Genomics

Severe Acute Respiratory Syndrome Coronavirus-2 genome sequence variations relate to morbidity and mortality in Coronavirus Disease-19

1. Poonam Mehta
2. Saumya Sarkar
3. Ujjala Ghoshal
4. Ankita Pandey
5. Ratender Singh
6. Dharamveer Singh
7. Rahul Vishvkarma
8. Uday Chand Ghoshal
9. Ranjeet Maurya
10. Rajesh Pandey
11. Ravishankar Ramachandran
12. Punyasloke Bhadury
13. Tapas K Kundu
14. Singh Rajender

Reviewed by ScreenIT

A population-level invasion by transposable elements triggers genome expansion in a fungal pathogen

1. Ursula Oggenfuss
2. Thomas Badet
3. Thomas Wicker
4. Fanny E Hartmann
5. Nikhil Kumar Singh
6. Leen Abraham
7. Petteri Karisto
8. Tiziana Vonlanthen
9. Christopher Mundt
10. Bruce A McDonald
11. Daniel Croll

• Curated by eLife

  Evaluation Summary:

  This study is of potential interest to a broad audience on evolutionary and population genomics, particularly scientists studying genome dynamics, including transposable elements (TE) and their evolution. It takes advantage of genomics datasets from a large population of wheat pathogens collected across the globe at different times (decades) to detect ongoing processes of genome expansion and potential selection mediated by TE insertions. The work provides empirical evidence that drastic demographic processes shape TE dynamics in nature and that these contribute to intraspecific variation in genome sizes, recapitulating the well-stablished association between TE content and genome size observed across the diversity of life forms.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1, Reviewer #2 and Reviewer #3 agreed to share their names with the authors.)

Reviewed by eLife

Genome-wide association study in quinoa reveals selection pattern typical for crops with a short breeding history

1. Dilan SR Patiranage
2. Elodie Rey
3. Nazgol Emrani
4. Gordon Wellman
5. Karl Schmid
6. Sandra M Schmöckel
7. Mark Tester
8. Christian Jung

• Curated by eLife

  Evaluation Summary:

  This is a comprehensive study of genomic and phenotypic diversity in the orphan crop quinoa. Based on whole genome resequencing of 310 accessions and field phenotyping of the same set of accessions for two years, the study identified the genetic basis of agronomically important traits. Based on this promising work, there will likely be scope for quick improvement of this orphan crop through breeding.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 and Reviewer #3 agreed to share their names with the authors.)

Reviewed by eLife

A phylogeny-based metric for estimating changes in transmissibility from recurrent mutations in SARS-CoV-2

1. Damien Richard
2. Liam P Shaw
3. Rob Lanfear
4. Russell Corbett-Detig
5. Angie Hinrichs
6. Jakob McBroome
7. Yatish Turakhia
8. Mislav Acman
9. Christopher J Owen
10. Cedric CS Tan
11. Lucy van Dorp
12. François Balloux

Reviewed by ScreenIT

Sequencing SARS-CoV-2 in a malaria research laboratory in Mali, West Africa: the road to sequencing the first SARS-CoV-2 genome in Mali

1. Antoine Dara
2. Bouréma Kouriba
3. Amadou Daou
4. Abdoul Karim Sangare
5. Djibril Kassogue
6. Charles Dara
7. Abdoulaye Djimde

Reviewed by ScreenIT

Multifractal Analysis of SARS-CoV-2 Coronavirus genomes using the wavelet transform

1. Sid-Ali Ouadfeul

Reviewed by ScreenIT

A repurposed, blood gene signature is associated with poor outcomes in SARS-CoV-2

1. Brenda M. Juan-Guardela
2. Jiehuan Sun
3. Tong Zhang
4. Bing Xu
5. Gaetane Michaud
6. Jose D. Herazo-Maya

Reviewed by ScreenIT

Patterns of within-host genetic diversity in SARS-CoV-2

1. Gerry Tonkin-Hill
2. Inigo Martincorena
3. Roberto Amato
4. Andrew RJ Lawson
5. Moritz Gerstung
6. Ian Johnston
7. David K Jackson
8. Naomi Park
9. Stefanie V Lensing
10. Michael A Quail
11. Sónia Gonçalves
12. Cristina Ariani
13. Michael Spencer Chapman
14. William L Hamilton
15. Luke W Meredith
16. Grant Hall
17. Aminu S Jahun
18. Yasmin Chaudhry
19. Myra Hosmillo
20. Malte L Pinckert
21. Iliana Georgana
22. Anna Yakovleva
23. Laura G Caller
24. Sarah L Caddy
25. Theresa Feltwell
26. Fahad A Khokhar
27. Charlotte J Houldcroft
28. Martin D Curran
29. Surendra Parmar
30. The COVID-19 Genomics UK (COG-UK) Consortium
31. Alex Alderton
32. Rachel Nelson
33. Ewan M Harrison
34. John Sillitoe
35. Stephen D Bentley
36. Jeffrey C Barrett
37. M Estee Torok
38. Ian G Goodfellow
39. Cordelia Langford
40. Dominic Kwiatkowski
41. Wellcome Sanger Institute COVID-19 Surveillance Team

• Curated by eLife

  Evaluation Summary:

  Tonkin-Hill and colleagues present a large set of deep sequencing data from acute SARS-CoV-2 infections with each sample sequenced in duplicate. They use these data to characterize the within-host mutational patterns and diversity and relate them to SARS-CoV-2 diversity in consensus sequences sampled around the globe. It further allows understanding how this variation can or cannot be used to understand transmission dynamics and other applications in genomic epidemiology.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #3 agreed to share their names with the authors.)

Reviewed by eLife, ScreenIT

Emerging SARS-CoV-2 Diversity Revealed by Rapid Whole-Genome Sequence Typing

1. Ahmed M Moustafa
2. Paul J Planet

Reviewed by ScreenIT

Single-nucleotide conservation state annotation of the SARS-CoV-2 genome

1. Soo Bin Kwon
2. Jason Ernst

Reviewed by ScreenIT