Sequencing Using a Two-Step Strategy Reveals High Genetic Diversity in the S Gene of SARS-CoV-2 after a High-Transmission Period in Tunis, Tunisia

• DOI: 10.1128/spectrum.00639-21
• Publication Date: 2021-11-10T15:31:46Z
• Authors: Wasfi Fares; Kais Ghedira; Mariem Gdoura; Anissa Chouikha; Sondes Haddad-Bou...; Marwa Khedhiri; Kaouthar Ayouni; Asma Lamari; Henda Touzi; Walid Hammemi; Zina Medeb; Amel Sadraoui; Nahed Hogga; Nissaf ben Alaya; Henda Triki
• Keywords: Male; 0301 basic medicine; Period (music); [SDV]Life Sciences [q-bio]; MESH: Spike Glycoprotein, Coronavirus; Evolutionary biology; Infectious disease (medical specialty); MESH: Base Sequence; FOS: Health sciences; spike protein; Gene; Genetic diversity; Agricultural and Biological Sciences; Computational biology; MESH: Aged, 80 and over; COVID-19 Testing; Sociology; MESH: Child; Pathology; MESH: COVID-19; Disease; DNA sequencing; MESH: Phylogeny; Child; MESH: High-Throughput Nucleotide Sequencing; Phylogeny; MESH: Aged; Aged, 80 and over; MESH: Middle Aged; Genome; Physics; High-Throughput Nucleotide Sequencing; Life Sciences; Middle Aged; QR1-502; FOS: Sociology; 3. Good health; Infectious Diseases; MESH: Young Adult; whole-genome sequencing; Child, Preschool; VOIs; Spike Glycoprotein, Coronavirus; Telecommunications; Medicine; Female; MESH: Genome, Viral; MESH: Tunisia; MESH: Whole Genome Sequencing; Research Article; Adult; Tunisia; MESH: Mutation; Adolescent; Population; Genome, Viral; Coronavirus Disease 2019 Research; Serogroup; Microbiology; 03 medical and health sciences; Virology; Health Sciences; Genetics; Humans; MESH: SARS-CoV-2; Viral Diseases in Livestock and Poultry; Biology; Aged; Demography; MESH: Adolescent; Genomic Sequencing; MESH: Humans; Base Sequence; SARS-CoV-2; Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); MESH: Child, Preschool; MESH: COVID-19 Testing; VOCs; COVID-19; Gastrointestinal Viral Infections and Vaccines Development; MESH: Adult; Outbreak; MESH: Serogroup; Acoustics; Transmission (telecommunications); Computer science; MESH: Male; Coronavirus disease 2019 (COVID-19); Whole genome sequencing; FOS: Biological sciences; Mutation; Animal Science and Zoology; MESH: Female; 2019-20 coronavirus outbreak

The method of choice for SARS-CoV-2 variant detection is whole-genome sequencing using next-generation sequencing (NGS) technologies. Resources for this technology remain limited in many low- and middle-income countries, where it is not possible to perform whole-genome sequencing for representative numbers of SARS-CoV-2-positive cases.