Volume 27, Number 7—July 2021
Research
Fatal Human Infection with Evidence of Intrahost Variation of Eastern Equine Encephalitis Virus, Alabama, USA, 2019
Holly R. Hughes
, Jason O. Velez, Emily H. Davis, Janeen Laven, Carolyn V. Gould, Amanda J. Panella, Amy J. Lambert, J. Erin Staples, and Aaron C. Brault
, Jason O. Velez, Emily H. Davis, Janeen Laven, Carolyn V. Gould, Amanda J. Panella, Amy J. Lambert, J. Erin Staples, and Aaron C. Brault
Table
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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