Presence and diversity of Leishmania RNA virus in an old zoonotic cutaneous leishmaniasis focus, northeastern Iran: haplotype and phylogenetic based approach

• Published in: International journal of infectious diseases 2020-12, Vol.101, p.6-13
• Main Authors: Saberi, Reza, Fakhar, Mahdi, Hajjaran, Homa, Ataei-Pirkooh, Angila, Mohebali, Mehdi, Taghipour, Niloofar, Ziaei Hezarjaribi, Hajar, Moghadam, Yousef, Bagheri, Abouzar
• Format: Article
• Language: English
• Subjects: Adult; Animals; Child; cutaneous leishmaniasis; Haplotypes; Humans; Iran; Leishmania; Leishmania - isolation & purification; Leishmania - virology; Leishmania RNA virus; Leishmaniasis, Cutaneous - parasitology; Leishmaniasis, Cutaneous - virology; Male; phylogenetic; Phylogeny; Polymerase Chain Reaction; RNA Viruses - genetics; RNA Viruses - isolation & purification; RNA, Viral - isolation & purification; Species Specificity; Viral Zoonoses - virology
• ISSN: 1201-9712; 1878-3511
• DOI: 10.1016/j.ijid.2020.08.033

•Leishmania RNA Virus 2 was detected in 59 (69.4%) of the Cutaneous Leishmaniasis cases studied.•For the first time, Leishmania RNA Virus 2 was reported in one L. tropica strain in Iran.•Ten unique haplotypes were identified based on the analyzed sequences of the RdRp gene. Leishmania RNA virus (LRV) is a double-stranded RNA (dsRNA) virus that circulates within many species of the Leishmania parasite. In this study, we aimed to investigate the presence of LRV2 circulating in Leishmania isolates in an old focus of ZCL located in northeastern of Iran. Leishmania isolates were collected from 85 patients that confirmed to have cutaneous leishmaniasis (CL) based on parasitological examination. To identify the Leishmania isolates, species-specific primer sets were applied for molecular identification. The presence of LRV2 was performed by RdRp-semi nested-PCR. The genetic diversity were calculated using MEGA and DnaSP. To assess haplotype diversity, 31 LRV2 strains in different regions were surveyed using analysis a 292-bp section of the RdRp sequences. Out of 85 patients, 83 (97.6 %) were diagnosed with L. major and 2 (2.4 %) with L. tropica. LRV2 virus was detected in 59 (69.4%) of the CL cases. For the first time, LRV2 was reported in one L. tropica strain in Iran. The current LRV2 sequences indicated the highest similarities to an Old World LRV2. Moreover, 10 unique haplotypes were identified based on the analyzed sequences of the RdRp gene. Our results indicated the highest occurrence of Leishmania/LRV2 co-circulation in this known ZCL focus from northeastern Iran. Phylogenetic analyses of LRV2 sequences confirmed that these isolates belong to the order of LRV2 from the Old World. This study offered an insight into LRV2 haplotype that the informative issue can be used for genetic research of LRV2 in other regions.