key: cord-0929615-40duserr
authors: Murat, Karamese; Didem, Ozgur; Ediz, Tutuncu Emin
title: Molecular Characterization, Phylogenetic and Variation Analyzes of SARS-CoV-2 strains in Turkey
date: 2020-09-11
journal: bioRxiv
DOI: 10.1101/2020.09.11.293183
sha: 924c2dcb41c1c6a2322cf2cb8442d44c0282ce08
doc_id: 929615
cord_uid: 40duserr

Introduction We present the sequence analysis for 47 complete genomes for SARS-CoV-2 isolates on Turkish patients. To identify their genetic similarity, phylogenetic analysis was performed by comparing the worldwide SARS-CoV-2 sequences, selected from GISAID, to the complete genomes from Turkish isolates. In addition, we focused on the variation analysis to show the mutations on SARS-CoV-2 genomes. Methods Illumina MiSeq platform was used for sequencing the libraries. The raw reads were aligned to the known SARS-CoV-2 genome (GenBank: MN908947.3) using the Burrows-Wheeler aligner (v.0.7.1). The phylogenetic tree was constructer using Phylip v.3.6 with Neighbor-Joining and composite likelihood method. The variants were detected by using Genome Analysis Toolkit-HaplotypeCaller v.3.8.0 and were inspected on GenomeBrowse v2.1.2. Results All viral genome sequences of our isolates was located in lineage B under the different clusters such as B.1 (n=3), B.1.1 (n=28), and B.1.9 (n=16). According to the GISAID nomenclature, all our complete genomes were placed in G, GR and GH clades. Five hundred forty-nine total and 53 unique variants were detected. All 47 genomes exhibited different kinds of variants. The distinct variants consist of 274 missense, 225 synonymous, and 50 non-coding alleles. Conclusion The results indicated that the SARS-CoV-2 sequences of our isolates have great similarity with all Turkish and European sequences. Further studies should be performed for better comparison of strains, after more complete genome sequences will be released. We also believe that collecting and sharing any data about SARS-CoV-2 virus and COVID-19 will be effective and may help the related studies.

To understand the transmission patterns and evolution of SARS-CoV-2 virus is crucial and necessary for creating better drug and vaccine designs for disease control and prevention (4) (5) (6) . The analysis of genetic sequence data from a pathogen is known as an important tool in infectious disease epidemiology (7, 8) . There are nearly 73.000 SARS-CoV-2 complete genome sequences available on the database of Global Initiative on Sharing All

Influenza Data (GISAID) (9). The availability of these genomic data has been helping hundreds of researchers to analyze the genomic diversity of SARS-CoV-2 virus. Firstly, Rambaut et al. (8) In this study, we performed the NGS analysis for 47 complete genomes for SARS-CoV-2 isolates on Turkish patients. To identify their genetic similarity, phylogenetic analysis was performed by comparing the worldwide SARS-CoV-2 sequences, selected from GISAID, to the complete genomes from Turkish isolates. In addition, we focused on the variation analysis to show the mutations on SARS-CoV-2 genomes. G  e  n  B  a  n  k  N  a  m  e  G  e  n  B  a  n  k  A  c  c  e  s  s  i  o  n  N  u  m  b  e  r  G  I  S  A  I  D  N  a  m  e  G  I  S  A  I  D  A  c  c  e  s  s  i  o  n  N  u  m  b  e  r  G  I  S  A  I  D  C  l  a  d  e   K  a  f  k  a  s  -S  A  R  S  C  o  V  2  -0  0  1  M  T  7  8  6  3  2  7  h  C  o  V  -1  9  /  T  u  r  k  e  y  /  K  U  -0  0  1  /  2  0  2  0  E  P  I  _  I  S  L  _  4  9  5 T  7  8  7  5  8  0  h  C  o  V  -1  9  /  T  u  r  k  e  y  /  K  U  -0  2  5  /  2  0  2  0  E  P  I  _  I  S  L  _  4  9  5  4  3  5  B  .  1  .  1  (  G  R  )  K  a  f  k  a  s  -S  A  R  S  C  o  V  2  -0  2  6  M  T  7  8  9  6  8  9  h  C  o  V  -1  9  /  T  u  r  k  e  y  /  K  U  -0  2  6  /  2  0  2  0  E  P  I  _  I  S  L  _  4  9  5  4  3  6  B  .  1  .  1  (  G  R  )  K  a  f  k  a  s  -S  A  R  S  C  o  V  2  -0  2  7  M  T  7  8  7  5  0  0  h  C  o  V  -1  9  /  T  u  r  k  e  y  /  K  U  -0  2  7  /  2  0  2  0  E  P  I  _  I  S  L  _  4  9  5  4  3  7  B  .  1  .  9  (  G  H  )  K  a  f  k  a  s  -S  A  R  S  C  o  V  2  -0  2  8  M  T  7  8  7  7  4  9  h  C  o  V  -1  9  /  T  u  r  k  e  y  /  K  U  -0  2  8  /  2  0  2  0  E  P  I  _  I  S  L  _  4  9  5  4  3  8  B  .  1  .  1  (  G  R  )  K  a  f  k  a  s  -S  A  R  S  C  o  V  2  -0  2  9  M  T  7  8  7  7  4  5  h  C  o  V  -1  9  /  T  u  r  k  e  y  /  K  U  -0  2  9  /  2  0  2  0  E  P  I  _  I  S  L  _  4  9  5  4  3  9  B  .  1  .  9  (  G  H  )  K  a  f  k  a  s  -S  A  R  S  C  o  V  2  -0  3  0  M  T  7  8  7  7  4  8  h  C  o  V  -1  9  /  T  u  r  k  e  y  /  K  U  -0  3  0  /  2  0  2  0  E  P  I  _  I  S  L  _  4  9  5  4  4  0  B  .  1  (  G  )  K  a  f  k  a  s  -S  A  R  S  C  o  V  2  -0  3  1  M  T  7  8  7  7  4  2  h  C  o  V  -1  9  /  T  u  r  k  e  y  /  K  U  -0  3  1  /  2  0  2  0  E  P  I  _  I  S  L  _  4  9  5  4  4  1  B  .  1  .  1  (  G  R  )  K  a  f  k  a  s  -S  A  R  S  C  o  V  2  -0  3  2  M  T  7  8  7  4  8  6  h  C  o  V  -1  9  /  T  u  r  k  e  y  /  K  U  -0  3  2  /  2  0  2  0  E  P  I  _  I  S  L  _  4  9  5  4  4 0  4  3  M  T  7  8  9  6  8  8  h  C  o  V  -1  9  /  T  u  r  k  e  y  /  K  U  -0  4  3  /  2  0  2  0  E  P  I  _  I  S  L  _  4  9  5  4  5  3  B  .  1  .  1  (  G  R  )  K  a  f  k  a  s  -S  A  R  S  C  o  V  2  -0  4  4  M  T  7  8  9  6  9  2  h  C  o  V  -1  9  /  T  u  r  k  e  y  /  K  U  -0  4  4  /  2  0  2  0  E  P  I  _  I  S  L  _  4  9  5  4  5  4  B  .  1  .  1  (  G  R  )  K  a  f  k  a  s  -S  A  R  S  C  o  V  2  -0  4  5  M  T  7  8  7  5  5  8  h  C  o  V  -1  9  /  T  u  r  k  e  y  /  K  U  -0  4  5  /  2  0  2  0  E  P  I  _  I  S  L  _  4  9  5  4  5  5  B  .  1  .  9  (  G  H  )  K  a  f  k  a  s  -S  A  R  S  C  o  V  2  -0  4  6  M  T  7  8  9  6  9  4  h  C  o  V  -1  9  /  T  u  r  k  e  y  /  K  U  -0  4  6  /  2  0  2  0  E  P  I  _  I  S  L  _  4  9  5  4  5  6  B  .  1  .  1  (  G  R  )  K  a  f  k  a  s  -S  A  R  S  C  o  V  2  -0  4  7  M  T  7  8  7  4  8  7  h  C  o  V  -1  9  /  T  u  r  k  e  y  /  K  U  -0  4  7  /  2  0  2  0  E  P  I  _  I  S  L  _  4  9  5  4  5  7  B  .  1  .  9  (  G  H  ) Five hundred forty-nine (549) total and 53 unique variants were detected as shown in T  a  b  l  e  2  :   C  o  d  i  n  g  a  n  d  n  o  n  -c  o  d  i  n  g  m  u  t  a  t  i  o  n  l  i  s  t  d  e  t  e  c  t  e  d  i  n  S  A  R  S  -C  o  V  -2  g  e  n  o  m  e  s  o  f  o  u  r  i  s  o  l  a  t  e  s  .   S  a  m  p  l  e  I  D  G  e  n  B  a  n  k  A  c  c  e  s  s  i  o  n   G  I  S  A  I  D  A  c  c  e  s  s  i  o  n   G  e  n  o  m  e  p  o  s  i  t  i  o  n  G  e  n  e  F  i  n  a  l  p  r  o  d  u  c  t  P  r  o  t  e  i  n  N  u  c  l  e  o  t  i  d  e  v  a  r  i  a  t  i  o  n   M  u  t  a  t  i  o  n  t  y  p  e  n   K  a  f  k  a  s  -S  A  R  S  C  o  V  2  -0  0  1   M  T  7  8  6  3  2  7  E  P  I  _  I  S  L  _  4  9  5  4 1 1 s  s  e  n  s  e  2  8   K  a  f  k  a  s  -S  A  R  S  C  o  V  2  -0  0  2   M  T  7  8  6  8  6  1  E  P  I  _  I  S  L  _  4  9  5  4  1  2   2  4  1  5  '  U  T  R  N  A  N  A  c  .  1  -2  5  C  >  T  N  o  n  -c  o  d  i  n  g  4  7   K  a  f  k  a  s  -S  A  R  S  C  o  V  2  -0  0  2  3  1  3  O  R  F  1  a  b  l  e  a  d  e  r  p  r  o  t  e  i  n  p  .  (  L  e  u  1  6  =  )  c  .  4  8  C  >  T  s  y  n  o  n  y  m  o  u  s  2  2   K  a  f  k  a  s  -S  A  R  S  C  o  V  2  -0  0  2  2  5  0  9  O  R  F  1  a  b  n  s  p  2  p  .  (  P  r  o  7  4  8  =  )  c  .  2  2  4  4  C  >  T  s  y  n  o  n  y  m  o  u  s  2  2   K  a  f  k  a  s  -S  A  R  S  C  o  V  2  -0  0  2  3  0  3  7  O  R  F  1  a  b  n  s  p  3  p  .  (  P  h  e  9  2  4  =  )  c  .  2  7  7  2  C  >  T  s  y  n  o  n  y  m  o  u  s  4  7   K  a  f  k  a  s  -S  A  R  S  C  o  V  2  -0  0  2  5  0  1  5  O  R  F  1  a  b  n  s  p  3  p  .  (  V  a  l  1  5  8  4  M  e  t  )  c  .  4  7  5  0  G  >  A  m  i  s  s  e  n  s  e  1  3   K  a  f  k  a  s  -S  A  R  S  C  o  V  2  -0  0  2  1  3  6 T  s  y  n  o  n  y  m  o  u  s  2  2   K  a  f  k  a  s  -S  A  R  S  C  o  V  2  -0  2  1  3  0  3  7  O  R  F  1  a  b  n  s  p  3  p  .  (  P  h  e  9  2  4  =  )  c  .  2  7  7  2  C  >  T  s  y  n  o  n  y  m  o  u  s  4 T  7  8  7  7  4  2  E  P  I  _  I  S  L  _  4  9  5  4 4 1 K  a  f  k  a  s  -S  A  R  S  C  o  V  2  -0  3  2  2  5  5  6  3  O  R  F  3  a  N  A  p  .  (  G  l  n  5  7  H  i  s  )  c  .  1  7  1  G  >  T  m  i  s  s  e  n  s  e  1  6   K  a  f  k  a  s  -S  A  R  S  C  o  V  2  -0  3  3   M  T  7  8  7  5  5  3  E  P  I  _  I  S  L  _  4  9  5  4  4  3   2  4  1  5  '  U  T  R  N  A  N  A  c  .  1  -2  5  C  >  T  N  o  n  -c  o  d  i  n  g  4 7 K  a  f  k  a  s  -S  A  R  S  C  o  V  2  -0  4  1  2  5  8  4  O  R  F  1  a  b  n  s  p  2  p  .  (  A  l  a  7  7  3  =  )  c  .  2  3  1  9  T  >  A  s  y  n  o  n  y  m  o  u  s  1   K  a  f  k  a  s  -S  A  R  S  C  o  V  2  -0  4  1  3  0  3  7  O  R  F  1  a  b  n  s  p  3  p  .  (  P  h  e  9  2  4  =  )  c  .  2  7  7  2  C  >  T  s  y  n  o  n  y  m  o  u  s  4 K  a  f  k  a  s  -S  A  R  S  C  o  V  2  -0  4  3  1  3  6  2  0  O  R  F  1  a  b  R  N  A  -d  e  p  R  N  A  -p  o  l  p  .  (  A  s  p  4  4  5  2  =  )  c  .  1  3  3  5  5  C  >  T  s  y  n  o  n  y  m  o  u  s  2  1   K  a  f  k  a  s  -S  A  R  S  C  o  V  2  -0  4  3  1  4  4  0  8  O  R  F  1  a  b  R  N  A  -d  e  p  R  N  A  -p  o  l  p  .  (  P  r  o  4  7  1  5  L  e  u  )  c  .  1  4  1  4  3  C  >  T  m  i  s  s  e  n  s  e  4 

2 B . 1 . 9 ( G H ) K a f k a s - S A R S C o V 2 - 0 3 3 M T 7 8 7 5 5 3 h C o V - 1 9 / T u r k e y / K U - 0 3 3 / 2 0 2 0 E P I _ I S L _ 4 9 5 4 4 3 B . 1 . 9 ( G H ) K a f k a s - S A R S C o V 2 - 0 3 4 M T 7 8 7 4 7 3 h C o V - 1 9 / T u r k e y / K U - 0 3 4 / 2 0 2 0 E P I _ I S L _ 4 9 5 4 4 4 B . 1 . 1 ( G R ) K a f k a s - S A R S C o V 2 - 0 3 5 M T 7 8 7 7 4 7 h C o V - 1 9 / T u r k e y / K U - 0 3 5 / 2 0 2 0 E P I _ I S L _ 4 9 5 4 4 5 B . 1 . 9 ( G H ) K a f k a s - S A R S C o V 2 - 0 3 6 M T 7 8 7 7 4 3 h C o V - 1 9 / T u r k e y / K U - 0 3 6 / 2 0 2 0 E P I _ I S L _ 4 9 5 4 4 6 B . 1 . 1 ( G R ) K a f k a s - S A R S C o V 2 - 0 3 7 M T 7 8 7 5 0 6 h C o V - 1 9 / T u r k e y / K U - 0 3 7 / 2 0 2 0 E P I _ I S L _ 4 9 5 4 4 7 B . 1 . 1 ( G R ) K a f k a s - S A R S C o V 2 - 0 3 8 M T 7 8 9 6 9 1 h C o V - 1 9 / T u r k e y / K U - 0 3 8 / 2 0 2 0 E P I _ I S L _ 4 9 5 4 4 8 B . 1 . 9 ( G H ) K a f k a s - S A R S C o V 2 - 0 3 9 M T 7 8 7 7 4 4 h C o V - 1 9 / T u r k e y / K U - 0 3 9 / 2 0 2 0 E P I _ I S L _ 4 9 5 4 4 9 B . 1 . 1 ( G R ) K a f k a s - S A R S C o V 2 - 0 4 0 M T 7 8 7 7 4 6 h C o V - 1 9 / T u r k e y / K U - 0 4 0 / 2 0 2 0 E P I _ I S L _ 4 9 5 4 5 0 B . 1 . 1 ( G R ) K a f k a s - S A R S C o V 2 - 0 4 1 M T 7 8 9 6 9 0 h C o V - 1 9 / T u r k e y / K U - 0 4 1 / 2 0 2 0 E P I _ I S L _ 4 9 5 4 5 1 B . 1 ( G H ) K a f k a s - S A R S C o V 2 - 0 4 2 M T 7 8 7 5 0 3 h C o V - 1 9 / T u r k e y / K U - 0 4 2 / 2 0 2 0 E P I _ I S L _ 4 9 5 4 5 2 B . 1 . 1 ( G R ) K a f k a s - S A R S C o V 2 -2 4 1 5 ' U T R N A N A c . 1 - 2 5 C > T N o n - c o d i n g 4 7 K a f k a s - S A R S C o V 2 - 0 0 1 3 1 3 O R F 1 a b l e a d e r p r o t e i n p . ( L e u 1 6 = ) c . 4 8 C > T s y n o n y m o u s 2 2 K a f k a s - S A R S C o V 2 - 0 0 1 2 5 0 9 O R F 1 a b n s p 2 p . ( P r o 7 4 8 = ) c . 2 2 4 4 C > T s y n o n y m o u s 2 2 K a f k a s - S A R S C o V 2 - 0 0 1 3 0 3 7 O R F 1 a b n s p 3 p . ( P h e 9 2 4 = ) c . 2 7 7 2 C > T s y n o n y m o u s 4 7 K a f k a s - S A R S C o V 2 - 0 0 1 1 3 6 2 0 O R F 1 a b R N A - d e p R N A - p o l p . ( A s p 4 4 5 2 = ) c . 1 3 3 5 5 C > T s y n o n y m o u s 2 1 K a f k a s - S A R S C o V 2 - 0 0 1 1 4 4 0 8 O R F 1 a b R N A - d e p R N A - p o l p . ( P r o 4 7 1 5 L e u ) c . 1 4 1 4 3 C > T m i s s e n s e 4 7 K a f k a s - S A R S C o V 2 - 0 0 1 1 4 7 2 4 O R F 1 a b R N A - d e p R N A - p o l p . ( P h e 4 8 2 0 = ) c . 1 4 4 5 9 C > T s y n o n y m o u s 2 2 K a f k a s - S A R S C o V 2 - 0 0 1 2 3 4 0 3 S N A p . ( A s p 6 1 4 G l y ) c . 1 8 4 1 A > G m i s s e n s e 4 7 K a f k a s - S A R S C o V 2 - 0 0 1 2 4 2 6 2 S N A p . ( M e t 9 0 0 I l e ) c . 2 7 0 0 G > T m i s s e n s e 2 3 K a f k a s - S A R S C o V 2 - 0 0 1 2 7 7 0 3 O R F 7 a N A p . ( V a l 1 0 4 P h e ) c . 3 1 0 G > T m i s s e n s e 2 3 K a f k a s - S A R S C o V 2 - 0 0 1 2 8 8 8 1 N N A p . ( A r g 2 0 3 L y s ) c . 6 0 8 G > A m i s s e n s e 2 8 K a f k a s - S A R S C o V 2 - 0 0 1 2 8 8 8 2 N N A p . ( A r g 2 0 3 = ) c . 6 0 9 G > A s y n o n y m o u s 2 8 K a f k a s - S A R S C o V 2 - 0 0 1 2 8 8 8 3 N N A p . ( G l y 2 0 4 A r g ) c . 6 1 0 G > C m i2 0 O R F 1 a b R N A - d e p R N A - p o l p . ( A s p 4 4 5 2 = ) c . 1 3 3 5 5 C > T s y n o n y m o u s 2 1 K a f k a s - S A R S C o V 2 - 0 0 2 1 4 4 0 8 O R F 1 a b R N A - d e p R N A - p o l p . ( P r o 4 7 1 5 L e u ) c . 1 4 1 4 3 C > T m i s s e n s e 4 7 K a f k a s - S A R S C o V 2 - 0 0 2 1 4 7 2 4 O R F 1 a b R N A - d e p R N A - p o l p . ( P h e 4 8 2 0 = ) c . 1 4 4 5 9 C > T s y n o n y m o u s 2 2 K a f k a s - S A R S C o V 2 - 0 0 2 2 3 4 0 3 S N A p . ( A s p 6 1 4 G l y ) c . 1 8 4 1 A > G m i s s e n s e 4 7 K a f k a s - S A R S C o V 2 - 0 0 2 2 4 2 6 2 S N A p . ( M e t 9 0 0 I l e ) c . 2 7 0 0 G > T m i s s e n s e 2 3 K a f k a s - S A R S C o V 2 - 0 0 2 2 7 7 0 3 O R F 7 a N A p . ( V a l 1 0 4 P h e ) c . 3 1 0 G > T m i s s e n s e 2 3 K a f k a s - S A R S C o V 2 - 0 0 2 2 8 8 8 1 N N A p . ( A r g 2 0 3 L y s ) c . 6 0 8 G > A m i s s e n s e 2 8 K a f k a s - S A R S C o V 2 - 0 0 2 2 8 8 8 2 N N A p . ( A r g 2 0 3 = ) c . 6 0 9 G > A s y n o n y m o u s 2 8 K a f k a s - S A R S C o V 2 - 0 0 2 2 8 8 8 3 N N A p . ( G l y 2 0 4 A r g ) c . 6 1 0 G > C m i s s e n s e 2 8 K a f k a s - S A R S C o V 2 - 0 0 3 2 4 1 5 ' U T R N A N A c . 1 - 2 5 C > T N o n - c o d i n g 4 7 K a f k a s - S A R S C o V 2 - 0 0 3 3 0 3 7 O R F 1 a bS A R S C o V 2 - 0 0 3 2 4 2 6 2 S N A p . ( M e t 9 0 0 I l e ) c . 2 7 0 0 G > T m i s s e n s e 2 3 K a f k a s - S A R S C o V 2 - 0 0 3 2 7 7 0 3 O R F 7 a N A p . ( V a l 1 0 4 P h e ) c . 3 1 0 G > T m i s s e n s e 2 3 K a f k a s - S A R S C o V 2 - 0 0 3 2 8 8 8 1 N N A p . ( A r g 2 0 3 L y s ) c . 6 0 8 G > A m i s s e n s e 2 8 K a f k a s - S A R S C o V 2 - 0 0 3 2 8 8 8 2 N N A p . ( A r g 2 0 3 = ) c . 6 0 9 G > A s y n o n y m o u s 2 8 K a f k a s - S A R S C o V 2 - 0 0 3 2 8 8 8 3 N N A p . ( G l y 2 0 4 A r g ) c . 6 1 0 G > C m i s s e n s e 2 8 K a f k a s - S A R S C o V 2 - 0 0 4 M T 7 8 6 3 2 9 E P I _ I S L _ 4 9 5 4 1 4 2 4 1 5 ' U T R N A N A c . 1 - 2 5 C > T N o n - c o d i n g 4 7 K a f k a s - S A R S C o V 2 - 0 0 4 3 0 3 7 O R F 1 a b n s p 3 p . ( P h e 9 2 4 = ) c . 2 7 7 2 C > T s y n o n y m o u s 4 7 K a f k a s - S A R S C o V 2 - 0 0 4 7 7 6 5 O R F 1 a b n s p 3 p . ( S e r 2 5 0 0 = ) c . 7 5 0 0 C > T s y n o n y m o u s 1 4 K a f k a s - S A R S C o V 2 - 0 0 4 8 3 2 6 O R F 1 a b n s p 3 p . ( A s p 2 6 8 7 = ) c . 8 0 6 1 C > T s y n o n y m o u s 1 4 K a f k a s - S A R S C o V 2 - 0 0 4 1 4 4 0 8 O R F 1 a b R N A - d e p R N A - p o l p . ( P r o 4 7 1 5 L e u ) c . 1 4 1 4 3 C > T m i s s e n s e 4 7 K a f k a s - S A R S C o V 2 - 0 0 4 1 7 6 9 0 O R F 1 a b h e l i c a s e p . ( S e r 5 8 0 9 L e u ) c . 1 7 4 2 5 C > T m i s s e n s e 1 4 K a f k a s - S A R S C o V 2 - 0 0 4 1 8 8 7 7 O R F 1 a b 3 ' - t o - 5 ' e x o n u c l e a s e p . ( L e u 6 2 0 5 = ) c . 1 8 6 1 2 C > T s y n o n y m o u s 1 5 K a f k a s - S A R S C o V 2 - 0 0 4 2 3 4 0 3 S N A p . ( A s p 6 1 4 G l y ) c . 1 8 4 1 A > G m i s s e n s e 4 7 K a f k a s - S A R S C o V 2 - 0 0 4 2 5 5 6 3 O R F 3 a N A p . ( G l n 5 7 H i s ) c . 1 7 1 G > T m i s s e n s e 1 6 K a f k a s - S A R S C o V 2 - 0 0 5 M T 7 8 6 7 9 7 E P I _ I S L _ 4 9 5 4 1 5 2 4 1 5 ' U T R N A N A c . 1 - 2 5 C > T N o n - c o d i n g 4 7 K a f k a s - S A R S C o V 2 - 0 0 5 3 1 3 O R F 1 a b l e a d eK a f k a s - S A R S C o V 2 - 0 0 5 2 3 4 0 3 S N A p . ( A s p 6 1 4 G l y ) c . 1 8 4 1 A > G m i s s e n s e 4 7 K a f k a s - S A R S C o V 2 - 0 0 5 2 4 2 6 2 S N A p . ( M e t 9 0 0 I l e ) c . 2 7 0 0 G > T m i s s e n s e 2 3 K a f k a s - S A R S C o V 2 - 0 0 5 2 7 7 0 3 O R F 7 a N A p . ( V a l 1 0 4 P h e ) c . 3 1 0 G > T m i s s e n s e 2 3 K a f k a s - S A R S C o V 2 - 0 0 5 2 8 8 8 1 N N A p . ( A r g 2 0 3 L y s ) c . 6 0 8 G > A m i s s e n s e 2 8 K a f k a s - S A R S C o V 2 - 0 0 5 2 8 8 8 2 N N A p . ( A r g 2 0 3 = ) c . 6 0 9 G > A s y n o n y m o u s 2 8 K a f k a s - S A R S C o V 2 - 0 0 5 2 8 8 8 3 N N A p . ( G l y 2 0 4 A r g ) c . 6 1 0 G > C m i s s e n s e 2 8 K a f k a s - S A R S C o V 2 - 0 0 6 2 4 1 5 ' U T R N A N A c . 1 - 2 5 C > T N o n - c o d i n g 4 7 K a f k a s - S A R S C o V 2 - 0 0 6 3 1 3 O R F 1 a b lK a f k a s - S A R S C o V 2 - 0 0 6 1 4 4 0 8 O R F 1 a b R N A - d e p R N A - p o l p . ( P r o 4 7 1 5 L e u ) c . 1 4 1 4 3 C > T m i s s e n s e 4 7 K a f k a s - S A R S C o V 2 - 0 0 6 1 4 7 2 4 O R F 1 a b R N A - d e p R N A - p o l p . ( P h e 4 8 2 0 = ) c . 1 4 4 5 9 C > T s y n o n y m o u s 2 2 K a f k a s - S A R S C o V 2 - 0 0 6 2 3 4 0 3 S N A p . ( A s p 6 1 4 G l y ) c . 1 8 4 1 A > G m i s s e n s e 4 7 K a f k a s - S A R S C o V 2 - 0 0 6 2 4 2 6 2 S N A p . ( M e t 9 0 0 I l e ) c . 2 7 0 0 G > T m i s s e n s e 2 3 K a f k a s - S A R S C o V 2 - 0 0 6 2 7 7 0 3 O R F 7 a N A p . ( V a l 1 0 4 P h e ) c . 3 1 0 G > T m i s s e n s e 2 3 K a f k a s - S A R S C o V 2 - 0 0 6 2 8 8 8 1 N N A p . ( A r g 2 0 3 L y s ) c . 6 0 8 G > A m i s s e n s e 2 8 K a f k a s - S A R S C o V 2 - 0 0 6 2 8 8 8 2 N N A p . ( A r g 2 0 3 = ) c . 6 0 9 G > A s y n o n y m o u s 2 8 K a f k a s - S A R S C o V 2 - 0 0 6 2 8 8 8 3 N N A p . ( G l y 2 0 4 A r g ) c . 6 1 0 G > C m i s s e n s e 2 8 K a f k a s - S A R S C o V 2 - 0 0 7 M T 7 8 6 3 3 4 E P I _ I S L _ 4 9 5 4 1 7 2 4 1 5 ' U T R N A N A c . 1 - 2 5 C > T N o n - c o d i n g 4 7 K a f k a s - S A R S C o V 2 - 0 0 7 3 0 3 7 O R F 1 a b n s p 3 p . ( P h e 9 2 4 = ) c . 2 7 7 2 C > T s y n o n y m o u s 4 7 K a f k a s - S A R S C o V 2 - 0 0 7 6 3 1 7 O R F 1 a b n s p 3 p . ( P r o 2 0 1 8 S e r ) c . 6 0 5 2 C > T m i s s e n s e 1 K a f k a s - S A R S C o V 2 - 0 0 7 7 7 6 5 O R F 1 a b n s p 3 p . ( S e r 2 5 0 0 = ) c . 7 5 0 0 C > T s y n o n y m o u s 1 4 K a f k a s - S A R S C o V 2 - 0 0 7 8 3 2 6 O R F 1 a b n s p 3 p . ( A s p 2 6 8 7 = ) c . 8 0 6 1 C > T s y n o n y m o u s 1 4 K a f k a s - S A R S C o V 2 - 0 0 7 1 4 4 0 8 O R F 1 a b R N A - d e p R N A - p o l p . ( P r o 4 7 1 5 L e u ) c . 1 4 1 4 3 C > T m i s s e n s e 4 7 K a f k a s - S A R S C o V 2 - 0 0 7 1 7 6 9 0 O R F 1 a b h e l i c a s e p . ( S e r 5 8 0 9 L e u ) c . 1 7 4 2 5 C > T m i s s e n s e 1 4 K a f k a s - S A R S C o V 2 - 0 0 7 1 8 8 7 7 O R F 1 a b 3 ' - t o - 5 ' e x o n u c l e a s e p . ( L e u 6 2 0 5 = ) c . 1 8 6 1 2 C > T s y n o n y m o u s 1 5 K a f k a s - S A R S C o V 2 - 0 0 7 2 3 4 0 3 S N A p . ( A s p 6 1 4 G l y ) c . 1 8 4 1 A > G m i s s e n s e 4 7 K a f k a s - S A R S C o V 2 - 0 0 7 2 5 5 6 3 O R F 3 a N A p . ( G l n 5 7 H i s ) c . 1 7 1 G > T m i s s e n s e 1 6 K a f k a s - S A R S C o V 2 - 0 0 8 M T 7 8 6 8 5 9 E P I _ I S L _ 4 9 5 4 1 8 2 4 1 5 ' U T R N A N A c . 1 - 2 5 C > T N o n - c o d i n g 4 7 K a f k a s - S A R S C o V 2 - 0 0 8 3 1 3 O R F 1 a b l e a d e r p r o t e i n p . ( L e u 1 6 = ) c . 4 8 C > T s y n o n y m o u s 2 2 K a f k a s - S A R S C o V 2 - 0 0 8 2 5 0 9 O R F 1 a b n s p 2 p . ( P r o 7 4 8 = ) c . 2 2 4 4 C > T s y n o n y m o u s 2 2 K a f k a s - S A R S C o V 2 - 0 0 8 3 0 3 7 O R F 1 a b n s p 3 p . ( P h e 9 2 4 = ) c . 2 7 7 2 C > T s y n o n y m o u s 4 7 K a f k a s - S A R S C o V 2 - 0 0 8 1 3 6 2 0 O R F 1 a b R N A - d e p R N A - p o l p . ( A s p 4 4 5 2 = ) c . 1 3 3 5 5 C > T s y n o n y m o u s 2 1 K a f k a s - S A R S C o V 2 - 0 0 8 1 4 4 0 8 O R F 1 a b R N A - d e p R N A - p o l p . ( P r o 4 7 1 5 L e u ) c . 1 4 1 4 3 C > T m i s s e n s e 4 7 K a f k a s - S A R S C o V 2 - 0 0 8 1 4 7 2 4 O R F 1 a b R N A - d e p R N A - p o l p . ( P h e 4 8 2 0 = ) c . 1 4 4 5 9 C > T s y n o n y m o u s 2 2 K a f k a s - S A R S C o V 2 - 0 0 8 2 3 4 0 3 S N A p . ( A s p 6 1 4 G l y ) c . 1 8 4 1 A > G m i s s e n s e 4 7 K a f k a s - S A R S C o V 2 - 0 0 8 2 4 2 6 2 S N A p . ( M e t 9 0 0 I l e ) c . 2 7 0 0 G > T m i s s e n s e 2 3 K a f k a s - S A R S C o V 2 - 0 0 8 2 7 7 0 3 O R F 7 a N A p . ( V a l 1 0 4 P h e ) c . 3 1 0 G > T m i s s e n s e 2 3 K a f k a s - S A R S C o V 2 - 0 0 8 2 8 8 8 1 N N A p . ( A r g 2 0 3 L y s ) c . 6 0 8 G > A m i s s e n s e 2 8 K a f k a s - S A R S C o V 2 - 0 0 8 2 8 8 8 2 N N A p . ( A r g 2 0 3 = ) c . 6 0 9 G > A s y n o n y m o u s 2 8 K a f k a s - S A R S C o V 2 - 0 0 8 2 8 8 8 3 N N A p . ( G l y 2 0 4 A r g ) c . 6 1 0 G > C m i s s e n s e 2 8 1 2 K a f k a s - S A R S C o V 2 - 0 0 9 M T 7 8 6 8 6 0 E P I _ I S L _ 4 9 5 4 1 9 2 4 1 5 ' U T R N A N A c . 1 - 2 5 C > T N o n - c o d i n g 4 7 K a f k a s - S A R S C o V 2 - 0 0 9 3 0 3 7 O R F 1 a b n s p 3 p . ( P h e 9 2 4 = ) c . 2 7 7 2 C > T s y n o n y m o u s 4 7 K a f k a s - S A R S C o V 2 - 0 0 9 1 4 4 0 8 O R F 1 a b R N A - d e p R N A - p o l p . ( P r o 4 7 1 5 L e u ) c . 1 4 1 4 3 C > T m i s s e n s e 4 7 K a f k a s - S A R S C o V 2 - 0 0 9 2 3 4 0 3 S N A p . ( A s p 6 1 4 G l y ) c . 1 8 4 1 A > G m i s s e n s e 4 7 K a f k a s - S A R S C o V 2 - 0 1 0 M T 7 8 6 3 3 5 E P I _ I S L _ 4 9 5 4 2 2 4 1 5 ' U T R N A N A c . 1 - 2 5 C > T N o n - c o d i n g 4 7 K a f k a s - S A R S C o V 2 - 0 1 0 3 1 3 O R F 1 a b l e a d e r p r o t e i n p . ( L e u 1 6 = ) c . 4 8 C > T s y n o n y m o u s 2 2 K a f k a s - S A R S C o V 2 - 0 1 0 2 5 0 9 O R F 1 a b n s p 2 p . ( P r o 7 4 8 = ) c . 2 2 4 4 C > T s y n o n y m o u s 2 2 K a f k a s - S A R S C o V 2 - 0 1 0 3 0 3 7 O R F 1 a b n s p 3 p . ( P h e 9 2 4 = ) c . 2 7 7 2 C > T s y n o n y m o u s 4 7 K a f k a s - S A R S C o V 2 - 0 1 0 4 4 6 5 O R F 1 a b n s p 3 p . ( S e r 1 4 0 0 = ) c . 4 2 0 0 A > G s y n o n y m o u s 1 K a f k a s - S A R S C o V 2 - 0 1 0 1 3 6 2 0 O R F 1 a b R N A - d e p R N A - p o l p . ( A s p 4 4 5 2 = ) c . 1 3 3 5 5 C > T s y n o n y m o u s 2 1 K a f k a s - S A R S C o V 2 - 0 1 0 1 4 4 0 8 O R F 1 a b R N A - d e p R N A - p o l p . ( P r o 4 7 1 5 L e u ) c . 1 4 1 4 3 C > T m i s s e n s e 4 7 K a f k a s - S A R S C o V 2 - 0 1 0 1 4 7 2 4 O R F 1 a b R N A - d e p R N A - p o l p . ( P h e 4 8 2 0 = ) c . 1 4 4 5 9 C > T s y n o n y m o u s 2 2 K a f k a s - S A R S C o V 2 - 0 1 0 2 3 4 0 3 S N A p . ( A s p 6 1 4 G l y ) c . 1 8 4 1 A > G m i s s e n s e 4 7 K a f k a s - S A R S C o V 2 - 0 1 0 2 4 2 6 2 S N A p . ( M e t 9 0 0 I l e ) c . 2 7 0 0 G > T m i s s e n s e 2 3 K a f k a s - S A R S C o V 2 - 0 1 0 2 7 7 0 3 O R F 7 a N A p . ( V a l 1 0 4 P h e ) c . 3 1 0 G > T m i s s e n s e 2 3 K a f k a s - S A R S C o V 2 - 0 1 0 2 8 8 8 1 N N A p . ( A r g 2 0 3 L y s ) c . 6 0 8 G > A m i s s e n s e 2 8 K a f k a s - S A R S C o V 2 - 0 1 0 2 8 8 8 2 N N A p . ( A r g 2 0 3 = ) c . 6 0 9 G > A s y n o n y m o u s 2 8 K a f k a s - S A R S C o V 2 - 0 1 0 2 8 8 8 3 N N A p . ( G l y 2 0 4 A r g ) c . 6 1 0 G > C m i s s e n s e 2 8 K a f k a s - S A R S C o V 2 - 0 1 1 M T 7 8 6 8 6 8 E P I _ I S L _ 4 9 5 4 2 1 2 4 1 5 ' U T R N A N A c . 1 - 2 5 C > T N o n - c o d i n g 4 7 K a f k a s - S A R S C o V 2 - 0 1 1 3 1 3 O R F 1 a b l e a d e r p r o t e i n p . ( L e u 1 6 = ) c . 4 8 C > T s y n o n y m o u s 2 2 K a f k a s - S A R S C o V 2 - 0 1 1 2 5 0 9 O R F 1 a b n s p 2 p . ( P r o 7 4 8 = ) c . 2 2 4 4 C > T s y n o n y m o u s 2 2 K a f k a s - S A R S C o V 2 - 0 1 1 3 0 3 7 O R F 1 a b n s p 3 p . ( P h e 9 2 4 = ) c . 2 7 7 2 C > T s y n o n y m o u s 4 7 K a f k a s - S A R S C o V 2 - 0 1 1 4 1 4 8 O R F 1 a b n s p 3 p . ( V a l 1 2 9 5 P h e ) c . 3 8 8 3 G > T m i s s e n s e 2 K a f k a s - S A R S C o V 2 - 0 1 1 5 0 1 5 O R F 1 a b n s p 3 p . ( V a l 1 5 8 4 M e t ) c . 4 7 5 0 G > A m i s s e n s e 1 3 K a f k a s - S A R S C o V 2 - 0 1 1 1 3 6 2 0 O R F 1 a b R N A - d e p R N A - p o l p . ( A s p 4 4 5 2 = ) c . 1 3 3 5 5 C > T s y n o n y m o u s 2 1 K a f k a s - S A R S C o V 2 - 0 1 1 1 4 4 0 8 O R F 1 a b R N A - d e p R N A - p o l p . ( P r o 4 7 1 5 L e u ) c . 1 4 1 4 3 C > T m i s s e n s e 4 7 K a f k a s - S A R S C o V 2 - 0 1 1 1 4 7 2 4 O R F 1 a b R N A - d e p R N A - p o l p . ( P h e 4 8 2 0 = ) c . 1 4 4 5 9 C > T s y n o n y m o u s 2 2 K a f k a s - S A R S C o V 2 - 0 1 1 2 3 4 0 3 S N A p . ( A s p 6 1 4 G l y ) c . 1 8 4 1 A > G m i s s e n s e 4 7 K a f k a s - S A R S C o V 2 - 0 1 1 2 4 2 6 2 S N A p . ( M e t 9 0 0 I l e ) c . 2 7 0 0 G > T m i s s e n s e 2 3 K a f k a s - S A R S C o V 2 - 0 1 1 2 7 7 0 3 O R F 7 a N A p . ( V a l 1 0 4 P h e ) c . 3 1 0 G > T m i s s e n s e 2 3 K a f k a s - S A R S C o V 2 - 0 1 1 2 8 1 6 6 O R F 8 N A p . ( G l n 9 1 = ) c . 2 7 3 G > A s y n o n y m o u s 2 K a f k a s - S A R S C o V 2 - 0 1 1 2 8 8 8 1 N N A p . ( A r g 2 0 3 L y s ) c . 6 0 8 G > A m i s s e n s e 2 8 K a f k a s - S A R S C o V 2 - 0 1 1 2 8 8 8 2 N N A p . ( A r g 2 0 3 = ) c . 6 0 9 G > A s y n o n y m o u s 2 8 1 3 K a f k a s - S A R S C o V 2 - 0 1 1 2 8 8 8 3 N N A p . ( G l y 2 0 4 A r g ) c . 6 1 0 G > C m i s s e n s e 2 8 K a f k a s - S A R S C o V 2 - 0 1 2 M T 7 8 7 6 4 7 E P I _ I S L _ 4 9 5 4 2 2 2 4 1 5 ' U T R N A N A c . 1 - 2 5 C > T N o n - c o d i n g 4 7 K a f k a s - S A R S C o V 2 - 0 1 2 3 1 3 O R F 1 a b l e a d e r p r o t e i n p . ( L e u 1 6 = ) c . 4 8 C > T s y n o n y m o u s 2 2 K a f k a s - S A R S C o V 2 - 0 1 2 2 5 0 9 O R F 1 a b n s p 2 p . ( P r o 7 4 8 = ) c . 2 2 4 4 C > T s y n o n y m o u s 2 2 K a f k a s - S A R S C o V 2 - 0 1 2 3 0 3 7 O R F 1 a b n s p 3 p . ( P h e 9 2 4 = ) c . 2 7 7 2 C > T s y n o n y m o u s 4 7 K a f k a s - S A R S C o V 2 - 0 1 2 1 3 6 2 0 O R F 1 a b R N A - d e p R N A - p o l p . ( A s p 4 4 5 2 = ) c . 1 3 3 5 5 C > T s y n o n y m o u s 2 1 K a f k a s - S A R S C o V 2 - 0 1 2 1 4 4 0 8 O R F 1 a b R N A - d e p R N A - p o l p . ( P r o 4 7 1 5 L e u ) c . 1 4 1 4 3 C > T m i s s e n s e 4 7 K a f k a s - S A R S C o V 2 - 0 1 2 1 4 7 2 4 O R F 1 a b R N A - d e p R N A - p o l p . ( P h e 4 8 2 0 = ) c . 1 4 4 5 9 C > T s y n o n y m o u s 2 2 K a f k a s - S A R S C o V 2 - 0 1 2 2 3 4 0 3 S N A p . ( A s p 6 1 4 G l y ) c . 1 8 4 1 A > G m i s s e n s e 4 7 K a f k a s - S A R S C o V 2 - 0 1 2 2 4 2 6 2 S N A p . ( M e t 9 0 0 I l e ) c . 2 7 0 0 G > T m i s s e n s e 2 3 K a f k a s - S A R S C o V 2 - 0 1 2 2 7 7 0 3 O R F 7 a N A p . ( V a l 1 0 4 P h e ) c . 3 1 0 G > T m i s s e n s e 2 3 K a f k a s - S A R S C o V 2 - 0 1 2 2 8 8 8 1 N N A p . ( A r g 2 0 3 L y s ) c . 6 0 8 G > A m i s s e n s e 2 8 K a f k a s - S A R S C o V 2 - 0 1 2 2 8 8 8 2 N N A p . ( A r g 2 0 3 = ) c . 6 0 9 G > A s y n o n y m o u s 2 8 K a f k a s - S A R S C o V 2 - 0 1 2 2 8 8 8 3 N N A p . ( G l y 2 0 4 A r g ) c . 6 1 0 G > C m i s s e n s e 2 8 K a f k a s - S A R S C o V 2 - 0 1 3 M T 7 8 7 5 6 4 E P I _ I S L _ 4 9 5 4 2 3 2 4 1 5 ' U T R N A N A c . 1 - 2 5 C > T N o n - c o d i n g 4 7 K a f k a s - S A R S C o V 2 - 0 1 3 3 0 3 7 O R F 1 a b n s p 3 p . ( P h e 9 2 4 = ) c . 2 7 7 2 C > T s y n o n y m o u s 4 7 K a f k a s - S A R S C o V 2 - 0 1 3 4 7 9 5 O R F 1 a b n s p 3 p . ( S e r 1 5 1 0 = ) c . 4 5 3 0 C > T s y n o n y m o u s 1 K a f k a s - S A R S C o V 2 - 0 1 3 1 1 0 8 3 O R F 1 a b n s p 6 p . ( L e u 3 6 0 6 P h e ) c . 1 0 8 1 8 G > T m i s s e n s e 3 K a f k a s - S A R S C o V 2 - 0 1 3 1 2 8 0 9 O R F 1 a b n s p 9 p . ( L e u 4 1 8 2 P h e ) c . 1 2 5 4 4 C > T m i s s e n s e 3 K a f k a s - S A R S C o V 2 - 0 1 3 1 4 4 0 8 O R F 1 a b R N A - d e p R N A - p o l p . ( P r o 4 7 1 5 L e u ) c . 1 4 1 4 3 C > T m i s s e n s e 4 7 K a f k a s - S A R S C o V 2 - 0 1 3 2 3 4 0 3 S N A p . ( A s p 6 1 4 G l y ) c . 1 8 4 1 A > G m i s s e n s e 4 7 K a f k a s - S A R S C o V 2 - 0 1 3 2 8 8 8 1 N N A p . ( A r g 2 0 3 L y s ) c . 6 0 8 G > A m i s s e n s e 2 8 K a f k a s - S A R S C o V 2 - 0 1 3 2 8 8 8 2 N N A p . ( A r g 2 0 3 = ) c . 6 0 9 G > A s y n o n y m o u s 2 8 K a f k a s - S A R S C o V 2 - 0 1 3 2 8 8 8 3 N N A p . ( G l y 2 0 4 A r g ) c . 6 1 0 G > C m i s s e n s e 2 8 K a f k a s - S A R S C o V 2 - 0 1 3 2 9 1 7 1 N N A p . ( H i s 3 0 0 T y r ) c . 8 9 8 C > T m i s s e n s e 2 K a f k a s - S A R S C o V 2 - 0 1 4 M T 7 8 6 8 6 6 E P I _ I S L _ 4 9 5 4 2 4 2 4 1 5 ' U T R N A N A c . 1 - 2 5 C > T N o n - c o d i n g 4 7 K a f k a s - S A R S C o V 2 - 0 1 4 3 1 3 O R F 1 a b l e a d e r p r o t e i n p . ( L e u 1 6 = ) c . 4 8 C > T s y n o n y m o u s 2 2 K a f k a s - S A R S C o V 2 - 0 1 4 2 5 0 9 O R F 1 a b n s p 2 p . ( P r o 7 4 8 = ) c . 2 2 4 4 C > T s y n o n y m o u s 2 2 K a f k a s - S A R S C o V 2 - 0 1 4 3 0 3 7 O R F 1 a b n s p 3 p . ( P h e 9 2 4 = ) c . 2 7 7 2 C > T s y n o n y m o u s 4 7 K a f k a s - S A R S C o V 2 - 0 1 4 1 3 6 2 0 O R F 1 a b R N A - d e p R N A - p o l p . ( A s p 4 4 5 2 = ) c . 1 3 3 5 5 C > T s y n o n y m o u s 2 1 K a f k a s - S A R S C o V 2 - 0 1 4 1 4 4 0 8 O R F 1 a b R N A - d e p R N A - p o l p . ( P r o 4 7 1 5 L e u ) c . 1 4 1 4 3 C > T m i s s e n s e 4 7 K a f k a s - S A R S C o V 2 - 0 1 4 1 4 7 2 4 O R F 1 a b R N A - d e p R N A - p o l p . ( P h e 4 8 2 0 = ) c . 1 4 4 5 9 C > T s y n o n y m o u s 2 2 K a f k a s - S A R S C o V 2 - 0 1 4 2 3 4 0 3 S N A p . ( A s p 6 1 4 G l y ) c . 1 8 4 1 A > G m i s s e n s e 4 7 1 4 K a f k a s - S A R S C o V 2 - 0 1 4 2 4 2 6 2 S N A p . ( M e t 9 0 0 I l e ) c . 2 7 0 0 G > T m i s s e n s e 2 3 K a f k a s - S A R S C o V 2 - 0 1 4 2 7 7 0 3 O R F 7 a N A p . ( V a l 1 0 4 P h e ) c . 3 1 0 G > T m i s s e n s e 2 3 K a f k a s - S A R S C o V 2 - 0 1 4 2 8 8 8 1 N N A p . ( A r g 2 0 3 L y s ) c . 6 0 8 G > A m i s s e n s e 2 8 K a f k a s - S A R S C o V 2 - 0 1 4 2 8 8 8 2 N N A p . ( A r g 2 0 3 = ) c . 6 0 9 G > A s y n o n y m o u s 2 8 K a f k a s - S A R S C o V 2 - 0 1 4 2 8 8 8 3 N N A p . ( G l y 2 0 4 A r g ) c . 6 1 0 G > C m i s s e n s e 2 8 K a f k a s - S A R S C o V 2 - 0 1 5 M T 7 8 7 6 4 8 E P I _ I S L _ 4 9 5 4 2 5 2 4 1 5 ' U T R N A N A c . 1 - 2 5 C > T N o n - c o d i n g 4 7 K a f k a s - S A R S C o V 2 - 0 1 5 3 1 3 O R F 1 a b l e a d e r p r o t e i n p . ( L e u 1 6 = ) c . 4 8 C > T s y n o n y m o u s 2 2 K a f k a s - S A R S C o V 2 - 0 1 5 2 5 0 9 O R F 1 a b n s p 2 p . ( P r o 7 4 8 = ) c . 2 2 4 4 C > T s y n o n y m o u s 2 2 K a f k a s - S A R S C o V 2 - 0 1 5 3 0 3 7 O R F 1 a b n s p 3 p . ( P h e 9 2 4 = ) c . 2 7 7 2 C > T s y n o n y m o u s 4 7 K a f k a s - S A R S C o V 2 - 0 1 5 5 0 1 5 O R F 1 a b n s p 3 p . ( V a l 1 5 8 4 M e t ) c . 4 7 5 0 G > A m i s s e n s e 1 3 K a f k a s - S A R S C o V 2 - 0 1 5 1 3 6 2 0 O R F 1 a b R N A - d e p R N A - p o l p . ( A s p 4 4 5 2 = ) c . 1 3 3 5 5 C > T s y n o n y m o u s 2 1 K a f k a s - S A R S C o V 2 - 0 1 5 1 4 4 0 8 O R F 1 a b R N A - d e p R N A - p o l p . ( P r o 4 7 1 5 L e u ) c . 1 4 1 4 3 C > T m i s s e n s e 4 7 K a f k a s - S A R S C o V 2 - 0 1 5 1 4 7 2 4 O R F 1 a b R N A - d e p R N A - p o l p . ( P h e 4 8 2 0 = ) c . 1 4 4 5 9 C > T s y n o n y m o u s 2 2 K a f k a s - S A R S C o V 2 - 0 1 5 2 3 4 0 3 S N A p . ( A s p 6 1 4 G l y ) c . 1 8 4 1 A > G m i s s e n s e 4 7 K a f k a s - S A R S C o V 2 - 0 1 5 2 4 2 6 2 S N A p . ( M e t 9 0 0 I l e ) c . 2 7 0 0 G > T m i s s e n s e 2 3 K a f k a s - S A R S C o V 2 - 0 1 5 2 7 7 0 3 O R F 7 a N A p . ( V a l 1 0 4 P h e ) c . 3 1 0 G > T m i s s e n s e 2 3 K a f k a s - S A R S C o V 2 - 0 1 5 2 8 8 8 1 N N A p . ( A r g 2 0 3 L y s ) c . 6 0 8 G > A m i s s e n s e 2 8 K a f k a s - S A R S C o V 2 -S A R S C o V 2 - 0 1 6 1 3 3 2 6 O R F 1 a b n s p 1 0 p . ( T h r 4 3 5 4 I l e ) c . 1 3 0 6 1 C > T m i s s e n s e 1 K a f k a s - S A R S C o V 2 - 0 1 6 1 4 4 0 8 O R F 1 a b R N A - d e p R N A - p o l p . ( P r o 4 7 1 5 L e u ) c . 1 4 1 4 3 C > T m i s s e n s e 4 7 K a f k a s - S A R S C o V 2 - 0 1 6 1 4 9 3 7 O R F 1 a b R N A - d e p R N A - p o l p . ( A s p 4 8 9 1 = ) c . 1 4 6 7 2 C > T s y n o n y m o u s 1 K a f k a s - S A R S C o V 2 - 0 1 6 1 6 9 1 4 O R F 1 a b h e l i2 4 1 5 ' U T R N A N A c . 1 - 2 5 C > T N o n - c o d i n g 4 7 K a f k a s - S A R S C o V 2 - 0 1 8 3 0 3 7 O R F 1 a b n s p 3 p . ( P h e 9 2 4 = ) c . 2 7 7 2 C > T s y n o n y m o u s 4 7 K a f k a s - S A R S C o V 2 - 0 1 8 7 7 6 5 O R F 1 a b n s p 3 p . ( S e r 2 5 0 0 = ) c . 7 5 0 0 C > T s y n o n y m o u s 1 4 K a f k a s - S A R S C o V 2 - 0 1 8 8 3 2 6 O R F 1 a b n s p 3 p . ( A s p 2 6 8 7 = ) c . 8 0 6 1 C > T s y n o n y m o u s 1 4 K a f k a s - S A R S C o V 2 - 0 1 8 1 4 4 0 8 O R F 1 a b R N A - d e p R N A - p o l p . ( P5 ' U T R N A N A c . 1 - 2 5 C > T N o n - c o d i n g 4 7 K a f k a s - S A R S C o V 2 - 0 1 9 3 0 3 7 O R F 1 a b n s p 3 p . ( P h e 9 2 4 = ) c . 2 7 7 2 C > T s y n o n y m o u s 4 7 K a f k a s - S A R S C o V 2 - 0 1 9 7 7 6 5 O R F 1 a b n s p 3 p . ( S e r 2 5 0 0 = ) c . 7 5 0 0 C > T s y n o n y m o u s 1 4 K a f k a s - S A R S C o V 2 - 0 1 9 8 3 2 6 O R F 1 a b n s p 3 p . ( A s p 2 6 8 7 = ) c . 8 0 6 1 C > T s y n o n y m o u s 1 4 K a f k a s - S A R S C o V 2 - 0 1 9 1 4 4 0 8 O R F 1 a b R N A - d e p R N A - p o l p . ( P r o 4 7 1 5 L e u ) c . 1 4 1 4 3 C > T m i s s e n s e 4 7 K a f k a s - S A R S C o V 2 - 0 1 9 1 7 6 9 0 O R F 1 a b h e l i7 K a f k a s - S A R S C o V 2 - 0 2 1 5 0 1 5 O R F 1 a b n s p 3 p . ( V a l 1 5 8 4 M e t ) c . 4 7 5 0 G > A m i s s e n s e 1 3 K a f k a s - S A R S C o V 2 - 0 2 1 1 3 6 2 0 O R F 1 a b R N A - d e p R N A - p o l p . ( A s p 4 4 5 2 = ) c . 1 3 3 5 5 C > T s y n o n y m o u s 2 1 K a f k a s - S A R S C o V 2 - 0 2 1 1 4 4 0 8 O R F 1 a b R N A - d e p R N A - p o5 ' U T R N A N A c . 1 - 2 5 C > T N o n - c o d i n g 4 7 K a f k a s - S A R S C o V 2 - 0 2 2 3 0 3 7 O R F 1 a b l e a d e' U T R N A N A c . 1 - 2 5 C > T N o n - c o d i n g 4 7 K a f k a s - S A R S C o V 2 - 0 2 3 3 1 3 O R F 1 a b N A p . ( L e u 1 6 = ) c . 4 8 C > T s y n o n y m o u s 2 3 K a f k a s - S A R S C o V 2 - 0 2 3 2 5 0 9 O R F 1 a b N A p . ( P r o 7 4 8 = ) c . 2 2 4 4 C > T s y n o n y m o u s 2 3 K a f k a s - S A R S C o V 2 - 0 2 3 3 0 3 7 O R F 1 a b N A p . ( P h e 9 2 4 = ) c . 2 7 7 2 C > T s y n o n y m o u s 2 8 K a f k a s - S A R S C o V 2 - 0 2 3 5 0 1 5 O R F 1 a b N A p . ( V a l 1 5 8 4 M e t ) c . 4 7 5 0 G > A m i s s e n s e 2 8 K a f k a s - S A R S C o V 2 - 0 2 3 1 1 0 8 3 O R F 1 a b N A p . ( L e u 3 6 0 6 P h e ) c . 1 0 8 1 8 G > T m i s s e n s e 2 8 K a f k a s - S A R S C o V 2 - 0 2 3 1 3 6 2 0 O R F 1 a b N A p . ( A5 ' U T R N A N A c . 1 - 2 5 C > T N o n - c o d i n g 4 7 K a f k a s - S A R S C o V 2 - 0 2 5 3 0 3 7 O R F 1 a b n s p 3 p . ( P h e 9 2 4 = ) c . 2 7 7 2 C > T s y n o n y m o u s 4 7 K a f k a s - S A R S C o V 2 - 0 2 5 1 3 7 2 0 O R F 1 a b R N A - d e p R N A - p o l p . ( PK a f k a s - S A R S C o V 2 - 0 2 6 2 8 8 8 1 N N A p . ( A r g 2 0 3 L y s ) c . 6 0 8 G > A m i s s e n s e 2 8 K a f k a s - S A R S C o V 2 - 0 2 6 2 8 8 8 2 N N A p . ( A r g 2 0 3 = ) c . 6 0 9 G > A s y n o n y m o u s 2 8 K a f k a s - S A R S C o V 2 - 0 2 6 2 8 8 8 3 N N A p . ( G l y 2 0 4 A r g ) c . 6 1 0 G > C m i s s e n s e 2 8 K a f k a s - S A R S C o V 2 - 0 2 7 M T 7 8 7 5 0 0 E P I _ I S L _ 4 9 5 4 3 7 2 1 0 5 ' U T R N A N A c . 1 - 5 6 G > T N o n - c o d i n g 1 K a f k a s - S A R S C o V 2 - 0 2 7 2 4 1 5 ' U T R N A N A c . 1 - 2 5 C > T N o n - c o d i n g 4 7 K a f k a s - S A R S C o V 2 - 0 2 7 2 0 8 6 O R F 1 a b n s p 2 p . ( G l n 6 0 7 H i s ) c . 1 8 2 1 G > T m i s s e n s e 1 K a f k a s - S A R S C o V 2 - 0 2 7 3 0 3 7 O R F 1 a b2 4 1 5 ' U T R N A N A c . 1 - 2 5 C > T N o n - c o d i n g 4 7 K a f k a s - S A R S C o V 2 - 0 3 0 3 0 3 7 O R F 1 a b n s p 3 p . ( P h e 9 2 4 = ) c . 2 7 7 2 C > T s y n o n y m o u s 4 7 K a f k a s - S A R S C o V 2 - 0 3 0 1 4 4 0 8 O R F 1 a b R N A - d e p R N A - p o l p . ( P r o 4 7 1 5 L e u ) c . 1 4 1 4 3 C > T m i s s e n s e 4 7 K a f k a s - S A R S C o V 2 - 0 3 0 2 3 4 0 3 S N A p . ( A s p 6 1 4 G l y ) c . 1 8 4 1 A > G m i s s e n s e 4 7 K a f k a s - S A R S C o V 2 - 0 3 1 M2 4 1 5 ' U T R N A N A c . 1 - 2 5 C > T N o n - c o d i n g 4 7 K a f k a s - S A R S C o V 2 - 0 3 1 3 0 3 7 O R F 1 a b n s p 3 p . ( P h e 9 2 4 = ) c . 2 7 7 2 C > T s y n o n y m o u s 4 7 K a f k a s - S A R S C o V 2 - 0 3 1 4 5 0 4 O R F 1 a b n s p 3 p . ( G l u 1 4 1 3 A s p ) c . 4 2 3 9 G > T m i2 4 1 5 ' U T R N A N A c . 1 - 2 5 C > T N o n - c o d i n g 4 7 K a f k a s - S A R S C o V 2 - 0 3 2 3 0 3 7 O R F 1 a b n s p 3 p . ( P h e 9 2 4 = ) c . 2 7 7 2 C > T s y n o n y m o u s 4 7 K a f k a s - S A R S C o V 2 - 0 3 2 7 7 6 5 O R F 1 a b n s p 3 p . ( S e r 2 5 0 0 = ) c . 7 5 0 0 C > T s y n o n y m o u s 1 4 K a f k a s - S A R S C o V 2 - 0 3 2 8 3 2 6 O R F 1 a b n s p 3 p . ( A s p 2 6 8 7 = ) c . 8 0 6 1 C > T s y n o n y m o u s 1 4 K a f k a s - S A R S C o V 2 - 0 3 2 1 3 5 1 7 O R F 1 a b R N A - d e p R N A - p o l p . ( TK a f k a s - S A R S C o V 2 - 0 3 3 3 0 3 7 O R F 1 a b n s p 3 p . ( P h e 9 2 4 = ) c . 2 7 7 2 C > T s y n o n y m o u s 4 7 K a f k a s - S A R S C o V 2 - 0 3 3 7 7 6 5 O R F 1 a b n s p 3 p . ( S e r 2 5 0 0 = ) c . 7 5 0 0 C > T s y n o n y m o u s 1 4 K a f k a s - S A R S C o V 2 - 0 3 3 8 3 2 6 O R F 1 a b n s p 3 p . ( A s p 2 6 8 7 = ) c . 8 0 6 1 C > T s y n o n y m o u s 1 4 K a f k a s - S A R S C o V 2 - 0 3 3 1 4 4 0 8 O R F 1 a b R N A - d e p R N A - p o l p . ( P r o 4 7 1 5 L e u ) c . 1 4 1 4 3 C > T m i s s e n s e 4 7 K a f k a s - S A R S C o V 2 - 0 3 3 1 7 6 9 0 O R F 1 a b h e l i2 4 1 5 ' U T R N A N A c . 1 - 2 5 C > T N o n - c o d i n g 4 7 K a f k a s - S A R S C o V 2 - 0 3 4 3 1 3 O R F 1 a b l e a d e r p r o t e i n p . ( L e u 1 6 = ) c . 4 8 C > T s y n o n y m o u s 2 2 K a f k a s - S A R S C o V 2 - 0 3 4 2 5 0 9 O R F 1 a b n s p 2 p . ( P r o 7 4 8 = ) c . 2 2 4 4 C > T s y n o n y m o u s 2 2 K a f k a s - S A R S C o V 2 - 0 3 4 3 0 3 7 O R F 1 a b n s p 3 p . ( P h e 9 2 4 = ) c . 2 7 7 2 C > T s y n o n y m o u s 4 7 K a f k a s - S A R S C o V 2 - 0 3 4 1 3 6 2 0 O R F 1 a b R N A - d e p R N A - p o l p . ( A s p 4 4 5 2 = ) c . 1 3 3 5 5 C > T s y n o n y m o u s 2 1 K a f k a s - S A R S C o V 2 - 0 3 4 1 4 4 0 8 O R F 1 a b R N A - d e p R N A - p o l p . ( P r o 4 7 1 5 L e u ) c . 1 4 1 4 3 C > T m i s s e n s e 4 7 K a f k a s - S A R S C o V 2 - 0 3 4 1 4 7 2 4 O R F 1 a b R N A - d e p R N A - p o l p . ( P2 4 1 5 ' U T R N A N A c . 1 - 2 5 C > T N o n - c o d i n g 4 7 K a f k a s - S A R S C o V 2 - 0 3 5 3 0 3 7 O R F 1 a b n s p 3 p . ( P h e 9 2 4 = ) c . 2 7 7 2 C > T s y n o n y m o u s 4 7 K a f k a s - S A R S C o V 2 - 0 3 5 7 7 6 5 O R F 1 a b n s p 3 p . ( S e r 2 5 0 0 = ) c . 7 5 0 0 C > T s y n o n y m o u s 1 4 K a f k a s - S A R S C o V 2 - 0 3 5 8 3 2 6 O R F 1 a b n s p 3 p . ( A s p 2 6 8 7 = ) c . 8 0 6 1 C > T s y n o n y m o u s 1 4 K a f k a s - S A R S C o V 2 - 0 3 5 1 2 1 1 1 O R F 1 a b2 4 1 5 ' U T R N A N A c . 1 - 2 5 C > T N o n - c o d i n g 4 7 K a f k a s - S A R S C o V 2 - 0 3 6 3 1 3 O R F 1 a b l e a d eA R S C o V 2 - 0 3 6 2 7 7 0 3 O R F 7 a N A p . ( V a l 1 0 4 P h e ) c . 3 1 0 G > T m i s s e n s e 2 3 K a f k a s - S A R S C o V 2 - 0 3 6 2 8 8 8 1 N N A p . ( A r g 2 0 3 L y s ) c . 6 0 8 G > A m i s s e n s e 2 8 K a f k a s - S A R S C o V 2 - 0 3 6 2 8 8 8 2 N N A p . ( A r g 2 0 3 = ) c . 6 0 9 G > A s y n o n y m o u s 2 8 K a f k a s - S A R S C o V 2 - 0 3 6 2 8 8 8 3 N N A p . ( G l y 2 0 4 A r g ) c . 6 1 0 G > C m i s s e n s e 2 8 K a f k a s - S A R S C o V 2 - 0 3 7 M T 7 8 7 5 0 6 E P I _ I S L _ 4 9 5 4 4 7 2 4 1 5 ' U T R N A N A c . 1 - 2 5 C > T N o n - c o d i n g 4 7 K a f k a s - S A R S C o V 2 - 0 3 7 3 1 3 O R F 1 a b l e a d e5 ' U T R N A N A c . 1 - 2 5 C > T N o n - c o d i n g 4 7 K a f k a s - S A R S C o V 2 - 0 3 9 3 1 3 O R F 1 a b l e a d eK a f k a s - S A R S C o V 2 - 0 3 9 5 0 1 5 O R F 1 a b n s p 3 p . ( V a l 1 5 8 4 M e t ) c . 4 7 5 0 G > A m i s s e n s e 1 3 K a f k a s - S A R S C o V 2 - 0 3 9 1 3 6 2 0 O R F 1 a b R N A - d e p R N A - p o l p . ( A s p 4 4 5 2 = ) c . 1 3 3 5 5 C > T s y n o n y m o u s 2 1 K a f k a s - S A R S C o V 2 - 0 3 9 1 4 4 0 8 O R F 1 a b R N A - d e p R N A - p o l p . ( P r o 4 7 1 5 L e u ) c . 1 4 1 4 3 C > T m i s s e n s e 4 7 K a f k a s - S A R S C o V 2 - 0 3 9 1 4 7 2 4 O R F 1 a b R N A - d e p R N A - p o l p . ( P h e 4 8 2 0 = ) c . 1 4 4 5 9 C > T s y n o n y m o u s 2 2 K a f k a s - S A R S C o V 2 - 0 3 9 2 3 4 0 3 S N A p . ( A s p 6 1 4 G l y ) c . 1 8 4 1 A > G m i s s e n s e 4 7 K a f k a s - S A R S C o V 2 - 0 3 9 2 4 2 6 2 S N A p . ( M e t 9 0 0 I l e ) c . 2 7 0 0 G > T m i s s e n s e 2 3 K a f k a s - S A R S C o V 2 - 0 3 9 2 7 7 0 3 O R F 7 a N A p . ( V a l 1 0 4 P h e ) c . 3 1 0 G > T m i s s e n s e 2 3 K a f k a s - S A R S C o V 2 - 0 3 9 2 8 8 8 1 N N A p . ( A r g 2 0 3 L y s ) c . 6 0 8 G > A m i2 4 1 5 ' U T R N A N A c . 1 - 2 5 C > T N o n - c o d i n g 4 7 K a f k a s - S A R S C o V 2 - 0 4 2 3 1 3 O R F 1 a b l e a d e

Complete genome data of a virus makes visible some epidemiological parameters including doubling time of an outbreak, reconstruction of transmission routes and the identification of possible sources and animal reservoirs

According to GISAID lineage, 47 in 47 of our SARS-CoV-2 genomes are in lineage B that mostly consists of European strains. According to the marker mutations

Moreover, most of European isolates have been placed in G, GR and GH clades in GISAID

The same researchers compared the two genomes regarding concurrent evolution and accumulation of mutations and reported that four mutations were detected in Italian sequence. Another study reported that because of the variations the first isolates of India were not showed high identity with Wuhan sequence (NC_045512) (15). Moreover, Bal et al. reported that the first three French sequences were located in European clade instead of reference Wuhan clade because of the three-nucleotide deletion in Orf1a at positions

In this study, we aimed to detect the variations of our SARS-CoV-2 isolates. According to the current literature, ORF genes have crucial role during COVID-19 (18). So in our study, 549 total and 53 unique variants were detected from 47 SARS-CoV-2 isolates (Table X). A study performed by Khailany et al. (19) reported that 156 total and 116 unique variants were found in 95 SARS-CoV-2 isolates. The same study also pointed out that the most frequently observed base changes was C>T same as our study

According to the global frequency of variations, most of our variants are novel; however, the studies on this issue in ongoing and more detailed information will be presented in near future. The Orf1ab is the longest and most important gene among coronaviruses (18)

Further studies should be performed for better comparison of strains, after more complete genome sequences will be released; however, these data may be useful to understand the dynamics of virus spread and may help the further vaccine and treatment studies

However, we believe that collecting and sharing any data about SARS-CoV-2 virus and COVID-19 will be effective and may help the related studies

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Phylogenetic analysis of the first four SARS-CoV-2 cases in Chile

Emergence of genomic diversity and recurrent mutations in SARS-CoV-2

Genomic and epidemiological monitoring of yellow fever virus transmission potential

Precision epidemiology for infectious disease control

Unifying the epidemiological and evolutionary dynamics of pathogens

A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology

Molecular characterization of SARS-CoV-2 in the first COVID-19 cluster in France reveals an amino acid deletion in nsp2

An emergent clade of SARS-CoV-2 linked to returned travellers from Iran

Virus Isolation from the First Patient with SARS-CoV-2 in Korea

Molecular and Phylogenetic analysis in COVID-19 patients: A preliminary report from Iran

Full-genome sequences of the first two SARS-CoV-2 viruses from India

Whole genome and phylogenetic analysis of two SARS-CoV-2 strains isolated in Italy in

Genomic characterization and phylogenetic analysis of SARS-COV-2 in Italy

Receptor Recognition by the Novel Coronavirus from Wuhan: an Analysis Based on Decade-Long Structural Studies of SARS Coronavirus

Genomic characterization of a novel SARS-CoV-2

Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant

Genetic diversity and evolution of SARS-CoV-2

We would like to thank all patients, clinicians, and laboratory technicians who contributed to this study.

The current study was supported by Kafkas University, Kars, Turkey; Scientific Research Project Council under the project number 2020-TS-26.

Availability of data and material: The data that support the findings of this study are openly available in NCBI GenBank and GISAID at https://submit.ncbi.nlm.nih.gov/subs/ and https://www.gisaid.org/.