Gradual emergence followed by exponential spread of the SARS-CoV-2 Omicron variant in Africa - Science - retracted after widespread criticism

[Mary Wilson]

1 Dec 2022
First Release
DOI: 10.1126/science.add873

CARLO FISCHER, TONGAI GIBSON MAPONGA, ANGES YADOULETON, NURO ABÍLIO, EMMANUEL ABOCE, PRAISE ADEWUMI, PEDRO AFONSO, JEWELNA AKORLI, SOA FY ANDRIAMANDIMBY , [...], AND JAN FELIX DREXLER +78 authors

Abstract

The geographic and evolutionary origins of the SARS-CoV-2 Omicron variant (BA.1), which was first detected mid-November 2021 in Southern Africa, remain unknown. We tested 13,097 COVID-19 patients sampled between mid-2021 to early 2022 from 22 African countries for BA.1 by real-time RT-PCR. By November-December 2021, BA.1 had replaced the Delta variant in all African sub-regions following a South-North gradient, with a peak Rt of 4.1. Polymerase chain reaction and near-full genome sequencing data revealed genetically diverse Omicron ancestors already existed across Africa by August 2021. Mutations, altering viral tropism, replication and immune escape, gradually accumulated in the spike gene. Omicron ancestors were therefore present in several African countries months before Omicron dominated transmission. These data also indicate that travel bans are ineffective in the face of undetected and widespread infection.

https://www.science.org/doi/10.1126/science.add8737#.Y4n9j1vz7Ok.twitter

 

[Pathfinder]

NEWS
06 December 2022

Surprising Omicron origins study comes under scrutiny

Sequences of early forms of the fast-spreading variant reported to have been circulating in West Africa could have resulted from contamination.

Smriti Mallapaty

A study that proposes that ancestors of the fast-spreading Omicron coronavirus variant were circulating undetected in Africa for months before the alarm was raised has prompted fierce discussion. The paper, published last week in Science, identifies sequences that the authors say are from Omicron’s predecessors, which they say were spreading from August 2021, some three months before researchers in South Africa and Botswana noted the variant’s arrival in November that year1. But many researchers think the sequences are probably the result of contamination in the laboratory.
...
https://www.nature.com/articles/d41586-022-04357-1

 

[Pathfinder]

Hattip Emily

‘We made a mistake.’ Omicron origin study retracted after widespread criticism; Contamination led to conclusion that SARS-CoV-2 variant evolved slowly in Africa, authors say

https://flutrackers.com/forum/forum/...ca-authors-say

 

[Mary Wilson]

Contamination leads to swift retraction for Science paper on the origins of Omicron in Africa


Dec 23 2022

The authors of a paper that proposed the Omicron variant of SARS-Cov-2 had evolved in Western Africa months before it was first detected in South Africa have retracted their study after discovering contamination in their samples, as several scientists had suggested on Twitter was the case.


The article, “Gradual emergence followed by exponential spread of the SARS-CoV-2 Omicron variant in Africa,” was published in Science on December 1 by a team led by Jan Felix Drexler of Charité – Universitätsmedizin Berlin.

Soon after publication, many geneticists expressed skepticism on social media about the study, including questioning whether the results came from contamination during the sequencing process.

Tulio de Oliveira, director of the Centre for Epidemic Response and Innovation and the KwaZulu-Natal Research Innovation and Sequencing Platform at the University of KwaZulu-Natal in South Africa, tweeted on December 4 about “weaknesses” in the study, including that “the quality of the sequences seems problematic”: ...

https://retractionwatch.com/2022/12...ce-paper-on-the-origins-of-omicron-in-africa/