Evaluation of Genomic Surveillance of SARS-CoV-2 Virus Isolates and Comparison of Mutational Spectrum of Variants in Bangladesh

Abstract

The SARS-CoV-2-induced disease, COVID-19, remains a worldwide public health concern due to its high rate of transmission, even in vaccinated and previously infected people. In the endemic state, it continues to cause significant pathology. To elu- cidate the viral mutational changes and screen the emergence of new variants of concern, we conducted this study in Bangladesh. The viral RNA genomes extracted from 25 ran- domly collected samples of COVID-19-positive patients from March 2021 to February 2022 were sequenced using Illumina COVID Seq protocol and genomic data processing, as well as evaluations performed in DRAGEN COVID Lineage software. In this study, the percentage of Delta, Omicron, and Mauritius variants identified were 88%, 8%, and 4%, respectively. All of the 25 samples had 23,403 A>G (D614G, S gene), 3037 C>T (nsp3), and 14,408 C>T (nsp12) mutations, where 23,403 A>G was responsible for increased transmis- sion. Omicron had the highest number of unique mutations in the spike protein (i.e., sub- stitutions, deletions, and insertions), which may explain its higher transmissibility and immune-evading ability than Delta. A total of 779 mutations were identified, where 691 substitutions, 85 deletions, and 3 insertion mutations were observed. To sum up, our study will enrich the genomic database of SARS-CoV-2, aiding in treatment strategies along with understanding the virus's preferences in both mutation type and mutation site for predicting newly emerged viruses' survival strategies and thus for preparing to coun- teract them.

Keywords: Bangladesh; COVID-19; Delta; Mauritius; Omicron; SARS-CoV-2; mutation.

Figure 1

Vaccination status of COVID-19 patients.

Figure 2

Distribution of SARS-CoV-2 variants in COVID-19 patients.

Figure 3

Needle plot of the visual representation of amino acid (AA) substitution (red lollipop) and deletion (blue lollipop) mutations in different domains and motifs of spike glycoprotein (S protein) of the Delta (a), Omicron (b), and Mauritius (c) variants of SARS-CoV-2 virus. Bold and blue font are used to refer to the most frequent mutations in a specific variant’s samples, while red color represents remarkable variants, and red-colored mutations are common for 3 variants. On the other hand, black and bold font represent common mutations for any of the 2 variants.

Figure 4

Lollipop plot representing the amino acid (AA) substitution and deletion mutations in nucleocapsid protein (N protein) of Delta (a), Omicron (b), and Mauritius (c) variants, where the red lollipop represents the aa substitution mutation, and deletion mutations are symbolized by the blue one. No deletion mutation was observed in the nucleocapsid protein of the Delta variant. Regarding the annotation of mutations, the bold red font represents the signature of important mutations reported in previous studies, while the bold blue font represents mutations that were found in a specific variant in highest frequency. Bold black font was used to refer to mutations that were present in 2 variants at least.

Figure 5

Substitution (red lollipop) and deletion (blue lollipop) mutations in ORF1a polyprotein region of the 3 variants, Delta (a), Omicron (b), and Mauritius (c), are shown in this needle plot. Annotation of mutations was performed based on the following font style—bold black font refers to mutations identified in at least 2 variants; bold blue font refers to mutations that were observed in highest frequency in a specific variant; bold red font indicates the noteworthy mutations and, in some cases, mutations that were found in 3 variants.

Figure 6

Exhibition of substitution mutations in ORF1b polyprotein region in Delta (a), Omicron (b), and Mauritius (c) viral genomes. No amino acid deletion was observed in this region of ORF1b gene. Here, the red lollipop presents the aa substitution mutation, and deletion mutations are symbolized by the blue one. For annotation of the mutations, bold black font refers to mutations that were present in 2 variants; the bold blue one represents mutations that were present in most of the samples of a specific variant; and bold red font implies the remarkable mutations and, in some cases, it refers to the mutations that were present in all 3 variants.

Figure 7

Amino acid (AA) substitution and AA deletion mutation numbers in different proteins of viral genomes.