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[Preprint]. 2024 Feb 15:2024.02.13.24302648.
doi: 10.1101/2024.02.13.24302648.

Gemykibivirus detection in acute encephalitis patients from Nepal

Eans Tara Tuladhar  1 , Smita Shrestha  1 , Susan Vernon  2 , Lindsay Droit  2 , Kathie A Mihindukulasuriya  2 , Mamta Tamang  1 , Lata Karki  1 , Annie Elong Ngono  3 , Bimlesh Jha  4 , Bal Krishna Awal  4 , Bimal Sharma Chalise  5 , Runa Jha  4 , Sujan Shresta  3 , David Wang  2 , Krishna Das Manandhar  1
Affiliations

Gemykibivirus detection in acute encephalitis patients from Nepal

Eans Tara Tuladhar et al. medRxiv. .

Update in

  • Gemykibivirus detection in acute encephalitis patients from Nepal.
    Tuladhar ET, Shrestha S, Vernon S, Droit L, Mihindukulasuriya KA, Tamang M, Karki L, Elong Ngono A, Jha B, Awal BK, Chalise BS, Jha R, Shresta S, Wang D, Manandhar KD. Tuladhar ET, et al. mSphere. 2024 Jul 30;9(7):e0021924. doi: 10.1128/msphere.00219-24. Epub 2024 Jun 21. mSphere. 2024. PMID: 38904383 Free PMC article.

Abstract

Acute Encephalitis Syndrome (AES) causes significant morbidity and mortality worldwide. In Nepal, Japanese encephalitis virus (JEV) accounts for ~ 5-20% of AES cases, but ~75% of AES cases are of unknown etiology. We identified a gemykibivirus in CSF collected in 2020 from a male child with AES using metagenomic next-generation sequencing. Gemykibiviruses are single stranded, circular DNA viruses in the family Genomoviridae. The complete genome of 2211 nucleotides was sequenced which shared 98.69% nucleotide identity to its closest relative, Human associated gemykibivirus 2 isolate SAfia-449D. Two real-time PCR assays were designed, and screening of 337 CSF and 164 serum samples from AES patients in Nepal collected in 2020 and 2022 yielded 11 CSF and 1 serum sample that were positive in both PCR assays. Complete genomes of 7 of the positives were sequenced. These results identify a candidate etiologic agent of encephalitis in Nepal.

Keywords: Gemykibivirus; acute encephalitis syndrome; emerging infection; metagenomic analysis.

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Figures

Figure 1.
Figure 1.
Phylogenetic trees of (A) amino acid sequences of the index case REP protein and representatives of each genus in the family Genomoviridae; (B) whole genome nucleotide sequences of the positive samples from Nepal compared to other genomes within the genus Gemykibivirus.
Figure 1.
Figure 1.
Phylogenetic trees of (A) amino acid sequences of the index case REP protein and representatives of each genus in the family Genomoviridae; (B) whole genome nucleotide sequences of the positive samples from Nepal compared to other genomes within the genus Gemykibivirus.
Figure 2.
Figure 2.
Schematic of the genome of Human gemykibivirus 2 Nepal/N0000051/2020.
Figure 3.
Figure 3.
Map of Nepal and locations of the gemykibivirus positive cases [shaded].
See this image and copyright information in PMC

References

    1. Why encephalitis matters? Report of the virtual meeting, 28–29 June 2022. Geneva: World Health Organization; 2023.
    1. Wang H, Zhao S, Wang S, Zheng Y, Wang S, Chen H, et al. Global magnitude of encephalitis burden and its evolving pattern over the past 30 years. J Infect. 2022. Jun;84(6):777–87. - PubMed
    1. Department of Health Services Annual Report 2078/79. Kathmandu: Government of Nepal Ministry of Health and Population; 2021/2022.
    1. Granerod J, Cunningham R, Zuckerman M, Mutton K, Davies NW, Walsh AL, et al. Causality in acute encephalitis: defining aetiologies. Epidemiol Infect. 2010. Jun;138(6):783–800. - PubMed
    1. Glaser CA, Honarmand S, Anderson LJ, Schnurr DP, Forghani B, Cossen CK, et al. Beyond viruses: clinical profiles and etiologies associated with encephalitis. Clin Infect Dis. 2006. Dec 15;43(12):1565–77. - PubMed

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