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Volume 27, Number 7—July 2021

Fatal Human Infection with Evidence of Intrahost Variation of Eastern Equine Encephalitis Virus, Alabama, USA, 2019

Holly R. HughesComments to Author , Jason O. Velez, Emily H. Davis, Janeen Laven, Carolyn V. Gould, Amanda J. Panella, Amy J. Lambert, J. Erin Staples, and Aaron C. Brault
Author affiliation: Centers for Disease Control and Prevention, Fort Collins, Colorado, USA

Main Article


Comparison of intrahost variability of eastern equine encephalitis virus variants in serum and cerebrospinal fluid from a woman in Alabama, USA, 2019*

Reference position† Serum consensus/SNV Serum SNV frequency, % CSF consensus/SNV CSF SNV frequency, % Protein Serum SNV amino acid substitution CSF SNV aa substitution
646 T/C 4.42 T/– NSP1 I208T
775 C/T 14.40 T/– NSP1 T251I
778 T/A 9.13 T/– NSP1 L252Q
1322 T/C 12.18 T/C 6.52 NSP1 P433 P433
1326 A/C 5.46 A/– NSP1 T435P
2719 T/– T/C 3.23 NSP2 L366P
2866 G/A 5.59 G/– NSP2 R415H
2871 G/C 6.74 G/– NSP2 E417Q
4443 T/C 7.75 T/C 7.34 NSP3 W147R W147R
4445 G/A 14.05 G/– NSP3 W147‡
5291 T/C 4.21 C/– NSP3 A429
5546 G/– G/A 4.87 Capsid T514
7768 C/– A/C 6.71 Capsid A66V
7774 G/– G/A 6.21 Capsid R68H
8662 C/T 41.71 C/– E2 A40V
8728 C/T 6.38 T/– E2 S62L
8827 A/G 4.17 A/– E2 H95R
9195 A/G 4.29 A/– E2 T218A
9200 T/A 6.37 T/A 3.05 E2 D219E D219E
9356 T/C 4.49 T/– E2 P271
10603 C/– C/A 3.81 E1 T210N
11091 A/G 2.72 A/– E1 S373G
11303 A/– T/C 4.82 3′ UTR
11312 C/A 15.18 C/A 12.14 3′ UTR
11450 T/– T/C 6.90 3′ UTR
11456 C/– A/G 36.61 3′ UTR

*Underlining indicates consensus nucleotide changes present in the serum compared with CSF sample. CSF, cerebrospinal fluid; NSP, nonstructural protein; SNV, single-nucleotide variants; UTR, untranslated region. Blank cells indicate not applicable in respective specimens. †Reference genome position based on isolate with GenBank accession no. KX029239. ‡Stop codon.

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Page created: May 14, 2021
Page updated: June 16, 2021
Page reviewed: June 16, 2021
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