China
Africa
Explore chapters and articles related to this topic
NGS technologies for detection of SARS-CoV-2 strains and mutations
Published in Sanjeeva Srivastava, Multi-Pronged Omics Technologies to Understand COVID-19, 2022
Manisha Choudhury, Ayushi Verma, Ankit Halder, Arup Acharjee
From the widespread infections of SARS-CoV-2, it is evident that it transmits to and within humans. In SARS-CoV-2, its genome shared nearly 96% identity with BatCoV RaTG13 isolated from Rhinolophus affinis found in Yunan Province in China. It was crucial to identify intermediate hosts, if any, to block the interspecies transmission. At almost the same time the outbreak occurred, SARS-CoV-like CoV from dead Malayan pangolins was extracted. The viral genome isolated from pangolin shared nearly 91.02% and 90.55% identical regions with the SARS-CoV-2 and BatCoV RaTG13 genomes, respectively. The S1 protein of Pangolin-CoV further supported this finding. Pangolin-CoV and SARS-CoV-2 shared the exact five amino acid sequences required to interact with human ACE2, but a slight variation of amino acids is present in RaTG13. The S1/S2 cleavage site remains intact in all three CoVs. Thus, it was concluded that the pangolin species possess reserves of SARS-CoV-2-like viruses (T. Zhang, Wu, and Zhang 2020) and are a probable intermediate species responsible for the outbreak.
COVID-19;-The origin, genetics,and management of the infection of mothers and babies
Published in Egyptian Journal of Basic and Applied Sciences, 2020
Hassan Ih El-Sayyad, Yousef Ka Abdalhafid
The seventh novel human infecting beta-coronavirus that causes pneumonia (SARS-CoV-2) originated in Wuhan, China. There is no correlation between COVID-19 and other respiratory diseases. A phylogenetic tree was constructed from the genome sequences depending on the presence and absence of homologs of ten SARS-CoV-2 proteins. The data suggests that SARS-CoV-2 is most closely related to Bat CoV RaTG13 and belongs to subgenus Sarbecovirus of Betacoronavirus, together with SARS-CoV and Bat-SARS-like CoV. The phylogenetic profiling cluster of homolog proteins of one annotated SARS-CoV-2 protein against other genome sequences revealed two clades of ten SARS-CoV-2 proteins. Clade 1 consisted of a group of conserved proteins in Orthocoronavirinae comprising Orf1ab polyprotein, nucleocapsid protein, spike glycoprotein, and membrane protein. Clade 2 comprised six proteins exclusive to Sarbecovirus and Hibecovirus. Two of six Clade 2 nonstructural proteins, NS7b and NS8, were exclusively conserved among SARS-CoV-2, BetaCoV_RaTG, and BatSARS-like Cov. NS7b and NS8 have previously been shown to affect immune response signaling in the SARS-CoV experimental model. Thus, we speculated that knowledge of the functional changes in the NS7b and NS8 proteins during evolution could provide important information to explore the human infective property of SARS-CoV-2 [97].