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

Abstract

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.

Within-host evolutionary dynamics and tissue compartmentalization during acute SARS-CoV-2 infection

“…The co-occurrence of the dip in S:P681H frequency with the emergence of S:Q677H and subsequent reversal are consistent with competition between these two substitutions. Both substitutions have proliferated at the global scale, suggesting that in some cases within-host and global dynamics may be aligned (Hodcroft et al 2021; Colson et al 2022; Ghosh et al 2021; Saxena et al 2022). Critically, S:Q677H peaked at a time (day 5 post-enrollment) when this participant was still viral culture positive (see figure 1 in (Ke, Martinez, Smith, Gibson, Achenbach, et al 2022)), indicating the potential for this de novo variant to be successfully transmitted.…”

Quantitative Reverse Transcription PCR Surveillance of SARS-CoV-2 Variants of Concern in Wastewater of Two Counties in Texas, United States

“… 28 However, studies in India have suggested that this was the dominant strain in some cities prior to May 2021. 47 The B.1.617.2 variant, and its sublineages, is of particular concern for public health and the health care system due to its increased transmissibility compared to B.1.1.7 48 and increased resistance to neutralization by antibodies from plasma and serum. 49 Symptomatic and asymptomatic individuals with this variant are associated with more onward transmissions than similar individuals infected with the alpha variant 50 and, further, have a higher risk of hospitalization, need for intensive care unit admission, and mortality, 51 although other factors also contribute to this such as comorbidities, age, and vaccination status.…”

“…Numerous targets, in addition to the P681R mutation, have been used to separate out the two lineages, including G142D and T478 K, which have also been used to screen patients with RT-qPCR. 47 The mutations L452R and E484Q within the receptor binding domain were specific to lineage B.1.617.1 (kappa) and B.1.617.3, while L452R and T478 K were specific to the lineage B.1.617.2, 59 although this mutation has also now been found in the B.1.617.1 (kappa), B.1.617.2 (delta), and B.1.427/B.1.429 (epsilon) variants. 60 In the present study, we used both targets (E484Q and P681R) initially to verify the presence of the B.1.617 lineage and later to differentiate between the kappa and delta variants when both variants were spreading, though a recent review reported that B.1.617.2 does not have the E484Q mutation.…”

“…The third COVID-19 wave, categorized by the dominance of the B.1.617.2 variant (delta), was first identified in India in late 2020 and then labeled a variant of interest (VOI) in April 2021 and a VOC on May 11, 2021 . However, studies in India have suggested that this was the dominant strain in some cities prior to May 2021 . The B.1.617.2 variant, and its sublineages, is of particular concern for public health and the health care system due to its increased transmissibility compared to B.1.1.7 and increased resistance to neutralization by antibodies from plasma and serum .…”

“…While the P681R mutation in the S protein of the B.1.617 lineage is unique and newly identified in this variant of concern, there are numerous lineages associated with this strain, with phylogenetic analysis confirming the spread of both B.1.617.1 (kappa) and B.1.617.2 (delta) in India in early 2021, before delta became the dominant strain worldwide. Numerous targets, in addition to the P681R mutation, have been used to separate out the two lineages, including G142D and T478 K, which have also been used to screen patients with RT-qPCR . The mutations L452R and E484Q within the receptor binding domain were specific to lineage B.1.617.1 (kappa) and B.1.617.3, while L452R and T478 K were specific to the lineage B.1.617.2, although this mutation has also now been found in the B.1.617.1 (kappa), B.1.617.2 (delta), and B.1.427/B.1.429 (epsilon) variants .…”