Mutational characterization of Omicron SARS-CoV-2 lineages circulating in Chhattisgarh, a central state of India

Genomic characterization of Influenza A (H1N1)pdm09 and SARS-CoV-2 from Influenza Like Illness (ILI) and Severe Acute Respiratory Illness (SARI) cases reported between July-December, 2022

Influenza Like Illness (ILI) and Severe Acute Respiratory Infection (SARI) cases are more prone to Influenza and SARS-CoV-2 infection. Accordingly, we genetically characterized Influenza and SARS-CoV-2 in 633 ILI and SARI cases by rRT-PCR and WGS. ILI and SARI cases showed H1N1pdm09 prevalence of 20.9% and 23.2% respectively. 135 (21.3%) H1N1pdm09 and 23 (3.6%) H3N2 and 5 coinfection (0.78%) of H1N1pdm09 and SARS-CoV-2 were detected. Phylogenetic analysis revealed H1N1pdm09 resemblance to clade 6B.1A.5a.2 and their genetic relatedness to InfA/Perth/34/2020, InfA/Victoria/88/2020 and InfA/Victoria/2570/2019. Pan 24 HA and 26 NA nonsynonymous mutations and novel HA (G6D, Y7F, Y78H, P212L, G339R, T508K and S523T) and NA (S229A) mutations were observed. S74R, N129D, N156K, S162N, K163Q and S164T alter HA Cb and Sa antibody recognizing site. Similarly, M19T, V13T substitution and multiple mutations in transmembrane and NA head domain drive antigenic drift. SARS-CoV-2 strains genetically characterized to Omicron BA.2.75 lineage containing thirty nonsynonymous spike mutations exhibited enhanced virulence and transmission rates. Coinfection although detected very minimal, the mutational changes in H1N1pdm09 and SARS-CoV-2 virus infected individuals could alter antibody receptor binding sites, allowing the viruses to escape immune response resulting in better adaptability and transmission. Thus continuous genomic surveillance is required to tackle any future outbreak.

Clustering analysis for the evolutionary relationships of SARS-CoV-2 strains

To explore the differences and relationships between the available SARS-CoV-2 strains and predict the potential evolutionary direction of these strains, we employ the hierarchical clustering analysis to investigate the evolutionary relationships between the SARS-CoV-2 strains utilizing the genomic sequences collected in China till January 7, 2023. We encode the sequences of the existing SARS-CoV-2 strains into numerical data through k-mer algorithm, then propose four methods to select the representative sample from each type of strains to comprise the dataset for clustering analysis. Three hierarchical clustering algorithms named Ward-Euclidean, Ward-Jaccard, and Average-Euclidean are introduced through combing the Euclidean and Jaccard distance with the Ward and Average linkage clustering algorithms embedded in the OriginPro software. Experimental results reveal that BF.28, BE.1.1.1, BA.5.3, and BA.5.6.4 strains exhibit distinct characteristics which are not observed in other types of SARS-CoV-2 strains, suggesting their being the majority potential sources which the future SARS-CoV-2 strains' evolution from. Moreover, BA.2.75, CH.1.1, BA.2, BA.5.1.3, BF.7, and B.1.1.214 strains demonstrate enhanced abilities in terms of immune evasion, transmissibility, and pathogenicity. Hence, closely monitoring the evolutionary trends of these strains is crucial to mitigate their impact on public health and society as far as possible.

A comprehensive profile of SARS-CoV-2 variants spreading during the COVID-19 pandemic: a genomic characterization study from Chhattisgarh State, India

SARS-CoV-2 has expressively changed its sequences during the COVID-19 pandemic situation by encompassing persistent evolutionary mutational changes resulting in the emergence of many clades and lineages. Evolution of these SARS-CoV-2 variants have significantly imparted fitness advantage to the virus, enhanced its transmissibility and severity of the disease. These new variants are a potential threat to the vaccine efficacy as well. It is therefore pertinent to monitor the evolution of these variants and their epidemiological and clinical impact, in a geographic setting. This study has thus looked into the geographic distribution and genetic diversity of SARS-CoV-2 variants and the evolutionary circulation of different clades in Chhattisgarh (CG) state from March 2020 to July 2023. A total of 3018 sequences were retrieved from the GISAID database, in which 558 were submitted by us. The demographic data revealed male preponderance of 56.45% versus 43.54% females, with the overall mean age of 36.5 years. SARS-CoV-2 sequences represented many variants viz., Delta (55%), Omicron (22%) and others (15%) with a small proportion of recombinant (5%), Kappa (2%), and Alpha (1%). The viral clades G was found predominant for a year from initial days of pandemic in March, 2020 to January, 2021 which then subsequently evoluted to subclade GK (Delta B.1.617.2) and remained in circulation in CG till November, 2021. From December 2021, the GRA (Omicron B.1.1.529) variant had replaced GK to become the dominant strain and continues to predominate in present time. GRA clade is however continuously encompassing new recombinant strains, having various non-synonymous mutations especially in spike protein. The non-synonymous mutation P314L in ORF1b, S84L in ORF8 and D614G in spike protein were found as the pan mutation carried over from clade G to GRA. The continuous evolution in SARS-CoV2 warrants periodical geographic genomic surveillance monitoring to timely detect any new variants having the potential of causing future outbreak.

Genome sequencing of SARS-CoV-2 omicron variants in Delhi reveals alterations in immunogenic regions in spike glycoprotein

The SARS-CoV-2 omicron variants keep accumulating a large number of mutations in the spike (S) protein, which contributes to greater transmissibility and a rapid rise to dominance within populations. The identification of mutations and their affinity to the cellular angiotensin-converting enzyme-2 (ACE-2) receptor and immune evasion in the Delhi NCR region was under-acknowledged. The study identifies some mutations (Y505 reversion, G339H, and R346T/N) in genomes from Delhi, India, and their probable implications for altering the immune response and binding affinity for ACE-2. The spike mutations have influenced the neutralizing activity of antibodies against the omicron variant, which shows partial immune escape. However, researchers are currently exploring various mitigation strategies to tackle the potential decline in efficacy or effectiveness against existing and future variants of SARS-CoV-2. These strategies include modifying vaccines to target specific variants, such as the omicron variant, developing multivalent vaccine formulations, and exploring alternative delivery methods. To address this, it is also necessary to understand the impact of these mutations from a different perspective, especially in terms of alterations in antigenic determinants. In this study, we have done whole genome sequencing (WGS) of SARS-CoV-2 in COVID-19 samples from Delhi, NCR, and analyzed the spike's mutation with an emphasis on antigenic alterations. The impact of mutation in terms of epitope formation, loss/gain of efficiency, and interaction of epitopes with antibodies has been studied. Some of the mutations or variant genomes seem to be the progenitors of the upcoming variants in India. Our analyses suggested that weakening interactions with antibodies may lead to immune resistance in the circulating genomes.

Genomic surveillance of genes encoding the SARS-CoV-2 spike protein to monitor for emerging variants on Jeju Island, Republic of Korea

Introduction

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been fueled by new variants emerging from circulating strains. Here, we report results from a genomic surveillance study of SARS-CoV-2 on Jeju Island, Republic of Korea, from February 2021 to September 2022.

Methods

A total of 3,585 SARS-CoV-2 positive samples were analyzed by Sanger sequencing of the gene encoding the spike protein before performing phylogenetic analyses.

Results

We found that the Alpha variant (B.1.1.7) was dominant in May 2021 before being replaced by the Delta variant (B.1.617.2) in July 2021, which was dominant until December 2021 before being replaced by the Omicron variant. Mutations in the spike protein, including N440K and G446S, have been proposed to contribute to immune evasion, accelerating the spread of Omicron variants.

Discussion

Our results from Juju Island, Republic of Korea, are consistent with and contribute to global surveillance efforts crucial for identifying new variants of concern of SARS-CoV-2 and for monitoring the transmission dynamics and characteristics of known strains.

Clinical and humoral immune response characterization of SARS-CoV-2 Omicron BA.2.38 infection in pediatric patients

Omicron variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a health concern for both unvaccinated and vaccinated individuals against coronavirus disease 2019 (COVID-19). To date, the humoral immune response following vaccination and natural infection remains uncharacterized in children ages 17 years and younger. To address this concern, we performed clinical and immunological analyses of IgM and IgG antibody responses to SARS-CoV-2 Omicron BA.2.38 infection in 64 pediatric patients. COVID-19 symptom severity decreased with age in pediatric patients, from 70.8% (17/24) in patients 0-2 years of age to 50% (6/12) and 50% (14/28) in patients 3-5 years and 6-17 years of age, respectively. Furthermore, fewer patients experienced symptoms when vaccinated with the CoronaVac or BBIBP-CorV vaccine (50%, 13/26) than unvaccinated patients (71%, 22/31). Using a protein array, we found that the Omicron BA.2.38 infection induced antibody responses to other Omicron variants (Omicron BA.1-BA.5), which increased with vaccination. Notably, non-Omicron and Omicron variants showed distinct serotypes. Altogether, our results provide insight into the clinical and immunological characteristics of pediatric patients with COVID-19 Omicron BA.2.38 who have and have not been vaccinated against COVID-19. These data may help develop more effective diagnostic tests and vaccines in the future.