Literature DB >> 33706862

Tracking SARS-CoV-2 lineage B.1.1.7 dissemination: insights from nationwide spike gene target failure (SGTF) and spike gene late detection (SGTL) data, Portugal, week 49 2020 to week 3 2021.

Vítor Borges1,2, Carlos Sousa2,3, Luís Menezes4, António Maia Gonçalves5, Miguel Picão6, José Pedro Almeida7, Margarida Vieita7, Rafael Santos7, Ana Rita Silva3, Mariana Costa3, Luís Carneiro3, Pedro Casaca8, Pedro Pinto-Leite8, André Peralta-Santos8, Joana Isidro1, Sílvia Duarte9, Luís Vieira9, Raquel Guiomar10, Susana Silva11, Baltazar Nunes11, João P Gomes1.   

Abstract

We show that the SARS-CoV-2 B.1.1.7 lineage is highly disseminated in Portugal, with the odds of B.1.1.7 proportion increasing at an estimated 89% (95% confidence interval: 83-95%) per week until week 3 2021. RT-PCR spike gene target late detection (SGTL) can constitute a useful surrogate to track B.1.1.7 spread, besides the spike gene target failure (SGTF) proxy. SGTL/SGTF samples were associated with statistically significant higher viral loads, but not with substantial shift in age distribution compared to non-SGTF/SGTL cases.

Entities:  

Keywords:  B.1.1.7 lineage; RT-PCR; SARS-CoV-2; genome sequencing; laboratory surveillance; spike gene target failure (SGTF); spike gene target late detection (SGTL)

Mesh：

Substances：

Year:  2021        PMID： 33706862      PMCID： PMC7953529          DOI： 10.2807/1560-7917.ES.2021.26.10.2100130

Source DB:  PubMed          Journal:  Euro Surveill        ISSN： 1025-496X


  3 in total

1.  Two-step strategy for the identification of SARS-CoV-2 variant of concern 202012/01 and other variants with spike deletion H69-V70, France, August to December 2020.

Authors:  Antonin Bal; Gregory Destras; Alexandre Gaymard; Karl Stefic; Julien Marlet; Sébastien Eymieux; Hadrien Regue; Quentin Semanas; Constance d'Aubarede; Geneviève Billaud; Frédéric Laurent; Claudia Gonzalez; Yahia Mekki; Martine Valette; Maude Bouscambert; Catherine Gaudy-Graffin; Bruno Lina; Florence Morfin; Laurence Josset
Journal:  Euro Surveill       Date:  2021-01

2.  S-Variant SARS-CoV-2 Lineage B1.1.7 Is Associated With Significantly Higher Viral Load in Samples Tested by TaqPath Polymerase Chain Reaction.

Authors:  Michael Kidd; Alex Richter; Angus Best; Nicola Cumley; Jeremy Mirza; Benita Percival; Megan Mayhew; Oliver Megram; Fiona Ashford; Thomas White; Emma Moles-Garcia; Liam Crawford; Andrew Bosworth; Sowsan F Atabani; Tim Plant; Alan McNally
Journal:  J Infect Dis       Date:  2021-05-28       Impact factor: 5.226

3.  Emergence of SARS-CoV-2 B.1.1.7 Lineage - United States, December 29, 2020-January 12, 2021.

Authors:  Summer E Galloway; Prabasaj Paul; Duncan R MacCannell; Michael A Johansson; John T Brooks; Adam MacNeil; Rachel B Slayton; Suxiang Tong; Benjamin J Silk; Gregory L Armstrong; Matthew Biggerstaff; Vivien G Dugan
Journal:  MMWR Morb Mortal Wkly Rep       Date:  2021-01-22       Impact factor: 17.586
  3 in total
  29 in total

Review 1.  Biological Properties of SARS-CoV-2 Variants: Epidemiological Impact and Clinical Consequences.

Authors:  Reem Hoteit; Hadi M Yassine
Journal:  Vaccines (Basel)       Date:  2022-06-09

2.  Simplified Cas13-based assays for the fast identification of SARS-CoV-2 and its variants.

Authors:  Pardis C Sabeti; Cameron Myhrvold; Jon Arizti-Sanz; A'Doriann Bradley; Yibin B Zhang; Chloe K Boehm; Catherine A Freije; Michelle E Grunberg; Tinna-Solveig F Kosoko-Thoroddsen; Nicole L Welch; Priya P Pillai; Sreekar Mantena; Gaeun Kim; Jessica N Uwanibe; Oluwagboadurami G John; Philomena E Eromon; Gregory Kocher; Robin Gross; Justin S Lee; Lisa E Hensley; Bronwyn L MacInnis; Jeremy Johnson; Michael Springer; Christian T Happi
Journal:  Nat Biomed Eng       Date:  2022-05-30       Impact factor: 29.234

3.  Impact of stringent non-pharmaceutical interventions applied during the second and third COVID-19 epidemic waves in Portugal, 9 November 2020 to 10 February 2021: an ecological study.

Authors:  Ana Rita Torres; Ana Paula Rodrigues; Mafalda Sousa-Uva; Irina Kislaya; Susana Silva; Liliana Antunes; Carlos Dias; Baltazar Nunes
Journal:  Euro Surveill       Date:  2022-06

4.  A SARS-CoV-2 mutant from B.1.258 lineage with ∆H69/∆V70 deletion in the Spike protein circulating in Central Europe in the fall 2020.

Authors:  Broňa Brejová; Kristína Boršová; Viktória Hodorová; Viktória Čabanová; Lenka Reizigová; Evan D Paul; Pavol Čekan; Boris Klempa; Jozef Nosek; Tomáš Vinař
Journal:  Virus Genes       Date:  2021-08-27       Impact factor: 2.332

5.  Mutation-Specific SARS-CoV-2 PCR Screen: Rapid and Accurate Detection of Variants of Concern and the Identification of a Newly Emerging Variant with Spike L452R Mutation.

Authors:  Huanyu Wang; Sophonie Jean; Richard Eltringham; John Madison; Pamela Snyder; Huolin Tu; Daniel M Jones; Amy L Leber
Journal:  J Clin Microbiol       Date:  2021-07-19       Impact factor: 5.948

Review 6.  One year into the pandemic: Short-term evolution of SARS-CoV-2 and emergence of new lineages.

Authors:  Fernando González-Candelas; Marie-Anne Shaw; Tung Phan; Urmila Kulkarni-Kale; Dimitrios Paraskevis; Fabio Luciani; Hirokazu Kimura; Manuela Sironi
Journal:  Infect Genet Evol       Date:  2021-04-26       Impact factor: 4.393

7.  Characteristics of SARS-CoV-2 variants of concern B.1.1.7, B.1.351 or P.1: data from seven EU/EEA countries, weeks 38/2020 to 10/2021.

Authors:  Tjede Funk; Anastasia Pharris; Gianfranco Spiteri; Nick Bundle; Angeliki Melidou; Michael Carr; Gabriel Gonzalez; Alejandro Garcia-Leon; Fiona Crispie; Lois O'Connor; Niamh Murphy; Joël Mossong; Anne Vergison; Anke K Wienecke-Baldacchino; Tamir Abdelrahman; Flavia Riccardo; Paola Stefanelli; Angela Di Martino; Antonino Bella; Alessandra Lo Presti; Pedro Casaca; Joana Moreno; Vítor Borges; Joana Isidro; Rita Ferreira; João Paulo Gomes; Liidia Dotsenko; Heleene Suija; Jevgenia Epstein; Olga Sadikova; Hanna Sepp; Niina Ikonen; Carita Savolainen-Kopra; Soile Blomqvist; Teemu Möttönen; Otto Helve; Joana Gomes-Dias; Cornelia Adlhoch
Journal:  Euro Surveill       Date:  2021-04

8.  Setting-Up a Rapid SARS-CoV-2 Genome Assessment by Next-Generation Sequencing in an Academic Hospital Center (LPCE, Louis Pasteur Hospital, Nice, France).

Authors:  Paul Hofman; Olivier Bordone; Emmanuel Chamorey; Jonathan Benzaquen; Renaud Schiappa; Virginie Lespinet-Fabre; Elisabeth Lanteri; Patrick Brest; Baharia Mograbi; Charlotte Maniel; Virginie Tanga; Maryline Allegra; Myriam Salah; Julien Fayada; Jacques Boutros; Sylvie Leroy; Simon Heeke; Véronique Hofman; Charles-Hugo Marquette; Marius Ilié
Journal:  Front Med (Lausanne)       Date:  2022-01-11

9.  Comparative Diagnostic Performance of a Novel Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) Kit for the Rapid Detection of SARS-CoV-2.

Authors:  Alexander Domnich; Andrea Orsi; Donatella Panatto; Vanessa De Pace; Valentina Ricucci; Patrizia Caligiuri; Giulia Guarona; Valerio Chessa; Diego Ferone; Simona Boccotti; Bianca Bruzzone; Giancarlo Icardi
Journal:  Pathogens       Date:  2021-12-15

10.  Comparative Effectiveness of Coronavirus Vaccine in Preventing Breakthrough Infections among Vaccinated Persons Infected with Delta and Alpha Variants.

Authors:  Irina Kislaya; Eduardo Freire Rodrigues; Vítor Borges; João P Gomes; Carlos Sousa; José P Almeida; André Peralta-Santos; Baltazar Nunes
Journal:  Emerg Infect Dis       Date:  2021-12-07       Impact factor: 6.883
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