pone.0256451.g001.tif (566.3 kB)

Maximum-Likelihood phylogenetic tree of SARS-CoV-2 sequences from Karachi.

figure

posted on 2021-08-31, 17:25 authored by Najia Karim Ghanchi, Asghar Nasir, Kiran Iqbal Masood, Syed Hani Abidi, Syed Faisal Mahmood, Akbar Kanji, Safina Razzak, Waqasuddin Khan, Saba Shahid, Maliha Yameen, Ali Raza, Javaria Ashraf, Zeeshan Ansar, Mohammad Buksh Dharejo, Nazneen Islam, Zahra Hasan, Rumina Hasan

The tree was constructed using 21 genomes from this study (AKU) (S2 Table) along with 58 other Pakistani and 449 full-length SARS-CoV-2 reference sequences (S1 File). AKU study sequences are indicated in blue, while other Pakistan sequences are shown in green. AKU sequences clustered with those from India (purple), Saudi Arabia (orange), United States (pink), China (light blue), Australia (turquoise), Bangladesh (yellow), France (light green) and also with other sequences from Pakistan (green). The root of the tree was determined using TreeRate tool by applying generalized midpoint rooting strategy. Nodes with significant (>0.90) aLRT-SH like support values are colored maroon. The tree was visualized and edited in Figtree software.