Genomic Epidemiology of SARS-CoV-2 Divulge B.1, B.1.36, and B.1.1.7 as the Most Dominant Lineages in First, Second, and Third Wave of SARS-CoV-2 Infections in Pakistan

Impact of Comorbidity on the Duration from Symptom Onset to Death in Patients with Coronavirus Disease 2019: A Retrospective Study of 104,753 Cases in Pakistan

(1) Background: The evidence indicates that comorbidities are associated with an increase in the risk of death from coronavirus disease 2019 (COVID-19). It is unclear whether such an association is different for various combinations of chronic disease comorbidities. (2) Methods: From 16 March 2020 to 30 November 2021, 104,753 patients with confirmed COVID-19 from Khyber Pakhtunkhwa Province, Pakistan, were studied to determine the association between comorbidities and the duration from symptom onset to death in patients with COVID-19 by stratifying their comorbidity status. (3) Results: The patients with comorbidities had an 84% (OR, 0.16; 95% CI, 0.14 to 0.17) decrease in the duration from symptom onset to death, as opposed to patients without a comorbidity. Among the patients with only one comorbidity, chronic lung disease (OR, 0.06; 95% CI, 0.03 to 0.09) had a greater impact on the duration from symptom onset to death than hypertension (OR, 0.15; 95% CI, 0.13 to 0.18) or diabetes (OR, 0.15; 95% CI, 0.12 to 0.18). The patients with both hypertension and diabetes had the shortest duration (OR, 0.17; 95% CI, 0.14 to 0.20) among the patients with two comorbidities. (4) Conclusions: Comorbidity yielded significant adverse impacts on the duration from symptom onset to death in COVID-19 patients in Pakistan. The impact varied with different combinations of chronic disease comorbidities in terms of the number and type of comorbidities.

Genomic Diversity and Evolution of SARS-CoV-2 Lineages in Pakistan

The emergence of SARS-CoV-2 variants has posed a challenge to disease control efforts worldwide. This study explored the genomic diversity and phylogenetic relationship of SARS-CoV-2 variants reported in Pakistan. Our objective was to understand the transmission dynamics of different lineages within the country. We retrieved and analyzed spike protein sequences from Pakistan and compared them with reference sequences reported worldwide. Our analysis revealed the clustering of Pakistan-origin isolates in nine different clades representing different regions worldwide, suggesting the transmission of multiple lineages within the country. We found 96 PANGO lineages of SARS-CoV-2 in Pakistan, and 64 of these corresponded to 4 WHO-designated variants: Alpha, Beta, Delta, and Omicron. The most dominant variants in Pakistan were Alpha (B.1.1.7), Beta (B.1.351), Delta (B.1.617.2, AY.108), and Omicron (BA.2.75, BA.5.2), and the N-terminal domain and receptor binding regions were the most hypervariable regions of the spike gene. Compared to the reference strain, characteristic substitutions were found in dominant variants. Our findings emphasize the importance of continuously monitoring and assessing nucleotide and residue substitutions over time to understand virus evolutionary trends better and devise effective disease control interventions.

COVID-19 Vaccines Status, Acceptance and Hesitancy among Maintenance Hemodialysis Patients: A Cross-Sectional Study and the Implications for Pakistan and Beyond

COVID-19 vaccine hesitancy continues to be a widespread problem in Pakistan due to various conspiracy beliefs, myths and misconceptions. Since the hemodialysis population is at a higher risk of contracting infections, we sought to investigate the current COVID-19 immunization status and reasons for any vaccine hesitancy among these patients in Pakistan. This cross-sectional study was conducted among maintenance hemodialysis patients at six hospitals in the Punjab Province of Pakistan. Data were collected anonymously using a questionnaire. A total of 399 hemodialysis patients took part in the survey, the majority of them were male (56%) and aged 45-64 years. A calculated 62.4% of the patients reported receiving at least one dose of the COVID-19 vaccine. Of those vaccinated (249), 73.5% had received two doses and 16.9% had received a booster dose. The most common reasons for vaccination were "being aware they were at high risk" (89.6%), "fear of getting infected" (89.2%) and "willingness to fight against COVID-19-pandemic" (83.9%). Of the 150 patients who had not yet been vaccinated, only 10 showed a willingness to take the COVID-19 vaccine. The major reasons for refusal included "COVID-19 is not a real problem" (75%), the "corona vaccine is a conspiracy (72.1%)" and "I don't need the vaccine" (60.7%). Our study revealed that only 62% patients receiving hemodialysis were partially or completely vaccinated against COVID-19. Consequently, there is a need to initiate aggressive approaches to educate this high-risk population in order to address their concerns with vaccine safety and efficacy as well as correct current myths and misconceptions to improve the COVID-19 immunization status in this population.

Molecular Characterization and Selection of Indigenous SARS-CoV-2 Delta Variant for the Development of the First Inactivated SARS-CoV-2 Vaccine of Pakistan

Vaccines are one of the efficient means available so far for preventing and controlling the infection rate of COVID-19. Several researchers have focused on the whole virus’s (SARS-CoV-2) inactivated vaccines which are economically efficient to produce. In Pakistan, multiple variants of SARS-CoV-2 have been reported since the start of the pandemic in February 2020. Due to the continuous evolution of the virus and economic recessions, the present study was designed to develop an indigenous inactivated SARS-CoV-2 vaccine that might help not only to prevent the COVID-19 in Pakistan, it will also save the country’s economic resources. The SARS-CoV-2 were isolated and characterized using the Vero-E6 cell culture system. The seed selection was carried out using cross-neutralization assay and phylogenetic analysis. The selected isolate of SARS-CoV-2 (hCoV-19/Pakistan/UHSPK3-UVAS268/2021) was inactivated using beta-propiolactone followed by vaccine formulation using Alum adjuvant, keeping the S protein concentration as 5 μg/dose. The vaccine efficacy was evaluated by in vivo immunogenicity testing in laboratory animals and in in vitro microneutralization test. The phylogenetic analysis revealed that all the SARS-CoV-2 isolates reported from Pakistan nested into different clades, representing multiple introductions of the virus into Pakistan. The antisera raised against various isolates from different waves in Pakistan showed a varied level of neutralization titers. However, the antisera produced against a variant (hCoV-19/Pakistan/UHSPK3-UVAS268/2021; fourth wave) efficiently neutralized (1:64–1:512) all the tested SARS-CoV-2 isolates. The inactivated whole virus vaccine of SARS-CoV-2 was safe and it also elicited a protective immune response in rabbits and rhesus macaques on the 35th-day post-vaccination. The activity of neutralizing antibodies of vaccinated animals was found at 1:256–1:1024 at 35 days post-vaccination, indicating the effectiveness of the double-dose regime of the indigenous SARS-CoV-2 vaccine.

Characterization and phylogenetic analysis of Iranian SARS-CoV-2 genomes: A phylogenomic study

Background and Aim

Characterization of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) based on analyzing the evolution and mutations of viruses is crucial for tracking viral infections, potential mutants, and other pathogens. The purpose was to study the complete sequences of SARS-CoV-2 to reveal genetic distance and mutation rate among different provinces of Iran.

Methods

As of March 2020-April 2021, a total of 131 SARS-CoV-2 whole genome sequences submitted from Tehran and 133 SARS-CoV-2 full-length sequences from 24 cities with high coverage submitted to EpiCoV GISAID database were analyzed to infer clades and mutation annotation compared with the wild-type variant Wuhan-Hu-1.

Results

The results of variant annotation were revealed 11,204 and 9468 distinct genomes were identified among the samples from different cities and Tehran, respectively. The phylogenetic analysis of genomic sequences showed the presence of eight GISAID clades, namely GH, GR, O, GRY, G, GK, L, and GV, and six Nextstrain clades; that is, 19A, 20A, 20B, 20I (alpha, V1), 20H (Beta, V2), and 21I (Delta) in Iran. The GH (GISAID clade), 20A (Nextstrain clade), and B.1 (Pango lineage) were predominant in Iran. Notably, analysis of the spike protein revealed D614G mutation (S_D614G) in 56% of the sequences. Also, the delta variant of the coronavirus, the super-infectious strain that was first identified among the sequences submitted from the southern cities of the country such as Zahedan, Yazd and Bushehr, and most likely from these places to other cities of Iran as well has expanded.

Conclusions

Our results indicate that most of the circulated viruses in Iran in the early time of the pandemic had collected in eight GISAID clades. Therefore, a continuous and extensive genome sequence analysis would be necessary to understand the genomic epidemiology of SARS-CoV-2 in Iran.

Strain Wars: Competitive interactions between SARS-CoV-2 strains are explained by Gibbs energy of antigen-receptor binding

Since the beginning of the COVID-19 pandemic, SARS-CoV-2 has mutated several times into new strains, with an increased infectivity. Infectivity of SARS-CoV-2 strains depends on binding affinity of the virus to its host cell receptor. In this paper, we quantified the binding affinity using Gibbs energy of binding and analyzed the competition between SARS-CoV-2 strains as an interference phenomenon. Gibbs energies of binding were calculated for several SARS-SoV-2 strains, including Hu-1 (wild type), B.1.1.7 (alpha), B.1.351 (beta), P.1 (Gamma), B.1.36 and B.1.617 (Delta). The least negative Gibbs energy of binding is that of Hu-1 strain, -37.97 kJ/mol. On the other hand, the most negative Gibbs energy of binding is that of the Delta strain, -49.50 kJ/mol. We used the more negative Gibbs energy of binding to explain the increased infectivity of newer SARS-CoV-2 strains compared to the wild type. Gibbs energies of binding was found to decrease chronologically, with appearance of new strains. The ratio of Gibbs energies of binding of mutated strains and wild type was used to define a susceptibility coefficient, which is an indicator of viral interference, where a virus can prevent or partially inhibit infection with another virus.