id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
cord-302813-963ypqow	Tegally, H.	Major new lineages of SARS-CoV-2 emerge and spread in South Africa during lockdown.	2020-10-30		.txt	text/plain	3543	200	59	Through the unprecedented sharing of SARS-CoV-2 sequences during this pandemic, including from one of the first cases in Wuhan, China (MN908947.3) 2 , genomic epidemiology investigations globally are playing a major role in characterizing and understanding this emerging virus [4] [5] [6] [7] [8] [9] . The profile of SARS-CoV-2 epidemiological progression in South Africa was largely influenced by the implementation of lockdown measures in the early phases of the epidemic and the subsequent easing of these measures. We focused on the three largest monophyletic lineage clusters (C.1, B.1.1.54, B.1.1.56,) that spread in South Africa during lockdown and then grew into large transmission clusters during the peak infections phase of the epidemic (Fig 1C) . Our analysis therefore shows that a number of SARS-CoV-2 lineages, each with unique mutations, emerged within localized epidemics during lockdown even as the introduction of new lineages from outside South Africa was being curbed.	./cache/cord-302813-963ypqow.txt	./txt/cord-302813-963ypqow.txt