Pango lineage designation and assignment using SARS-CoV-2 spike gene nucleotide sequences.
BMC Genomics
; 23(1): 121, 2022 Feb 11.
Artículo
en Inglés
| MEDLINE | ID: covidwho-1690976
ABSTRACT
BACKGROUND:
More than 2 million SARS-CoV-2 genome sequences have been generated and shared since the start of the COVID-19 pandemic and constitute a vital information source that informs outbreak control, disease surveillance, and public health policy. The Pango dynamic nomenclature is a popular system for classifying and naming genetically-distinct lineages of SARS-CoV-2, including variants of concern, and is based on the analysis of complete or near-complete virus genomes. However, for several reasons, nucleotide sequences may be generated that cover only the spike gene of SARS-CoV-2. It is therefore important to understand how much information about Pango lineage status is contained in spike-only nucleotide sequences. Here we explore how Pango lineages might be reliably designated and assigned to spike-only nucleotide sequences. We survey the genetic diversity of such sequences, and investigate the information they contain about Pango lineage status.RESULTS:
Although many lineages, including the main variants of concern, can be identified clearly using spike-only sequences, some spike-only sequences are shared among tens or hundreds of Pango lineages. To facilitate the classification of SARS-CoV-2 lineages using subgenomic sequences we introduce the notion of designating such sequences to a "lineage set", which represents the range of Pango lineages that are consistent with the observed mutations in a given spike sequence.CONCLUSIONS:
We find that many lineages, including the main variants-of-concern, can be reliably identified by spike alone and we define lineage-sets to represent the lineage precision that can be achieved using spike-only nucleotide sequences. These data provide a foundation for the development of software tools that can assign newly-generated spike nucleotide sequences to Pango lineage sets.Palabras clave
Texto completo:
Disponible
Colección:
Bases de datos internacionales
Base de datos:
MEDLINE
Asunto principal:
SARS-CoV-2
/
COVID-19
Tipo de estudio:
Estudio observacional
/
Ensayo controlado aleatorizado
Tópicos:
Variantes
Límite:
Humanos
Idioma:
Inglés
Revista:
BMC Genomics
Asunto de la revista:
Genética
Año:
2022
Tipo del documento:
Artículo
País de afiliación:
S12864-022-08358-2
Similares
MEDLINE
...
LILACS
LIS