome To 1995

We bring on Lingzi Xiaoli and Jill Hagey to talk about their benchmark datasets for SARS-CoV-2.  Find out more at https://github.com/CDCgov/datasets-sars-cov-2

* Previous paper for bacterial datasets can be found at https://peerj.com/articles/3893/
* Jill can be found on Twitter at @JillHagey and jvhagey.github.io
* Lingzi can be found on LinkedIn at https://www.linkedin.com/in/lingzi-xiaoli-27b87174/

80 Benchmark datasets for SARS-CoV-2

We bring on Lingzi Xiaoli and Jill Hagey to talk about their benchmark datasets for SARS-CoV-2.  Find out more at https://github.com/CDCgov/datasets-sars-cov-2.  See our previous episode for part 1 of the conversation.

* Previous paper for bacterial datasets can be found at https://peerj.com/articles/3893/
* Jill can be found on Twitter at @JillHagey and jvhagey.github.io
* Lingzi can be found on LinkedIn at https://www.linkedin.com/in/lingzi-xiaoli-27b87174/

81 The people behind the benchmark datasets for SARS-CoV-2

We chat to Justin O'Grady, Andrew Page and Alison Mather about how they went about sequencing 1500 SARS-CoV-2 genomes from one small region in the UK (Norfolk), and how they went about using the data for genomic epidemiology to help get a detailed, near real-time view of the pandemic as it unfolded.

Some of the key points are that in Norfolk and surrounding regions: 
100 distinct UK lineages were identified.
16 UK lineages found in key workers were not observed in patients or in community care. 
172 genomes from SARS-CoV-2 positive samples sequenced per 100,000 population representing 42.6% of all positive cases.
SARS-CoV-2 genomes from 1035 cases sequenced to a high quality.
Only 5 countries, out of 103, have sequenced more SARS-CoV-2 genomes than have been sequenced in Norfolk for this paper.
Samples covered the entire first wave, March to August 2020.
Stable evolutionary rate of 2 SNPs per month.
D614G mutation is the dominant genotype and associated with increased transmission.
No evidence of reinfection in 42 cases with longitudinal samples.
WGS identified a sublineage associated with care facilities.
WGS ruled out nosocomial outbreaks. 
Rapid WGS confirmed the relatedness of cases from an outbreak at a food processing facility.

The manuscript is available from: https://www.medrxiv.org/content/10.1101/2020.09.28.20201475v1

31 Large scale sequencing of SARS-CoV-2 genomes from one region

Nick Loman, Sam Nicholls and Radosław Popławski join us to discuss building systems to support the analysis of hundreds of thousands of SARS-CoV-2 genomes in the middle of a pandemic, without using Excel.

Preprint about MAJORA: Continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance: https://doi.org/10.1101/2020.10.06.328328

COGUK website: https://www.cogconsortium.uk/

32 Looking behind Majora's Mask and nation wide tracking of SARS-CoV-2 genomics

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

40 A crash course in SARS-CoV-2 bioinformatics

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

39 Explaining the naming of SARS-CoV-2 new variants

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/

41 SARS-CoV-2 Phylogenomics questions answered

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

42 Overcoming barriers to SARS-CoV-2 data analysis

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/

43 Why use genomics in an epidemic? with Sam Sheppard

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

44 How to sequence SARS-CoV-2 using the ARTIC protocol with Joshua Quick

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

46 SARS-CoV-2 genomics resources

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

47 SARS-CoV-2 Rapid roundup and questions answered

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

48 SARS-CoV-2 More Variants of Concern and updates from Africa

We are joined by Peter van Heusden to discuss all the latest developments in SARS-CoV-2 genomics, particularly around tools and resources. We also discuss the challenges of building and sharing data in large scale sequencing endeavours.

Tools and resources: 
Nextalign github.com/nextstrain/nextclade/releases

COG mutation explorer http://sars2.cvr.gla.ac.uk/cog-uk/

Grinch https://cov-lineages.org

New US tool for variants: https://www.cdc.gov/coronavirus/2019-ncov/transmission/variant-cases.html 
https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/variant-surveillance/global-variant-map.html 

Online lineage assignment: https://pangolin.cog-uk.io/

CoronaHiT paper published: https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-021-00839-5

49 SARS-CoV-2 Tools and resources update

Microbial Bioinformatics is a rapidly changing field marrying computer science and microbiology. Join us as we share some tips and tricks we’ve learnt over the years. If you’re student just getting to grips to the field, or someone who just wants to keep tabs on the latest and greatest - this podcast is for you. 

The hosts are Dr. Lee Katz from the Centres for Disease Control and Prevention (US), Dr. Nabil-Fareed Alikhan from the University of Oxford (UK), and Prof. Andrew Page from Theiagen Genomics (UK) and bring together years of experience in microbial bioinformatics.

The opinions expressed here are our own and do not necessarily reflect the views of Centres for Disease Control and Prevention, University of Oxford or Theiagen Genomics.

Intro music : Werq - Kevin MacLeod (incompetech.com)
Licensed under Creative Commons: By Attribution 3.0 License
http://creativecommons.org/licenses/by/3.0/

Outro music : Scheming Weasel (faster version) - Kevin MacLeod (incompetech.com)
Licensed under Creative Commons: By Attribution 3.0 License
http://creativecommons.org/licenses/by/3.0/

Question and comments? microbinfie@gmail.com

SARS-CoV-2 bioinformatics

Micro Binfie Podcast