New papillomaviruses identified in Malayan and Chinese pangolins

Papillomaviruses are non-enveloped double-stranded DNA (dsDNA) viruses with a circular genome. Infection with these viruses can lead to diverse clinical symptoms ranging from subclinical, cutaneous, and mucosal warts to cancerous lesions in vertebrate hosts.

A new study published in the journal Biology Letters identifies two new papillomavirus lineages by mining genome data from Chinese and Malayan pangolins.

Study: Discovery of new papillomaviruses in critically endangered Malayan and Chinese pangolins.  Image Credit: 2630ben/

She studies: Discovery of new papillomaviruses in critically endangered Malayan and Chinese pangolins. Image Credit: 2630ben/

What are pangolins?

Pangolins are nocturnal, scaly, insectivorous mammals that belong to the order Pholidota. The Phataginus And Smutsia genera are found in Africa, while the Manis genera are found in Asia.

Four different pangolin species reside in Asia, including the Philippine pangolin (Manis culionensis), Indian pangolin (Manis crassicaudata), Malayan pangolin (Manis javanica) and Chinese pangolin (Pentadactyla manis). The International Union for Conservation of Nature (IUCN) has designated the Philippine, Malayan and Chinese pangolins as critically endangered species due to their population declines due to overexploitation and trafficking of their scales.

Recently, pangolins emerged as potential hosts of viral diseases after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-related coronaviruses were reported in Malayan pangolins. Additionally, pangolins have also been implicated as hosts for other ribonucleic acid (RNA) viruses such as picornavirus, pneumovirus, reovirus, flavivirus, and canine distemper virus.Paramyxoviridae).

The diversity of DNA viruses and their association with disease in pangolins remains unclear.

About the studio

Researchers in the current study discovered an unidentified papillomavirus contig in pangolins and subsequently examined this sample using the tblastn algorithm. Annotation of contig 7307-bp was performed using the PuMA pipeline, which matched a complete human papillomavirus genome encoding proteins E1, E2, E6, E7, L1 and L2, along with two splicing products .

Next, short-read data from the resequenced genomes of 22 Chinese pangolins and 72 Malayan pangolins were examined. First, the short-read sequences with more than 100 significant matches were downloaded, followed by their again montage.

Genomic sequences were sorted into forward, orphan and reverse reads. Finally, annotation of complete viral genomes contigs was performed using PuMA.

Examination of L1 gene contigs revealed an intact L1 open reading frame. Isoelectric point and molecular weight estimation of the predicted protein products was performed using ExPASy. Magic-BLAST was used to calculate the coverage of the assembled sequences.

Bayesian phylogeny of E1 and L1 proteins was performed to study the systematics of these viruses using papillomaviruses recognized by ICTV and Tupaia belangeri papillomavirus 1 (TbelPV1) and Tupaiabelangeri papillomavirus 2 (TbelPV2).

Study results

Significant HPV hits were identified in 11 of 22 Chinese pangolin samples and 36 of 73 Malayan pangolin samples. All samples with known geographic provinces were from the Yunnan province of China.

Specifically, one Chinese pangolin sample and ten Malayan pangolin samples had more than 100 significant hits. These samples were subsequently screened for genome assembly, in which two new papillomavirus genomes were assembled, along with the reassembled genome for the reference contig.

The complete L1 gene was assembled for three of these samples. Furthermore, three different contigs of the L1 gene were assembled from a single Chinese pangolin.

The assembled genome was between 7,253 and 7,437 base pairs (bp), with a guanine-cytosine (GC) content ranging from 39.84% to 40.09%.

All three genomes contained proteins E1, E2, E6, E7, L1 and L2, as well as two splicing products. Furthermore, seven of the eight L1 sequences were classified into a monophyletic group and grouped as a sister lineage of TbelPV1. The E1 clade has also been positioned as a sister to TbelPV1.

Just one protein sequence from a Chinese pangolin belonged to several clades, including Dyodeltapapilloma virus, alpha papillomavirusAnd Omegapapillomavirus.


The current study identifies Southeast Asian pangolins as hosts of highly prevalent and diverse human papillomaviruses. These results underline the importance of in silicon extraction of host sequencing data to screen for new viruses. Further studies are needed to better understand the impact of papillomaviruses on pangolins and to develop conservation strategies for these animals.

Magazine reference:

  • Barreat, JGN, Kamada, AJ, Reuben de Souza, C., et al. (2023). Discovery of new papillomaviruses in critically endangered Malayan and Chinese pangolins. Biology Letters. doi:10.1098/rsbl.2022.0464.

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