Whole genome comparison of Pakistani Corona virus with Chinese and US Strains along with its predictive severity of COVID-19

Response of vaccination on community transmission of COVID-19: a dynamical approach

Due to the severity of COVID-19, vaccination campaigns have been or are underway in most parts of the world. In the current circumstances, it is obligatory to examine the response of vaccination on transmission of the SARS-CoV-2 virus when there are many vaccines available. Considering the importance of vaccination, a dynamic model has been proposed to provide an insight in the same direction. A mathematical model has been developed where six population compartments viz. susceptible, infected, vaccinated, home-isolated, hospitalized and recovered population are considered. Moreover, two novel parameters are included in the model to ascertain the effectiveness and speed of the vaccination campaign. Reproduction number and local stability of both the disease-free and endemic equilibrium points are studied to examine the nature of population dynamics. Graphical results for the community stage of COVID-19 infection are simulated and compared with real data to ascertain the validity of our model. The data is then studied to understand the impact of vaccination. These numerical results evidently demonstrate that home isolation and hospitalization should continue for the infected people until the transmission of the virus from person to person reduces sufficiently after completely vaccinating every nation. This model also recommends that all type of prevention measures should still be taken to avoid any type of critical situation due to infection and also reduce the death rate.

Insect cell expression and purification of recombinant SARS-COV-2 spike proteins that demonstrate ACE2 binding

The COVID-19 pandemic caused by SARS-CoV-2 infection has led to socio-economic shutdowns and the loss of over 5 million lives worldwide. There is a need for the identification of therapeutic targets to treat COVID-19. SARS-CoV-2 spike is a target of interest for the development of therapeutic targets. We developed a robust SARS-CoV-2 S spike expression and purification protocol from insect cells and studied four recombinant SARS-CoV-2 spike protein constructs based on the original SARS-CoV-2 sequence using a baculovirus expression system: a spike protein receptor-binding domain that includes the SD1 domain (RBD) coupled to a fluorescent tag (S-RBD-eGFP), spike ectodomain coupled to a fluorescent tag (S-Ecto-eGFP), spike ectodomain with six proline mutations and a foldon domain (S-Ecto-HexaPro(+F)), and spike ectodomain with six proline mutations without the foldon domain (S-Ecto-HexaPro(-F)). We tested the yield of purified protein expressed from the insect cell lines Spodoptera frugiperda (Sf9) and Trichoplusia ni (Tni) and compared it to previous research using mammalian cell lines to determine changes in protein yield. We demonstrated quick and inexpensive production of functional glycosylated spike protein of high purity capable of recognizing and binding to the angiotensin converting enzyme 2 (ACE2) receptor. To further confirm functionality, we demonstrate binding of eGFP fused construct of the spike ectodomain (S-Ecto-eGFP) to surface ACE2 receptors on lung epithelial cells by flow cytometry analysis and show that it can be decreased by means of receptor manipulation (blockade or downregulation).

Genomic Characterization of SARS-CoV2 from Peshawar Pakistan Using Next-Generation Sequencing

This study aimed to characterize the whole genome of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2) isolated from an oropharyngeal swab specimen of a Pashtun Pakistani patient using next-generation sequencing. Upon comparing the SARS-CoV2 genome to the reference genome, a total of 10 genetic variants were identified. Among the 10 genetic variants, 1 missense mutation (c.1139A > G, p.Lys292Glu) in the Open Reading Frame 1ab (ORF1ab) positioned at 112 in the non-structural protein 2 (NSP2) was found to be unique. Phylogenetic analysis (n = 84) revealed that the current SARS-CoV2 genome was closely clustered with 8 Pakistani strains belonging to Punjab, Federal Capital, Azad Jammu and Kashmir (AJK), and Khyber Pakhtunkhwa (KP). In addition, the current SARS-CoV2 genome was very similar to the genome of SARS-CoV2 reported from Guam, Taiwan, India, the USA, and France. Overall, this study reports a slight mismatch in the SARS-CoV2 genome, indicating the presence of a single unique missense mutation. However, phylogenetic analysis revealed that the current SARS-CoV2 genome was closely clustered with 8 other Pakistani strains.