Whole genome analysis of Human Mastadenovirus D causing Keratoconjunctivitis in India - A multicentre study

Authors

  • Ferdinamarie S Philomenadin RVRDL, Department of Microbiology, JIPMER, Pondicherry, India
  • Mini P Singh Department of Virology, PGIMER, Chandigarh, India
  • Jayanthi Shastri Department of Microbiology, TNMC & BYL Nair Hospital, Mumbai, India
  • Anil C Phukan Department of Microbiology, NEIGRIHMS, Shillong, India
  • Muruganandam Nagarajan Regional Medical Research Centre, Port Blair, A & N, India https://orcid.org/0000-0003-0430-221X
  • Subashini Kaliaperumal Department of Ophthalmology, JIPMER, Puducherry, India https://orcid.org/0000-0002-2399-9529
  • Radha Kanta Ratho Department of Virology, PGIMER, Chandigarh, India
  • Jagat Ram Department of Ophthalmology, PGIMER, Chandigarh, India
  • Madhav J Sathe Department of Microbiology, TNMC & BYL Nair Hospital, Mumbai, India
  • Avinash Ingole Department of Ophthalmology, BYL Nair Hospital & TNMC, Mumbai, India
  • Darshana B Rathod Department of Ophthalmology, BYL Nair Hospital & TNMC, Mumbai, India
  • Benjamin Nongrum Department of Ophthalmology, NEIGRIHMS, Shillong, India
  • Rehnuma Parvez Regional Medical Research Centre, Port Blair, A & N, India
  • Vineeta Malik Regional Medical Research Centre, Port Blair, A & N, India
  • Rahul Dhodapkar RVRDL, Department of Microbiology, JIPMER, Pondicherry, India https://orcid.org/0000-0002-8984-3332

DOI:

https://doi.org/10.3855/jidc.18905

Keywords:

Human mastadenovirus D, keratoconjunctivitis, recombinants, HAdV-54, India

Abstract

Introduction: Human mastadenovirus (HAdV) types 8, 37, 64 have been considered the major contributors in Epidemic keratoconjunctivitis (EKC) epidemics, but recent surveillance data have shown the involvement of emerging recombinants, including HAdV-53, HAdV-54, and HAdV-56. In our initial work, positive samples for adenovirus revealed that our strains were closer to HAdV-54 than HAdV-8. Hence, the current study aimed to use whole genome technology to identify the HAdV strain correctly.

Methodology: Oxford Nanopore technique was used, wherein a Targeted sequencing approach using long-range PCR amplification was performed. Primers were designed using HAdV-54 (AB448770.2) and HAdV-8 (AB897885.1) as reference sequences. Amplicons were sequenced on the GridION sequencer. Sequences were annotated using Gatu software, and similarities with standard reference sequence was calculated using Bioedit software. The phylogenetic tree was built after alignment in MEGA v7.0 using Neighbour joining method for each of the genes: Penton, Hexon, and Fiber. The effect of novel amino acid changes was evaluated using the PROVEAN tool. The Recombination Detection Program (RDP) package Beta 4.1 was used to identify recombinant sequences.

Results: Of the five samples sequenced, OL450401, OL540403, and OL540406 showed nucleotide similarity to HAdV-54 in the penton region. Additionally, OL450401 showed a statistically significant recombination event with HAdV-54 as minor and HAdV-8 as major parents. This was further supported by phylogenetic analysis as well.

Conclusions: In the present study, we have found evidence of a shift from HAdV-8 towards HAdV-54, thus stressing the need for surveillance of HAdVs and to stay updated on the rise of new recombinants.

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Published

2024-03-31

How to Cite

1.
Philomenadin FS, Singh MP, Shastri J, Phukan AC, Nagarajan M, Kaliaperumal S, Ratho RK, Ram J, Sathe MJ, Ingole A, Rathod DB, Nongrum B, Parvez R, Malik V, Dhodapkar R (2024) Whole genome analysis of Human Mastadenovirus D causing Keratoconjunctivitis in India - A multicentre study. J Infect Dev Ctries 18:450–457. doi: 10.3855/jidc.18905

Issue

Vol. 18 No. 03: March 2024

Section

Original Articles

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Copyright (c) 2024 Ferdinamarie Sharmila P, Mini Pritam, Jayanthi Shastri, Anil Chandra Phukan, Muruganandam Nagarajan, Subashini Kaliaperumal, Radha Kanta Ratho, Jagat Ram, Madhav Jagannath Sathe, Avinash Ingole, Darshana Babubhai Rathod, Benjamin Nongrum, Rehnuma Parvez, Vineeta Malik, Rahul Dhodapkar

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