Complete genome sequencing of SARS‑CoV‑2 strains: A pilot survey in Palestine reveals spike mutation H245N

Abstract

Objectives: SARS‑CoV‑2, severe respiratory syndrome coronavirus‑2, is an RNA virus that emerged from China sweeping the globe in the form of a pandemic that became an international public health concern. This pilot study aimed to describe the genetic variation and molecular epidemiology of SARS‑CoV‑2 in Palestine in fall 2020. Results: To achieve these aims, whole genome sequencing of SARS‑CoV‑2, phylogenetic analysis, haplotype net‑working and genetic diversity analysis were performed. These analyses revealed a unique spike mutation H245N that has never been reported before. The phylogenetic analysis depicted that three clusters existed in Palestinian SARS‑ CoV‑2 genome sequences, in which cluster‑I comprised the majority of clusters by 90%. Congruently, the haplotype network analysis depicted the same three clusters with a total of 39 haplotypes. The genetic diversity analysis showed that Cluster‑I is highly diverse as confirmed by statistically significant mutation rate indices, Tajima’s D and Fu‑Li’s‑F tests (−2.11 and 2.74, respectively), highest number of mutations (Eta=120), highest number of haplotypes (h=17), and highest average number of nucleotide differences between any two sequences (S=118). The study confirmed the high genetic diversity among the Palestine