![]() The Delta variant comprises several descendants of B.1.617.2, such as AY.4 and AY.12. As of 12 August 2021, it was present in 115 countries. The Delta variant lineage harbors 29 mutations as compared to the Wuhan-Hu-1 reference virus sequence ( e.g., S:P681R and S:L452R Table 1). Since then, this variant has been detected in most countries and has rapidly become dominant worldwide ( 5– 7). In October 2020, the Delta variant, corresponding to the Pangolin lineage B.1.617.2, was first detected in India. Such efforts have permitted the discovery of emerging variants, such as Alpha, Beta, and Delta, and to follow their progression in the human population. Tools such as Nextstrain or Pangolin were developed to characterize emerging variants ( 3, 4). There is a worldwide effort to monitor the emergence and evolution of SARS-CoV-2 genotypes due to the implications these new variants have for public health, society, and scientific research. The spike (S) protein, encoded by the S gene, has a key role in receptor recognition and cell membrane fusion process, and the emergence of new variants often relies on the appearance of mutations within this region, the predominant antigen of the virus ( 1, 2). SARS-CoV-2 is a positive-strand RNA virus of the Betacoronavirus genus from Coronaviridae family. This discovery rapidly evolved in the global COVID-19 pandemic. In late 2019, SARS-CoV-2 was detected in Wuhan (Hubei province, China). Candidate primers were tested on few clinical samples, highlighting the need to further pursue primer optimization and validation on a larger and diverse set of samples. Because information about protocols from individual laboratories is generally difficult to obtain, the aims of the study were to identify whether large under-sequenced regions were present in deposited Delta variant genome sequences (from April to August 2021), to investigate the extent of the coverage dropout among all the currently available Delta sequences in six countries, and to propose simple PCR primer modifications to sequence the missing region, especially for the first circulating Delta variants observed in 2021 in Switzerland. In this study, we investigated whether the sequencing community adopted the new sets of primers, especially in the context of the spread of the Delta lineage, in July 2021. A new set of primers (v4) was designed to circumvent this issue in June 2021. The ARTIC v3 protocol for SARS-CoV-2 whole-genome sequencing, which relies on a large number of PCR primers, was among the first available early in the pandemic, but may be prone to coverage dropouts that result in incomplete genome sequences. The SARS-CoV-2 Delta variant, corresponding to the Pangolin lineage B.1.617.2, was first detected in India in July 2020 and rapidly became dominant worldwide. Institute for Infectious Diseases, University of Bern, Bern, Switzerland.Leib, Pascal Bittel, Stefan Neuenschwander and Alban Ramette * Terrazos Miani, Christian Baumann, Carole Grädel, Ronald Dijkman, Franziska Suter-Riniker, Stephen L. Loïc Borcard, Sonja Gempeler, Miguel A. ![]()
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |