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Volume 25, Number 5—May 2019
Dispatch

Nipah Virus Sequences from Humans and Bats during Nipah Outbreak, Kerala, India, 2018

Pragya D. Yadav, Anita M. Shete, G. Arun Kumar, Prasad Sarkale, Rima R. Sahay, Chandni Radhakrishnan, Rajen Lakra, Prachi Pardeshi, Nivedita Gupta, Raman R. Gangakhedkar, V.R. Rajendran, Rajeev Sadanandan, and Devendra T. MouryaComments to Author 
Author affiliations: Indian Council of Medical Research–National Institute of Virology, Pune, India (P.D. Yadav, A.M. Shete, P. Sarkale, R.R. Sahay, R. Lakra, P. Pardeshi, D.T. Mourya); Manipal Centre for Virus Research, Manipal, India (G.A. Kumar); Government Medical College Kozhikode, Kozhikode, India (C. Radhakrishnan, V.R. Rajendran); Indian Council of Medical Research, New Delhi, India (N. Gupta, R.R. Gangakhedkar); Health & Family Welfare, Kerala (R. Sadanandan)

Main Article

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.

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Page created: April 18, 2019
Page updated: April 18, 2019
Page reviewed: April 18, 2019
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