Evidence map›Paper›PMID 37952911›Full record

ArticleInternational journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases2024

Rapid dynamic changes of FL.2 variant: A case report of COVID-19 breakthrough infection.

Wonderful T Choga, Gobuiwang Khilly Kurusa Gasenna, James Emmanuel San, Tidimalo Ookame, Irene Gobe, Mohammed Chand, Badisa Phafane, Kedumetse Seru, Patience Matshosi, Boitumelo Zuze and 20 more

Abstract readCase Reports
PubMed Full text at PMC Publisher
In one paragraph

Article in International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

30 authors.

Wonderful T ChogaBotswana Harvard AIDS Institute Partnership, Gaborone, Botswana; School of Allied Health Sciences, Faculty of Health Sciences, Gaborone, Botswana; Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.
Gobuiwang Khilly Kurusa GasennaLenmed-Bokamoso Private Hospital, Gaborone, Botswana.
James Emmanuel SanCentre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory. Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
Tidimalo OokameMinistry of Health and Wellness, Gaborone, Botswana.
Irene GobeSchool of Allied Health Sciences, Faculty of Health Sciences, Gaborone, Botswana.
Mohammed ChandDiagnofirm Medical Laboratories, Plot 12583, Nyerere Drive MiddleStar, Gaborone, Botswana.
Badisa PhafaneDiagnofirm Medical Laboratories, Plot 12583, Nyerere Drive MiddleStar, Gaborone, Botswana.
Kedumetse SeruBotswana Harvard AIDS Institute Partnership, Gaborone, Botswana.
Patience MatshosiBotswana Harvard AIDS Institute Partnership, Gaborone, Botswana.
Boitumelo ZuzeBotswana Harvard AIDS Institute Partnership, Gaborone, Botswana.
Nokuthula NdlovuBotswana Harvard AIDS Institute Partnership, Gaborone, Botswana.
Teko MatsuruBotswana Harvard AIDS Institute Partnership, Gaborone, Botswana.
Dorcas MaruapulaBotswana Harvard AIDS Institute Partnership, Gaborone, Botswana.
Ontlametse T BarengBotswana Harvard AIDS Institute Partnership, Gaborone, Botswana; School of Allied Health Sciences, Faculty of Health Sciences, Gaborone, Botswana.
Kutlo MachekeNational Health laboratory, Gaborone, Botswana.
Lesego Kuate-LereNational Health laboratory, Gaborone, Botswana.
Labapotswe TlaleNational Health laboratory, Gaborone, Botswana.
Onalethata LesetediNational Health laboratory, Gaborone, Botswana.
Modiri TauNational Health laboratory, Gaborone, Botswana.
Mpaphi B MbulawaNational Health laboratory, Gaborone, Botswana.
Pamela Smith-LawrenceNational Health laboratory, Gaborone, Botswana.
Mogomotsi MatshabaBotswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana; Department of Pediatrics, Baylor College of Medicine, Houston, USA.
Roger ShapiroBotswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, USA.
Joseph MakhemaBotswana Harvard AIDS Institute Partnership, Gaborone, Botswana.
Darren P MartinInstitute of Infectious Diseases and Molecular Medicine, Division of Computational Biology, Department of Integrative Biomedical Sciences, University of Cape Town, South Africa.
Tulio de OliveiraCentre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory. Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa; Department of Global Health, University of Washington, Seattle, USA.
Richard J LessellsCentre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory. Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
Shahin LockmanBotswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, USA.
Simani GaseitsiweBotswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, USA.
Sikhulile MoyoBotswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, USA; School of Health Systems and Public Health, University of Pretoria, South Africa; Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa. Electronic address: smoyo@bhp.org.bw.

Funding

Training in HIV Genomics, Treatment, and Cure Research in BotswanaD43TW009610 · FIC · THE BOTSWANA HARVARD HEALTH PARTNERSHIP · PI SHAHIN LOCKMAN, Joseph Moeketsi Makhema · 2013 to 2026
$4.4M
Mentoring in Patient-Oriented HIV Research in the Era of Universal ARTK24AI131928 · NIAID · BRIGHAM AND WOMEN'S HOSPITAL · PI SHAHIN LOCKMAN · 2017 to 2026
$1.9M
Expansion of research and mentoring to improve birth outcomes and treatment outcomes among HIV-affected children in BotswanaK24AI131924 · NIAID · HARVARD UNIVERSITY D/B/A HARVARD SCHOOL OF PUBLIC HEALTH · PI Roger L Shapiro · 2018 to 2026
$1.6M
Viral Diversity an Innovative Biomarker for Refining Estimates of HIV IncidenceK43TW012350 · FIC · THE BOTSWANA HARVARD HEALTH PARTNERSHIP · PI Sikhulile Moyo · 2022 to 2026
$682k
FIC NIH HHS D43 TW009610FIC NIH HHS K43 TW012350NIAID NIH HHS K24 AI131924NIAID NIH HHS K24 AI131928Wellcome Trust
6 · The paper itself

Abstract

We investigated intra-host genetic evolution using two SARS-CoV-2 isolates from a fully vaccinated (primary schedule x2 doses of AstraZeneca plus a booster of Pfizer), >70-year-old woman with a history of lymphoma and hypertension who presented a SARS-CoV-2 infection for 3 weeks prior to death due to COVID-19. Two full genome sequences were determined from samples taken 13 days apart with both belonging to Pango lineage FL.2: the first detection of this Omicron sub-variant in Botswana. FL.2 is a sub-lineage of XBB.1.9.1. The repertoire of mutations and minority variants in the Spike protein differed between the two time points. Notably, we also observed deletions within the ORF1a and Membrane proteins; both regions are associated with high T-cell epitope density. The internal milieu of immune-suppressed individuals may accelerate SARS-CoV-2 evolution; hence, close monitoring is warranted.

Indexed as

COVID-19AgedBotswanaBreakthrough InfectionsFemaleHumansSARS-CoV-2BotswanaEvolutionFL.2ImmunocompromisedSARS-CoV-2

Identifiers

PMID37952911
PMCPMC10719116

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.