Molecular and Serological Characterization of the SARS-CoV-2 Delta Variant in Bangladesh in 2021

• Published in: Viruses Vol. 13; no. 11; p. 2310
• Main Authors: Ghosh, Asish Kumar, Kaiser, Marco, Molla, Md. Maruf Ahmed, Nafisa, Tasnim, Yeasmin, Mahmuda, Ratul, Rifat Hossain, Sharif, Md. Mohiuddin, Akram, Arifa, Hosen, Nur, Mamunur, Rashid, Amin, Md. Robed, Islam, Alimul, Hoque, Md. Ehsanul, Landt, Olfert, Lytton, Simon D.
• Format: Journal Article
• Language: English
• Published: Basel MDPI AG 19.11.2021; MDPI
• Subjects: amino acid mutations; Amino acids; anti-N-protein IgG; anti-S-protein IgG; antibodies; antibody formation; Antibody response; Bangladesh; Coronaviruses; COVID-19; COVID-19 infection; COVID-19 vaccines; delta variant; Developing countries; Disease transmission; Genomes; Immunoglobulin A; Immunoglobulin G; Infections; Influenza; LDCs; Manufacturers; Melting curve; Mutation; Nucleotide sequence; nucleotide sequences; Pandemics; Phylogenetics; Polymerase chain reaction; Proteins; SARS-CoV-2; Severe acute respiratory syndrome coronavirus 2; Software; Spike protein; Vaccination; viral load; Viruses; Bangladesh; United States > US; China; Germany; India
• ISSN: 1999-4915; 1999-4915
• DOI: 10.3390/v13112310

Novel SARS-CoV-2 variants are emerging at an alarming rate. The delta variant and other variants of concern (VoC) carry spike (S)-protein mutations, which have the potential to evade protective immunity, to trigger break-through infections after COVID-19 vaccination, and to propagate future waves of COVID-19 pandemic. To identify SARS CoV-2 variants in Bangladesh, patients who are RT-PCR-positive for COVID-19 infections in Dhaka were screened by a RT-PCR melting curve analysis for spike protein mutations. To assess the anti-SARS CoV-2 antibody responses, the levels of the anti-S -proteins IgA and IgG and the anti-N-protein IgG were measured by ELISA. Of a total of 36 RT-PCR positive samples (75%), 27 were identified as delta variants, with one carrying an additional Q677H mutation and two with single nucleotide substitutions at position 23029 (compared to Wuhan-Hu-1 reference NC 045512) in the genome sequence. Three (8.3%) were identified as beta variants, two (5.5%) were identified as alpha variants, three (8.3%) were identified as having a B.1.1.318 lineage, and one sample was identified as an eta variant (B.1.525) carrying an additional V687L mutation. The trend of higher viral load (lower Cp values) among delta variants than in the alpha and beta variants was of borderline statistical significance (p = 0.045). Prospective studies with larger Bangladeshi cohorts are warranted to confirm the emergence of S-protein mutations and their association with antibody response in natural infection and potential breakthrough in vaccinated subjects.