Volume 27, Number 10—October 2021
Research Letter
SARS-CoV-2 Neutralization Resistance Mutations in Patient with HIV/AIDS, California, USA
Seth A. Hoffman, Cristina Costales, Malaya K. Sahoo, Srikanth Palanisamy, Fumiko Yamamoto, ChunHong Huang, Michelle Verghese, Daniel A. Solis, Mamdouh Sibai, Aruna Subramanian, Lucy S. Tompkins, Philip Grant, Robert W. Shafer, and Benjamin A. Pinsky
Table
Mutations in severe acure respiratory syndrome coronavirus 2 sequences from a patient with HIV/AIDS, California, USA*
| Nucleotide mutation | Translation | Variant reads/read depth (%) |
|
|---|---|---|---|
| Day 30 | Day 45 | ||
| Day 45 sample only | |||
| 21606G>T | S: C15F | ND | 661/1,493 (44.3) |
| d21982_12 | S: del_141–144 | ND | 248/1,420 (17.5) |
| 22304T>A | S: Y248N | ND | 333/2,488 (13.4) |
| ins_22304_12 (TAT>TTACTCAGTTTTAAT) | S: ins_248_Y->LLSFN | ND | 919/2,065 (44.5) |
| 23012G>C |
S: E484Q |
ND |
1,088/1,607 (67.7) |
| Day 30 sample only | |||
| 26801C>T | Membrane protein: L93L | 753/2,196 (34.3) | ND |
| 27146A>G |
Membrane protein: T208T |
567/1,843 (30.8) |
ND |
| Both samples | |||
| 241C>T | 5′ untranslated region | 1,206/1,213 (99.4) | 848/851 (99.6) |
| 829C>T | NSP2: N8N | 862/866 (99.5) | 652/653 (99.8) |
| 2258G>A | NSP2: V485I | 3,280/3,293 (99.6) | 1,524/1,528 (99.7) |
| 3037C>T | NSP3: F106F | 1,781/1,783 (99.9) | 1,139/1,142 (99.7) |
| 6441A>G | NSP3: K1241R | 2,385/2,389 (99.8) | 1,499/1,500 (99.9) |
| 8140C>T | NSP3: S1807S | 2,491/2,505 (99.4) | 1,399/1,410 (99.2) |
| 9204A>G | NSP4: D217G | 1,395/1,401 (99.6) | 651/653 (99.7) |
| 10015C>T | NSP4: Y487Y | 527/530 (99.4) | 244/245 (99.6) |
| 10641C>T | NSP5: T196M | 516/517 (99.8) | 176/179 (98.3) |
| 13858G>T | NSP12: D131Y (or RdRp D140Y) | 3,814/3,832 (99.5) | 3,081/3,100 (99.4) |
| 14408C>T | NSP12: P314L (or RdRp P323L) | 3,923/3,938 (99.6) | 2,872/2,890 (99.4) |
| 18288A>G | NSP14: V83V | 2,498/2,521 (99.1) | 1,868/1,886 (99.0) |
| 20268A>G | NSP15: L216L | 1,655/1,662 (99.6) | 873/885 (98.6) |
| 23403A>G | S: D614G | 2,991/3,018 (99.1) | 1,792/1,800 (99.6) |
| 28744C>T | NP: I157I | 5,669/5,704 (99.4) | 4,311/4,343 (99.3) |
| 28854C>T | NP: S194L | 5,681/5,706 (99.6) | 4,477/4,498 (99.5) |
| 29384G>T | NP: D371Y | 5,843/5,889 (99.2) | 4,779/4,807 (99.4) |
| 29445C>T | NP: T391I | 5,928/6,006 (98.7) | 4,641/4,670 (99.4) |
*Compared with the reference Wuhan-Hu-1 (GenBank accession no. NC_045512.2) sequence. Patient samples collected 30 (hCoV-19/USA/CA-Stanford-07_S25/2021, GISAID accession no. EPI_ISL_2009057) and 45 (hCoV-19/USA/CA-Stanford-07_S24/2021, GISAID accession no. EPI_ISL_2009056) days after symptom onset. ND, not detected; NP, nucleoprotein; NSP, nonstructural protein; RdRp, RNA-dependent RNA polymerase; S, spike protein.
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