Contents lists available at ScienceDirect Virus Research journal homepage: www.elsevier.com/locate/virusres Characterization and genome analysis of B1 sub-cluster mycobacteriophage PDRPxv Avni Sinha a,1 , Kandasamy Eniyan a,b,1 , Prasanth Manohar b , Nachimuthu Ramesh b , Urmi Bajpai a, * a Department of Biomedical Science, Acharya Narendra Dev College (University of Delhi) Govindpuri, Kalkaji, New-Delhi, 110019, India b Antibiotic Resistance and Phage Therapy Laboratory, School of Bioscience and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India ARTICLE INFO Keywords: PDRPxv Lytic phage ORFs B1 Sub-cluster Adsorption Burst size ABSTRACT Mycobacteriophages are viruses specific to mycobacteria that have gained attention as alternative therapeutic strategies for treating antibiotic-resistant infections. Mycobacteriophages are highly diverse and have been grouped into 29 clusters, 71 sub-clusters and 10 singletons based on the genome sequence. Here, we annotate the genome of PDRPxv, a lytic mycobacteriophage isolated from New Delhi; it belongs to the Siphoviridae family as determined by transmission electron microscopy. This phage survives at higher temperatures (up to 55 °C) and in alkaline conditions (up to pH11). PDRPxv phage genome is 69,171 bp in length with 66.35 % GC content and encodes 107 putative open reading frames and belongs to the B1 sub-cluster. Genome annotation indicated that genes for DNA encapsidation, structural proteins, replication/transcription and lysis of the host are present in functional clusters. Structural proteins encoded by Gp10-Gp12, Gp18, Gp25 and Gp28-Gp33 were identified by mass spectrometry. Interestingly, no gene encoding a holin function was found. Single-step growth curve re- vealed that PDRPxv has an adsorption time of 45 min, a latency time of 135 min and an average burst size of 99 phage particles per infected cell. The short latency period and the large burst size mark the lytic nature of the PDRPxv phage, which could therefore be a promising therapeutic candidate against pathogenic Mycobacterium species. 1. Introduction The emergence of drug-resistant strains of M. tuberculosis has cre- ated an alarming situation (WHO, 2017). Exploring alternative options to combat and manage the disease are of paramount importance. Bac- teriophages, the natural killers of the bacteria, and their lytic enzymes such as endolysins, ectolysins, depolymerases are gaining traction as potential alternates/complements to antibiotics due to their anti- bacterial activity. It is known that about 10 23 phage infections may occur per second (Hendrix et al., 1999); this high rate of infection causes extensive horizontal gene exchange between bacteriophages and their hosts, which accounts for the mosaic nature of phage genomes (Hendrix et al., 2000; Pedulla et al., 2003). Mycobacteriophages are specific to mycobacterial spp. that include fast dividing non-pathogenic M. smegmatis and slow growing pathogenic M. tuberculosis. Enormous genetic diversity is observed amongst mycobacteriophages, which are hence classified into 29 distinct clusters, where 12 of the clusters (A–D, F–H, I, K–M, P) are also further divided into sub-clusters. Additionally, there are 10 singletons that do not share homology with any of the reported phages. According to Actinobacteriophage Database (http:// phagesdb.org/), so far 11,160 mycobacteriophages have been isolated from various environmental sources but only about 17 % have been sequenced so far. Their genome size ranges between 41-165 kb (with an average GC content of 50–70 %). Given the small size of phage genomes and the current low cost of DNA sequencing, the published sequence information of phage genomes represents only a tiny fraction. In this report, we are describing whole genome analysis and anno- tation and one step growth curve of PDRPxv, a lytic mycobacter- iophage, which we isolated from a soil sample, collected from New Delhi. The phage belongs to cluster B1 and its genome is a contig of 69171 bases, containing a total of 107 ORFs. 2. Material and methods 2.1. Bacterial strains, soil samples and culture media M. smegmatis mc 2 155 strain was used as host for the phage isolation. The cells were grown in Middlebrook 7H9 Medium (HiMedia, India) https://doi.org/10.1016/j.virusres.2020.197884 Received 15 October 2019; Received in revised form 21 January 2020; Accepted 21 January 2020 ⁎ Corresponding author. E-mail address: urmibajpai@andc.du.ac.in (U. Bajpai). 1 Both the authors contributed equally. Virus Research 279 (2020) 197884 Available online 22 January 2020 0168-1702/ © 2020 Published by Elsevier B.V. T