Viral Metagenomics Revealed Sendai Virus and Coronavirus Infection of Malayan Pangolins (Manis javanica).

Ping Liu,Jin-Ping Chen,Wu Chen

doi:10.3390/v11110979

Abstract

Pangolins are endangered animals in urgent need of protection. Identifying and cataloguing the viruses carried by pangolins is a logical approach to evaluate the range of potential pathogens and help with conservation. This study provides insight into viral communities of Malayan Pangolins (Manis javanica) as well as the molecular epidemiology of dominant pathogenic viruses between Malayan Pangolin and other hosts. A total of 62,508 de novo assembled contigs were constructed, and a BLAST search revealed 3600 ones (≥300 nt) were related to viral sequences, of which 68 contigs had a high level of sequence similarity to known viruses, while dominant viruses were the Sendai virus and Coronavirus. This is the first report on the viral diversity of pangolins, expanding our understanding of the virome in endangered species, and providing insight into the overall diversity of viruses that may be capable of directly or indirectly crossing over into other mammals.

Highlights

The Malayan pangolin (Manis javanica), a representative mammal species of the order Pholidota, is one of the only eight pangolin species worldwide
A total of 21 organ samples of lung, lymph and spleen from 11 dead Malayan pangolins that could not be rescued by the Guangdong Wildlife Rescue Center were used to reveal viral diversity of pangolins
The whole genome and individual gene phylogenies for Sendai virus sequences assembled in this study all showed that the Sendai virus from Malayan pangolin had the closest relationship with the strain isolated from humans (AB005795.1), which strongly suggests the possibility that the Sendai virus is transmitted between pangolins and humans

Summary

Introduction

The Malayan pangolin (Manis javanica), a representative mammal species of the order Pholidota, is one of the only eight pangolin species worldwide. The skin of pangolins is covered by large and overlapping keratinized scales [2]. Because of the huge demand for their meat as a delicacy and their scales for use in traditional medicines, pangolins are the most poached and trafficked mammal in the world. That is why all the eight pangolin species are included in the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Concerted efforts have been made to conserve and rescue these species in captivity in China because of their threatened status and continuing decline of the population size in the wild. A previous study reported a complete genome sequence of Parainfluenza Virus 5 (PIV5) from a Sunda

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