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.