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Distinct from the PANGOLIN tool, Pango lineages are regularly, manually curated based on the current globally circulating diversity. A large phylogenetic tree is constructed from an alignment containing publicly available SARS-CoV-2 genomes, and sub-clusters of sequences in this tree are manually examined and cross-referenced against epidemiological information to designate new lineages; these ...
The closest known viral relatives of SARS-CoV-2 are RaTG13 and BANAL-52, sampled from horseshoe bat droppings in Yunnan province in China and Feuang, Laos, respectively. The evolutionary distance between SARS-CoV-2 and RaTG13 is estimated to be about 50 years (between 38 and 72 years). [18] [19]
As time went on, the evolution of SARS-CoV-2's genome (by means of random mutations) led to mutant specimens of the virus (i.e., genetic variants), observed to be more transmissible, to be naturally selected. Notably, both the Alpha and the Delta variants were observed to be more transmissible than previously identified viral strains. [13]
The most similar known viruses to SARS-CoV-2 include bat coronaviruses RpYN06 with 94.5% identity, [15] and RmYN02 with 93% identity [18] RaTG13 was not the direct progenitor of SARS-CoV-2. [19] Temmam et al. found no serological evidence for exposure to BANAL-52 among bat handlers and guano collectors in the area of Laos where it was sampled ...
The mutation rate estimated from early cases of SARS-CoV-2 was of 6.54 × 10 −4 per site per year. [86] Coronaviruses in general have high genetic plasticity, [89] but SARS-CoV-2's viral evolution is slowed by the RNA proofreading capability of its replication machinery. [90]
From the early outbreak of the COVID-19 pandemic, rumors and speculation arose about the possible lab origins of SARS-CoV-2, the causative agent of the COVID-19 disease.. Different versions of the lab origin hypothesis present different scenarios in which a bat-borne progenitor of SARS-CoV-2 may have spilled over to humans, including a laboratory-acquired infection of a natural or engineered vir
The team at PANGO behind manually curating the phylogenetic tree of SARS-CoV-2 noted the earliest sequence was from 7 December 2020. They proposed a new designation for the variant containing the mutations at the spike protein including G142D, L452R, E484Q, D614G, P681R among others and this variant went to be assigned PANGO lineage B.1.617 on ...
Throughout the COVID-19 pandemic, the genome of SARS-CoV-2 viruses has been sequenced many times, resulting in identification of thousands of distinct variants. In a World Health Organization analysis from July 2020, ORF1ab was the most frequently mutated gene, followed by the S gene encoding the spike protein.