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Volume 32, Number 7—July 2026

Dispatch

Nipah Virus Shedding in Urine from Fruit Bats, Sri Lanka, 2018–2019

Claudia Kohl1Comments to Author , Sahan Siriwardana1, Therese Muzeniek, Thejanee Perera, Dilara Bas, Mizgin Öruc, Annika Brinkmann, Beate Becker-Ziaja, Franziska Schwarz, Hamsananthy Jeevatharan, Jagathpriya Weerasena, Shiroma Handunnetti, Inoka C. Perera, Gayani Premawansa, Sunil Premawansa, Wipula Yapa, and Andreas Nitsche
Author affiliation: Robert Koch Institute, Berlin, Germany (C. Kohl, T. Muzeniek, T. Perera, D. Bas, M. Öruc, A. Brinkmann, B. Becker-Ziaja. F. Schwarz, A. Nitsche); University of Colombo, Columbo, Sri Lanka (S. Siriwardana, T. Perera, J. Weerasena, S. Handunetti, I.C. Perera, S. Premawansa, W. Yapa); Ministry of Health, Colombo (H. Jeevatharan); Colombo North Teaching Hospital, Ragama, Sri Lanka (G. Premawansa)

Main Article

Table 2

Sequencing results for NiV-positive bat urine samples in study of NiV shedding in urine from fruit bats, Sri Lanka, 2018–2019*

Characteristic Bat urine pools tested positive for NiV
S03-P2 S18-08
Origin Pteropus medius, Colombo P. medius, Colombo
Sampling date
 June 2018
 March 2019
PCR
Henipa PCR
Ct value 33 35
Mean duplicates 8 6
NiV in-house
Ct value 32 37
Mean duplicates
 3
 7
Illumina sequencing, shotgun†
Trimmed reads 5,094,516 5,633,085
NiV reads 128 20
Longest contig 481 nt (accession no. PP893187.1) 255 nt (accession no. PP893189.1)
Highest % ID nt
 98.96% MCL-18-H-1088 (accession no. MHK523642)‡
 99.61% (accession no. MN549404.1)§
NiVliSeq, amplicon-based approach¶
Genome length and coverage 93% query, 189-fold average (>10-fold) 98% query, 8,783-fold average (>10-fold)
Highest % ID nt
 98.34%‡
 98.43%‡
Novel strain Nipah virus strain C-18-B-0302 Sri Lanka
(accession no. PP893186.1)		 Nipah virus strain C-19-B-1808 Sri Lanka
(accession no. PP893188.1)

*Ct, cycle threshold; NiV, Nipah virus; % ID, percentage identity of nucleotide and amino acid sequence between pool and reference strain. †Illumina, https://www.illumina.com. ‡Reference strain MH396625 (GenBank accession no.) from a human patient during the 2018 outbreak in Kerala, India. §Reference strain from a bat in India. ¶ AmpliSeq primer panel spanning the whole NiV genome using Primer3 version 2.3.7 (Figure 1; Appendix Table).

Main Article

1These first authors contributed equally to this article.

Page created: April 13, 2026
Page updated: June 26, 2026
Page reviewed: June 26, 2026
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