Evolutionary dynamics of SARS-CoV-2 circulating in Yogyakarta and Central Java, Indonesia: sequence analysis covering furin cleavage site (FCS) region of the spike protein

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a new virus responsible for the COVID-19 pandemic. The emergence of the new SARS-CoV-2 has been attributed to the possibility of evolutionary dynamics in the furin cleavage site (FCS) region. This study aimed to analyze the sequence of the FCS region in the spike protein of SARS-CoV-2 isolates that circulated in the Special Region of Yogyakarta and Central Java provinces in Indonesia. The RNA solution extracted from nasopharyngeal swab samples of confirmed COVID-19 patients were used and subjected to cDNA synthesis, PCR amplification, sequencing, and analysis of the FCS region. The sequence data from GISAID were also retrieved for further genome analysis. This study included 52 FCS region sequences. Several mutations were identified in the FCS region, i.e., D614G, Q675H, Q677H, S680P, and silent mutation in 235.57 C > T. The most important mutation in the FCS region is D614G. This finding indicated the G614 variant was circulating from May 2020 in those two provinces. Eventually, the G614 variant totally replaced the D614 variant from September 2020. All Indonesian SARS-CoV-2 isolates during this study and those deposited in GISAID showed the formation of five clade clusters from the FCS region, in which the D614 variant is in one specific cluster, and the G614 variant is dispersed into four clusters. The data indicated there is evolutionary advantage of the D614G mutation in the FCS region of the spike protein of SARS-CoV-2 circulating in the Special Region of Yogyakarta and Central Java provinces in Indonesia.

Keywords: D614G mutation; Furin cleavage site; SARS-CoV-2; Spike protein.

Fig. 1

The geographical distribution of the D614G variants reported in Indonesia from April 2020 to January 2021. The GISAID database showed that the D614 variant has been found in 25 provinces in Indonesia and it was subsequently replaced by the new G614 variant, including in the Special Region of Yogyakarta and Central Java provinces (inset). Sequence data from this study showed that during May to October 2020, the D614 variant remained circulating in Special Region of Yogyakarta in exceedingly small numbers (the last date of collected sample was August 2020), while all analyzed samples in Central Java were the G614 variant. Blue dots: D614 variants, Orange dots: G614 variants

Fig. 2

The location of the D614G mutant variant reported in Indonesia from April 2020 to January 2021. The D614G mutant variant has been found in 25 provinces in Indonesia based on this study and GISAID data

Fig. 3

The phylodynamic of D614G mutant in the Special Region of Yogyakarta and Central Java provinces. The G614 mutation was found in the Special Region of Yogyakarta as early as in May 6, 2020 (A) and May 12, 2020 in Central Java (B)

Fig. 4

The proportion of D614G variant in Indonesia based on this study and GISAID data. The G614 variant in Indonesia was first reported since April 2020 and increasingly found to be the predominant variant. The D614 variant was no longer reported in September 2020 as indicated by this study and GISAID data analyzed from March 2020 to January 2021

Fig. 5

Phylogeny tree of 52 research samples. maximum likelihood (ML) tree from furin cleavage site (FCS) region of research samples (red dot) with several FCS SARS-CoV-2 strains originating from the GeneBank (black dots were originated from Indonesia and blue dots were from another country) showed 4 different mutations in the FCS region, Q675H, Q677H, one mutation near the furin cleavage PRRAR was S680P, and one silent mutation in 23,557 C > T

Fig. 6

The distribution of mutations in the FCS region in Indonesian samples. Analysis of the maximum clade credibility (MCC) tree in the research samples and the Indonesian samples obtained from GISAID data showed the formation of five clusters from the FCS region, with S680P and Q677H in the same cluster