Mutation analysis
Frequent mutations in Turkish isolates
In total, 170 Genome sequences of SARS-COV-2 from different countries were collected from GISAID (https://www.gisaid.org/) and GenBank (http://www.ncbi.nlm.nih.gov/genbank/) sources. In this analysis, 80 SARS- COV-2 genomes sequences submitted from Turkey were investigated to detect different mutations in spike protein (S), nucleocapsid protein (N) and non-structural proteins (Nsp2, Nsp3, Nsp4, Nsp6, NSP12/RdRP) (Table 2).
Table 2 List of mutations identified in 80 SARS-COV-2 genomes of Turkey. The unique mutations in S protein, NSsp2, Nsp3, Nsp4, Nsp12 are marked with *.
|
List of mutations
|
Amino acid change
|
Gene
|
Type of Mutation
|
Number of Isolates
|
|
23403 A>G
|
D614G
|
S
|
Missense
|
59
|
|
14408 C>T
|
P4715L
|
orf1ab
|
Missense
|
58
|
|
3037C>T
|
|
orf1ab
|
Synonymous
|
57
|
|
241 C>T
|
|
5'UTR
|
Non coding
|
42
|
|
25563G>T
|
Q57H
|
ORF3a
|
Missense
|
31
|
|
18877C>T
|
L6205L/L280L
|
orf1ab
|
Synonymous
|
29
|
|
11083G>T
|
L3606F
|
orf1ab
|
Missense
|
25
|
|
28688T>C
|
|
N
|
Synonymous
|
23
|
|
28881 G>A
|
R203K
|
N
|
Missense
|
23
|
|
28882G>A
|
|
N
|
Synonymous
|
23
|
|
28883 G>C
|
G204R
|
N
|
Missense
|
23
|
|
29742G>T
|
|
3'UTR
|
Non coding
|
22
|
|
1397G>A
|
V378I
|
Orf1ab
|
Missense
|
21
|
|
C26549T
|
|
M
|
Synonymous
|
13
|
|
26735C>T
|
|
M
|
Synonymous
|
13
|
|
884C>A
|
R207S
|
Orf1ab/Nsp2
|
Missense
|
11*
|
|
8653G>T
|
M2796I
|
Orf1ab/Nsp4
|
Missense
|
11*
|
|
19839T>C
|
|
Orf1ab
|
Synonymous
|
11
|
|
7765C>A
|
|
Orf1ab/Nsp3
|
Synonymous
|
09*
|
|
17690C>T
|
S5809L
|
Orf1ab
|
Missense
|
08
|
|
228C>T
|
|
5'UTR
|
|
08
|
|
28854C>T
|
S194L
|
N
|
Missense
|
08*
|
|
22444C>T
|
D294D
|
S
|
Synonymous
|
08*
|
|
2113C>T
|
|
Orf1ab/Nsp2
|
Synonymous
|
07*
|
|
12809C>T
|
L4182F
|
orf1ab
|
Missense
|
04
|
|
10702C>T
|
|
Orf1ab
|
Synonymous
|
04
|
|
26551T>C
|
V10A
|
M
|
Missense
|
04
|
|
22964A>T
|
I468V
|
S
|
Missense
|
04*
|
|
5736 C>T
|
A1824V
|
Orf1ab/Nsp3
|
Missense
|
03*
|
|
13476C>T
|
|
orf1ab
|
Synonymous
|
03*
|
|
3903C>T
|
P1213L
|
orf1ab/Nsp3
|
Missense
|
03*
|
|
881G>A
|
A206T
|
orf1ab/Nsp2
|
Missense
|
03*
|
|
25611C>A
|
|
ORF3a
|
Synonymous
|
03
|
|
8782 C>T
|
|
Orf1ab
|
Synonymous
|
02*
|
|
1059C>T
|
T265I
|
orf1ab
|
Missense
|
02*
|
|
23874C>T
|
A771V
|
S
|
Missense
|
02*
|
|
25275C>T
|
T1238I
|
S
|
Missense
|
01*
|
|
23929C>T
|
Y789Y
|
S
|
Synonymous
|
01*
|
|
22468G>A
|
T302T
|
S
|
Synonymous
|
01*
|
|
25314G>T
|
G1251V
|
S
|
Missense
|
01*
|
|
2416C>T
|
Y717Y
|
orf1ab/Nsp2
|
Synonymous
|
01*
|
|
13730C>T
|
A4489V
|
orf1ab
|
Missense
|
01
|
|
28144T>C
|
L84S
|
ORF8
|
Missense
|
01
|
|
5182T>C
|
|
orf1ab
|
Synonymous
|
03
|
|
27103>T
|
A194V
|
M
|
Missense
|
01
|
|
5477 C>T
|
H1738Y
|
orf1ab
|
Missense
|
01
|
|
6402C>T
|
P2046L
|
orf1ab
|
Missense
|
01
|
|
12741C>A
|
T4159K
|
ORF1ab/Nsp8
|
Missense
|
01
|
|
2997C>T
|
S911F
|
orf1ab
|
Missense
|
01
|
|
13376A>G
|
T4371A
|
orf1ab
|
Missense
|
01
|
|
19484C>T
|
A6407V
|
orf1ab
|
Missense
|
01
|
|
1437C>T
|
S391F
|
orf1ab
|
Missense
|
01
|
|
C7834T
|
|
orf1ab
|
Synonymous
|
01
|
|
944G>A
|
G227S
|
orf1ab
|
Missense
|
01
|
|
26735C>T
|
|
M
|
Synonymous
|
01
|
|
14178C>T
|
|
orf1ab
|
Synonymous
|
01
|
|
25549C>T
|
L53F
|
ORF3a
|
Missense
|
01
|
|
16247C>T
|
A5328V
|
orf1ab
|
Missense
|
01
|
|
6078C>T
|
A1938V
|
orf1ab
|
Missense
|
01
|
|
16616C>T
|
T5451I
|
orf1ab
|
Missense
|
01
|
|
27354A>G
|
|
ORF6
|
Synonymous
|
01
|
|
20464G>A
|
D6734N
|
orf1a
|
Missense
|
01
|
|
9667T>C
|
|
orf1ab
|
Synonymous
|
01
|
|
29197C>T
|
|
N
|
Synonymous
|
01
|
|
7303C>T
|
|
orf1ab
|
Synonymous
|
01
|
|
3464C>T
|
H1067Y
|
orf1ab
|
Missense
|
01
|
|
5192C>T
|
|
orf1ab
|
Synonymous
|
01
|
|
20629C>T
|
H6789Y
|
orf1ab
|
Missense
|
01
|
|
20799T>C
|
|
orf1ab
|
Synonymous
|
01
|
|
28391C>T
|
R40C
|
N
|
Missense
|
01
|
|
25611C>A
|
|
ORF3a
|
Synonymous
|
03
|
|
20668G>A
|
A6802T
|
orf1ab
|
Missense
|
01
|
|
27476C>T
|
T28I
|
ORF7a
|
Missense
|
01
|
Based on mutation analysis, 59/80 isolates from turkey have shown a signature 23403A > G (D614G) mutation in the Spike glycoprotein (S) which is clear indicative of a very frequent mutation (73%). Most samples with D614G mutations had high associations with two other mutations (3037 C>T and 14408C > T) in orf1ab region (Table 2). These co-occurring mutations have been recently described as one of major SARS-CoV-2 variant occurring in Europe. For example, Yin [11] detected 15 high frequency SNPs among 558 SARS-COV-2 strains, with most common being 241C > T, 3037C > T, 14408C > T, and 23403A > G in European viral isolates, where the COVID-19 infections by SARS-CoV-2 are generally more severe than other geographical regions.
Regarding the orf1ab region, we also identified previously reported SNPs at the sites 14408 (C>T), 3037 (C>T), 11083 (G>T), 1397 (G>A), 18877 (C>T), 1059 (T>A) and 8782 (C>T). In a report by Banerjee et al. [12], 1134 coding region of orf1ab polyprotein across various states of USA were studied in which four signature mutations T265I (Nsp 2), P4715L (Nsp 12) and P5828L and Y5865C (both at Nsp 13) were identified. In present analysis, 14408C>T (P4715L) and 3037 C>T (F106F) variants of ORF1ab were remarkable to occur at high frequency and presumed to be linked, causing mutations in the RNA dependent RNA polymerase (RdRp/NSP12) site and Nsp3 gene respectively. RdRP/NSP12 is key component of replication/transcription machinery, therefore mutant leucine at 4715 position within RdRP/NSP12 may potentially affect its function, thus increasing the viral mutation rates. Moreover, the proline to leucine was consistently observed as frequent mutation in Europe (51.6%), and North America (58.1%) in previous reports [12, 13]. The variation C3037T was reported to cause synonymous mutation in region encoding Nsp3 and was seen in 57 isolates (71%) from Turkey. Consistent with other studies, the combination of variants at position C3037T, C14408T and A23403G were most common mutations (73%), that exist together in isolates from Turkey.
Other key variants observed in present report includes 25563G>T (Q57H) in ORF3a, along with consecutive series of three variants at position 28881 (G>A), 28882 (G>A) and 28883(G>C) in N proteins. The triple site mutation 28881-28883 that brings change in two amino acid 203-204:RG>KR, is known to play a critical role in virion assembly and structure and had been abundantly seen in US strain previously [14], but also observed recently in Spain, Greece, Vietnam and South America, Mexico, Australia, New Zealand, Belgium, Brazil and Peru [15, 16]. According to GISAID repository, these mutations in N protein were first described in isolates from Netherlands (EPI_ISL_413565) with travel history to Italy, whereas the same mutation was detected in one Italian sample from Abruzzo region (EPI_ISL_436718). In present study, this tri-nucleotide mutation in N protein was observed in eight samples from Turkey with one patient (EPI_ISL_429870) having travel history to Saudi Arabia. This mutation was accompanied by other three mutations such as 241:C>T, 3037:C>T and 14408:C>T. As reported before, the mutated 203/204 region of N protein affects the SR (serine-arginine)-rich motif of the protein (a crucial region for controlling viral transcription and replication) by introducing lysin in between them that might hamper the phosphorylation at serine residue required for normal functioning of N protein [17]. In an investigation by Tylor et al. (2009) [18], significant reduction in pathogenicity has been observed with the deletion of SR domain, therefore it is important to target 203-204:RG>KR positions of the N protein to design the drugs for controlling the disease.
The missense mutation G11083T conferring amino acid change from leucine (L) to phenylalanine (F) in non- structural protein 6 (Nsp6) protein at position 3606 was appeared in 25 samples. In comparison to other countries, it has been observed in Spain, Italy and Iran as well in this study. Previously, it was reported as infrequent mutation from Japan, Netherland and Australia [19,20]. Another substitution (G>A) was found within Nsp2 encoding region of ORF1a at position 1397 and was seen in 26% (21/80) of isolates, which lead to an amino acid change from valine to isoleucine (V378I) having similar isoelectric point. In the study of Pachetti et al. [13], V378I substitution was mainly observed in Oceania viral isolates and less frequently in Asia and North America.
Novel mutations in spike protein
Notably, seven novel mutations were identified in spike (S) protein at different positions which include two synonymous mutations (22444C>T and 23929C>T) and four substitutional mutations (I468V, A771V, T1238I, G1251V) (Table 2). Among synonymous SNPs, C23929T (Y789Y) mutant was observed in only one Turkish sequence (EPI_ISL_455719) of S protein, which was previously reported with high prevalence in Indian strain (39.13%) and one in USA strain (EPI ISL 436898) [12, 21], but not in any other European strain so far. Although, no change in amino acid (Y789Y) at this site, but it was established as a signature SNP in Indian strains, therefore it can be used to trace and monitor the transmission of SARS-CoV-2 within community [21, 22]. The present study also revealed C22444T (S protein) along with C28854T substitution (N protein) as un-common co-evolved mutation both in viral isolates from Turkey (8 samples) and Saudi Arabia (9 samples) (Table S1), which may provide an evidence for travel- associated origin of these mutations to Turkey from Saudi Arabia. However, C22444T mutation has not been detected in any other European isolate or USA so far but in few Indian strains [12]. On the other hand, C28854T was previously seen in 6/95 samples from different countries [23].
Effect of novel missense mutations in spike protein
D614G characteristic SNP has been considered to play a key role in virus entry and pathogenesis by binding with host ACE2 receptor via variable amino acid residues from 331 to 524 of S protein called receptor-binding domain (RBD) in S1 subunit [24-25]. Strikingly, a substitutional mutation (I468V) at 468th position was found in four Turkish isolates (EPI_ISL_437316, EPI_ISL_437322, EPI_ISL_437323 and EPI_ISL_437324) in RBD of the spike protein which was not previously reported in strains of any other country. At this site, isoleucine (I) was replaced by valine (V) at position 468. Since both amino acids are hydrophobic in nature having C beta branched residues, thus any change due to this mutation did not cause any functional change in protein, as predicted by our secondary structure analysis (Fig. 1A). Despite these, this site is more prone to mutate further that may change the binding property of S protein to ACE2 receptor. However, the impact of such mutation is needed to explore further to unrevealed the crucial role of this binding site for interaction with host ACE2. Similarly, two strains (EPI_ISL_437314, EPI_ISL_437316) showed a missense mutation at position 771 exchanging alanine (A) with valine (V) in S protein. From the results of secondary structure data, it was demonstrated that helix structure has been replaced at positions 770 and 771 due to addition of two sheets at these sites (Fig. 1B). Alanine to valine substitution as residue 771 was previously seen in one Belgium strain [21].
Additionally, threonine (polar amino acid) to Isoleucine (non-polar amnio acid) substitution due to T1238I mutation and change of glycine to bulkier valine at position 1251 (G1251V) were specifically found in EPI_ISL_429870 and EPI_ISL_437317 strains respectively. The detailed secondary structure analysis revealed that change of threonine to Isoleucine makes it hydrophobic and induce structural alteration in that domain with an addition of helix at position 1238 (Fig. 1C), while G1251V mutant have attained changes in secondary structure at mutation locus with six additional sheets from position 1448 to 1253 and a helix at site 1254 (Fig. 1D). Some of earlier reports suggests that substitutional mutations like threonine to Isoleucine and alanine to valine in EBOV glycoprotein (GP) has increased the viral infectivity of Ebola virus in humans [26, 27], therefore, it is assumed that mutant residues at 771, 1238 and 1254 positions in spike protein may lead to an alteration in the way the spike interacts with the receptor, changing the infectivity as these mutations lies in S2 subunit of S protein, but this require further research and more sequencing.
Novel mutations in Nsp2
In total five uncommon mutations within the Nsp2 region (C1059T, C2416T, G881A, C884T, C2113T) were identified in this report (Table 2). Some of these infrequent mutations (C8782T and T1059A) were appeared to be predominate in other countries [28, 29]. Nsp2 is postulated to have an important role in the host cell survival pathway via interaction with prohibitin (PHB) and prohibitin 2(PHB2) [30]. A change of nonpolar amino acid (Alanine) to a polar amino acid (Threonine) at position 206 (G881A mutation) within Nsp2 gene was uniquely appeared in three sequences (EPI_ISL_480239, EPI_ISL_428723, EPI_ISL_429863) from Turkey only. Similarly, 884C>T mutation that resulted in the change of arginine codon (R) to cysteine (C) at position 207 were displayed by 11 Turkish viral isolates and one Pakistani strain (MT240479.1) (Table S1). Furthermore, two samples of Turkey (EPI_ISL_437309; EPI_ISL_437315), along with one strain from Spain (EPI_ISL_428688) and Denmark (EPI_ISL_437668) showed substitutional change (Threonine to Isoleucine) at site 265 (C1059T mutation). In addition, a synonymous mutation (2416C>T) was reported in two infected individuals (EPI_ISL_428712; EPI_ISL_437332) from turkey with travel history from Iran and in three samples (EPI_ISL_468162; EPI_ISL_468161; EPI_ISL_468160) from Pakistan. Previously, T265I mutation was detected exclusively in American population at frequency of 43 % making it a signature SNP for USA, whereas it was found in very low frequency in Asia (4.8%) [30]. Likewise, a change in nucleotide (C>T) was observed at position 2113 in seven Turkish samples and two isolates of Saudi Arabia, but none from any other sequence in this report.
Effect of missense mutations on Nsp2
Our secondary structure prediction analysis showed that A206T, R207C and T265I mutations has caused structural alterations within Nsp2 domain (Fig. 1E). For example, a loss in α-helix was noted at positions 203, 204 and 206 with addition of two sheets at 203 and 204 due to mutation of A206T. Similarly, R207C mutation resulted in substitution of α-helix with a sheet structure at position 204 and an additional turn at 210 position (Fig. 1F). Further, there is an addition of sheet structure at position 266 when threonine is substituted by isoleucine in mutant T265I (Fig. 1G). Since all these mutations were identified in Nsp2 domain that may cause structural alterations, therefore it is essential to consider these mutational spectra while designing new antiviral therapeutics targeting viral orf1ab. However, further experimental work is required to study the effect of these mutations on SRAS-CoV-2.
Novel mutations in Nsp3
In SARS-CoV virus, NSP3 has been proposed to work with NSP4 and NSP6 to induce double membrane vesicles (DMV), that serve as important unit for replication/transcription complex [31]. In this report, some novel variants in Nsp3 region were also detected at the sites 3903 (C>T), 5736 (C>T) and 7765 (C>A). Out of these three mutations, two were missense mutations (C3903Tand C5736T) that brings amino acid changes from proline to leucine (P1213L) and alanine to valine (A1824V) respectively and each were exclusively seen in isolates from Turkey only, while C7765A was a silent mutation and was observed in 11 % (9/80) of Turkish samples, while only one viral isolate from Saudi Arabia (EPI_ISL_437463) had this variation (Table S1).
Effect of missense mutations on Nsp3
In mutant A1824V, there is loss of turn and addition of a sheet structure at position 1825 as shown by secondary structure prediction (Fig. 1H), that might result in significant functional implications, whereas, no substantial change in secondary structure was observed for mutant P1213L (Fig. 1I). It is important to evaluate these mutations in Nsp3, as this gene has been reported to harbour many mutations that resulted in the evolution of beta coronaviruses with extensive selection pressure [32].
Novel mutations in Nsp4 and Nsp12
Apart from frequent mutations, two mutations in NSP4 (C8782T and G8653T) and one in NSP12/RdRP gene (13730C>T) were found completely unique to Turkey. A silent mutation at site 8782 (C>T) within Nsp4 was displayed by two infected individuals (EPI_ISL_428718 and EPI_ISL_437317) from Turkey and seven samples from Spain, describing it as infrequent mutation, however, it was present at high frequency in both Oceania and North America isolates in previous reports [13]. G8653T is another Nsp4 mutation (missense) which substitute methionine (M) into isoleucine (I) at site 2796 and was found in 11 Turkish strains, not observed in any other viral isolates from Europe so far. However, this mutation was detected by Joshi and Paul [33] in nine Indian samples and two isolates from Kuwait. At NSP12/RdRP gene, alanine/valine substitution was observed at site 4489 in a single sequence (EPI_ISL_455719, Turkey / Mardin) on April 9th, 2020 which was not found in any other sequence in this report. In a previous report by Maitra et al. [34], this unique mutation was also depicted in two infected individuals of India.
Effect of missense mutations on Nsp4 and Nsp12/RdRp
Further, our secondary structure prediction analysis showed that mutant M2796I causes changes in secondary structure within Nsp4 as there is replacement of α-helix with sheet structure at position 2795 and addition of turn at 2798 site (Fig. 1J), which might affect the interaction between Nsp3 and Nsp4 and viral replication in SARS-CoV-2. Normally, valine side chain is larger than alanine, and substitution of valine in Nsp12 resulted in the of loss of α-helixes at position 4486,4487, and 4488 with the addition of five sheets from positions 4486 to 4490 as revealed by our secondary structure predications (Fig. 1K), therefore, this substitution might have functional consequences that can potentially affect the viral replication and mutagenic capabilities of SARS-CoV-2.
Importantly, it will be quite interesting to validate the effects of these substitutions on non-structural proteins as one of previous study proposed that alanine/valine substitution in NS2A (non-structural protein) in Zika virus impairs viral RNA synthesis and results in viral attenuation (Márquez -Jurado et al., 2018) [35]. Similarly, valine substitution in RdRp protein in Indian SARS-CoV-2 isolates has caused structural alteration that impairs packing of the protein (Chand et al. 2020) [36]. Thus, functional characterization of these mutations investigated in our study needs to be carried out to understand the exact role of these mutations and to develop strategies for vaccine designing that target this virus.
Transmission and phylogenetic analysis
Interestingly, 13 viral isolates of turkey harboring 23403 A>G, 3037 C>T, and 14408 C>T concurrent mutations having travel history from Saudi Arabia (Table 3). Of these, 6 cases were reported from Ankara city while remaining were from Aksaray, Sakarya, Tekirdag, Kocaeli, Kastamonu, Konya and Afyon. Similarly, 6 samples had association with Iran travel history and maximum cases (5/6) were noted from Istanbul mentioned in GISAID. Among Iran-travel linked isolates, 4 samples (EPI_ISL_437319, EPI_ISL_437324, EPI_ISL_437325,EPI_ISL_437327) are defined by the presence of three co-mutations (G1397A, T28688C and G29742T, a Europe based introduction), while remaining 2 samples (EPI_ISL_437326, EPI_ISL_437332) lacked these mutations (Table 3). However, G1397A and T28688C substitution was also observed in one patient who had travelled to Taiwan, this probably suggesting the spread of COVID-19 infection to Turkey from multiple countries especially from Saudi Arabia and Iran. In a similar analysis, Eden et al. [22] provided an evidence for travel associated SARS-CoV-2 origin to Australia from Iran. Our findings may also contribute to better understand the diversity of circulating SARS-COV-2 and origin of imported cases to Turkey.
Table 3 List of Turkish strains with travel history.
|
Accession
|
Virus name
|
Location
|
Collection date
|
Travelling history
|
|
EPI_ISL_429866
|
hCoV-19/Turkey/HSGM- 4236/2020
|
Turkey / Afyon/west
|
2020-03-16
|
Saudi Arabia
|
|
EPI_ISL_429869
|
hCoV-19/Turkey/HSGM- 4701/2020
|
Turkey / Konya
|
2020-03-17
|
Saudi Arabia
|
|
EPI_ISL_428716
|
hCoV-19/Turkey/HSGM- 5711/2020
|
Turkey / Ankara
|
2020-03-18
|
Saudi Arabia
|
|
EPI_ISL_428714
|
hCoV-19/Turkey/HSGM- 5602/2020
|
Turkey / Kastamonu
|
2020-03-18
|
Saudi Arabia
|
|
EPI_ISL_429862
|
hCoV-19/Turkey/HSGM- 8970/2020
|
Turkey / Ankara
|
2020-03-22
|
Saudi Arabia
|
|
EPI_ISL_437332
|
hCoV-19/Turkey/HSGM- 4698/2020
|
Turkey / Istanbul
|
2020-03-18
|
Iran
|
|
EPI_ISL_428718
|
hCoV-19/Turkey/HSGM- 5770/2020
|
Turkey / Kocaeli
|
2020-03-19
|
Saudi Arabia
|
|
EPI_ISL_437328
|
hCoV-19/Turkey/HSGM- 7668/2020
|
Turkey / Tekirdag
|
2020-03-19
|
Saudi Arabia
|
|
EPI_ISL_437326
|
hCoV-19/Turkey/HSGM- 1432/2020
|
Turkey / Istanbul
|
2020-03-19
|
Iran
|
|
EPI_ISL_437325
|
hCoV-19/Turkey/HSGM- 1495/2020
|
Turkey / Istanbul
|
2020-03-19
|
Iran
|
|
EPI_ISL_437324
|
hCoV-19/Turkey/HSGM- 1476/2020
|
Turkey / Istanbul
|
2020-03-19
|
Iran
|
|
EPI_ISL_437327
|
hCoV-19/Turkey/HSGM- 1458/2020
|
Turkey / Agri
|
2020-03-19
|
Iran
|
|
EPI_ISL_437323
|
hCoV-19/Turkey/HSGM- 1481/2020
|
Turkey / Istanbul
|
2020-03-19
|
Taiwan
|
|
EPI_ISL_437319
|
hCoV-19/Turkey/HSGM- 1490/2020
|
Turkey / Istanbul
|
2020-03-19
|
Iran
|
|
EPI_ISL_429870
|
hCoV-19/Turkey/HSGM- 8990/2020
|
Turkey / Sakarya
|
2020-03-22
|
Saudi Arabia
|
|
EPI_ISL_428723
|
hCoV-19/Turkey/HSGM- 8964/2020
|
Turkey / Aksaray
|
2020-03-22
|
Saudi Arabia
|
|
EPI_ISL_429871
|
hCoV-19/Turkey/HSGM- 10241/2020
|
Turkey / Ankara
|
2020-03-23
|
Saudi Arabia
|
|
EPI_ISL_437317
|
hCoV-19/Turkey/HSGM- 1027/2020
|
Turkey / Ankara
|
2020-03-27
|
Saudi Arabia
|
|
EPI_ISL_437329
|
hCoV-19/Turkey/HSGM- 6204/2020
|
Turkey / Ankara
|
2020-03-19
|
Saudi Arabia
|
|
EPI_ISL_437331
|
hCoV-19/Turkey/HSGM- 1014/2020
|
Turkey / Ankara
|
2020-03-25
|
Saudi Arabia
|
Phylogenetic analysis of SARS-COV-2 genomes suggests that Turkish strain shares close relationships with isolates from Saudi Arabia predicting the possibility of common origin (Fig. 1 A and B). However, the viral genomes of Turkey were dispersed throughout the phylogenetic tree indicating multiple independent introductions to the country. In phylogram two distinct clades were categorized as Cluster 1 and Cluster 2. The first cluster 1 had a key mutation at 1397G>A, 11083G>T, 28688T>C, and 29742G>T, while second cluster had 23403 A>G, 3037 C>T, and 14408 C>T dominant mutations. Moreover, majority of viral isolates in Turkey showed L type characteristics and form monophyletic clade, while S type were present in limited numbers. SNP with “T” at site 28144 encoding leucine were classified as L type, while “C” at this position encoding serine is referred as S type. Comparatively, L type was speculated more aggressive and contagious than S type [12]. Thus, it appears that L strain is predominant strain circulating among Turkish population. In addition, samples having travel connection to Saudi Arabia and Iran were showing monophyletic origin within their respective clusters in phylogenetic tree.
In conclusion, the functional characterization of novel mutations investigated in our study needs to be carried out to understand the exact role of these variations. Furthermore, the above-mentioned mutations might pave way towards the identification of less virulent strains and development of vaccines for large repertoire of strains. Phylogenetic and transmission analysis revealed that spread of SARS-COV-2 to Turkey was due to multiple independent sources of introductions and viral isolates of Saudi Arabia and Turkey are closely related with one another.