Substitution spectra of SARS-CoV-2 genome from Pakistan reveals insights into the evolution of variants across the pandemic

Changing morbidity and mortality due to COVID-19 across the pandemic has been linked with factors such as the emergence of SARS-CoV-2 variants and vaccination. Mutations in the Spike glycoprotein enhanced viral transmission and virulence. We investigated whether SARS-CoV-2 mutation rates and entropy were associated COVID-19 in Pakistan, before and after the introduction of vaccinations. We analyzed 1,705 SARS-CoV-2 genomes using the Augur phylogenetic pipeline. Substitution rates and entropy across the genome, and in the Spike glycoprotein were compared between 2020, 2021 and 2022 (as periods A, B and C). Mortality was greatest in B whilst cases were highest during C. In period A, G clades were predominant, and substitution rate was 5.25 × 10-4 per site per year. In B, Delta variants dominated, and substitution rates increased to 9.74 × 10-4. In C, Omicron variants led to substitution rates of 5.02 × 10-4. Genome-wide entropy was the highest during B particularly, at Spike E484K and K417N. During C, genome-wide mutations increased whilst entropy was reduced. Enhanced SARS-CoV-2 genome substitution rates were associated with a period when more virulent SARS-CoV-2 variants were prevalent. Reduced substitution rates and stabilization of genome entropy was subsequently evident when vaccinations were introduced. Whole genome entropy analysis can help predict virus evolution to guide public health interventions

Higher interferon gamma response to mycobacterium tuberculosis antigen is associated with less severe COVID-19

Background: Mycobacterium tuberculosis (Mtb) and SARS-CoV-2 are both respiratory pathogens and their interaction in host is not well understood, especially in case of latent tuberculosis (LTBi). LTBi is known to alter host immune response and its impact on outcome of COVID-19 disease is still under debate.Objectives: This study was designed to compare the interferon-gamma (IFN-γ) response against Mtb antigens in healthy individuals and COVID-19 patients and its association with disease severity. We also compared IgG response against receptor-binding domain (RBD) protein of SARS-CoV-2 virus in the presence or absence of LTBi.Methods: A total of 275 participants as 147 healthy controls and 128 COVID-19 patients were recruited. COVID-19 patients were categorized according to the WHO ordinary scale in 1–3 (ambulatory: n = 103) or 4–7 (hospitalized: n = 25) disease severity. LTBi was screened through X DOT TB-an ELISPOT assay using whole blood. IFN-γ response was compared as spot forming units in PBMCs of X DOT TB assay supernatants. Anti-RBD and anti-Rubella IgG levels were measured through ELISA.Results: We found the frequency of LTBi was lower (18%) among COVID-19 than in the HC group (32%; P \u3c 0.001). All LTBi-positive COVID-19 had mild disease. COVID-19 frequency and severity increased with age as well as with comorbidities, independently of the LTBi status (P \u3c 0.05). Levels of Mtb-specific IFN-g secreting cells were lower in the COVID-19 than in healthy controls (HC) individuals (P = 0.04). Severe COVID-19 cases showed lower IFN-γ responses to Mtb than those with mild disease (P = 0.02). The anti-Sars-Cov-2 RBD IgG levels did not differ between LTBi positive or negative individuals (P = NS). Anti-Rubella IgG titers in LTBi positive or negative individuals were similar (P = NS).Conclusion: Our study has shown low detection of latent TB in COVID-19 individuals as compared to healthy controls. We further observed no detection of LTBi in hospitalized COVID-19 which is suggestive of downregulated T-cell response in severe COVID-19. There was no difference in IgG response against SARS-Cov-2 RBD or Rubella in the presence or absence of LTBi. Further studies are required to study the underlying differential molecular pathways regulated in these individuals

Substitution spectra of SARS-CoV-2 genome from Pakistan reveals insights into the evolution of variants across the pandemic

Abstract Changing morbidity and mortality due to COVID-19 across the pandemic has been linked with factors such as the emergence of SARS-CoV-2 variants and vaccination. Mutations in the Spike glycoprotein enhanced viral transmission and virulence. We investigated whether SARS-CoV-2 mutation rates and entropy were associated COVID-19 in Pakistan, before and after the introduction of vaccinations. We analyzed 1,705 SARS-CoV-2 genomes using the Augur phylogenetic pipeline. Substitution rates and entropy across the genome, and in the Spike glycoprotein were compared between 2020, 2021 and 2022 (as periods A, B and C). Mortality was greatest in B whilst cases were highest during C. In period A, G clades were predominant, and substitution rate was 5.25 × 10–4 per site per year. In B, Delta variants dominated, and substitution rates increased to 9.74 × 10–4. In C, Omicron variants led to substitution rates of 5.02 × 10–4. Genome-wide entropy was the highest during B particularly, at Spike E484K and K417N. During C, genome-wide mutations increased whilst entropy was reduced. Enhanced SARS-CoV-2 genome substitution rates were associated with a period when more virulent SARS-CoV-2 variants were prevalent. Reduced substitution rates and stabilization of genome entropy was subsequently evident when vaccinations were introduced. Whole genome entropy analysis can help predict virus evolution to guide public health interventions