Volume 25, Number 5—May 2019
Dispatch
Nipah Virus Sequences from Humans and Bats during Nipah Outbreak, Kerala, India, 2018
Table 1
Details of persons suspected to have secondary Nipah virus infection, Kerala state, India, 2018*
| Serial no. |
MCL no. |
GenBank accession no. |
Relationship to index case-patient |
District |
Age, y/sex |
Onset date |
Sample collection date |
POD |
Sample type |
qRT-PCR results |
Ct |
IgM ELISA |
OD† |
Generation of Nipah case |
Outcome |
| 1‡ |
MCL-18-H-1085 | NA | Elder brother |
Kozhikode |
27/M |
May 13 | May 17 | 5 | Serum | Pos | 36.9 | Pos | 0.669 | Secondary |
Died |
| MCL-18-H-1086 | NA | Throat swab | Neg | ND | ND | ND | |||||||||
| MCL-18-H-1087§ | MH423323 | Urine | Neg | ND | ND | ND | |||||||||
| MCL-18-H-1197¶ |
MH523640 |
Jun 4 |
23 |
Lung tissue |
Pos |
26 |
ND |
ND |
|||||||
| 2‡ |
MCL-18-H-1088¶# | Throat swab, MH396625; virus isolate, MH523642¶ | Father |
Kozhikode |
59/M |
May 15 |
May 17 |
3 |
Throat swab | Pos | 34 | ND | ND | Secondary |
Died |
| MCL-18-H-1089 |
NA |
Urine |
Neg |
No Ct |
ND |
ND |
|||||||||
| 3‡ |
MCL-18-H-1090 | NA | Paternal aunt |
Kozhikode |
53/F |
May 15 |
May 17 |
3 |
Serum | Neg | No Ct | Neg | ND | Secondary |
Died |
| MCL-18-H-1091 | NA | Throat swab | Pos | 36.7 | ND | ND | |||||||||
| MCL-18-H-1092 |
NA |
Urine |
Pos |
37.8 |
ND |
ND |
|||||||||
| 4 |
MCL-18-H-1093** | NA | Neighbor |
Kozhikode |
18/F |
May 14 |
May 17 |
4 |
Serum | Neg | ND | ND | ND | NA |
NA |
| MCL-18-H −1094 | NA | Throat swab | Neg | ND | ND | ND | |||||||||
| MCL- 18-H −1095 |
NA |
Urine |
Neg |
ND |
ND |
ND |
|||||||||
| 5‡ |
MCL −18-H −1199 |
NA |
Attendant of another patient where the index case-patient was initially admitted (TH) |
Kozhikode |
48/F |
May 16 |
May 19 |
4 |
Throat swab |
Pos |
34 |
ND |
ND |
Secondary |
Died |
| 6‡ |
MCL-18-H-1200 | NA | Truck driver who visited GMC where index case-patient was later admitted |
Kozhikode |
52/M |
May 15 |
May 20 |
6 |
Urine | Neg | No Ct | ND | ND | Secondary |
Died |
| MCL-18-H-1201 |
NA |
Blood |
ND |
ND |
Pos |
0.767 |
|||||||||
| 7‡ |
MCL-18-H-1202 | NA | Nurse in GMC |
Mallapuram |
27/M |
May 14 | May 21 | 8 | Urine | Pos | 34 | ND | ND | Secondary |
Survived |
| MCL-18-H-1246 |
NA |
Jun 9 |
27 |
Serum |
ND |
ND |
Pos |
0.674 |
|||||||
| 8‡ |
MCL-18-H-1203 | NA | Staff nurse at TH |
Kozhikode |
31/F |
May 15 |
May 19 |
5 |
Throat swab | Pos | 25 | ND | ND | Secondary |
Died |
| MCL-18-H-1204 |
NA |
Urine |
Neg |
ND |
ND |
ND |
|||||||||
| 9‡ |
MCL-18-H-1205 | NA | Automobile driver/ neighbor of index case-patient |
Kozhikode |
26/M |
May 14 |
May 19 |
6 |
Blood | ND | No Ct | Pos | 0.996 | Secondary |
Died |
| MCL-18-H-1206 | NA | Throat swab | ND | ND | ND | ND | |||||||||
| MCL-18-H-1207 |
NA |
Urine |
Pos |
36 |
ND |
ND |
|||||||||
| 10‡ | MCL-18-H-1208 | NA | Nursing student in GMC | Kozhikode | 19/F | May 14 | May 21 | 8 | Blood | ND | ND | Pos | 0.652 | Secondary | Survived |
| MCL-18-H-1209§ | MH523641 | Throat swab | Pos | 30 | ND | ND | |||||||||
| MCL-18-H-1210 | NA | Urine | Pos | 37 | ND | ND | |||||||||
| MCL-18-H-1242 | NA | Jun 9 | 27 | Serum | ND | ND | Pos | 0.642 |
*Ct, cycle threshold; GMC, Government Medical College, Kozhikode; MCL, maximum containment laboratory; ND, not done; Neg, negative; OD, optical density at 450 nm; POD, postonset day; pos, positive; rRT-PCR, real-time reverse transcription PCR; TH, Taluka Hospital, Perambra, Kozhikode.
†Sum of OD should be >0.45 for IgM positive for Nipah case.
‡All clinical samples of Nipah virus positive cases were tested and found to be negative for anti-Nipah IgG.
§Retrieval of the partial sequence through Sanger sequencing (GenBank accession no. MH423323).
¶Retrieval of the full genome through next-generation sequencing (GenBank accession nos. MH523640, MH396625, MH523642, and MH523641).
#Virus isolation on VeroCCL81 cell line from a throat swab of the sample (GenBank accession no. MH523642).
**Sample no 1093 is positive by anti-Japanese encephalitis IgM ELISA.