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Epidemiological Study of Betacoronaviruses in Captive Malayan Pangolins

Our take —

Researchers have found additional evidence of coronavirus infection in pangolins sampled in southern China. The detected viruses were most similar to a virus previously detected in pangolins from 2019; the pangolin viruses are genetically similar to SARS-CoV-2 but are more distantly related than viruses detected in bats. The results suggest that coronavirus infection in pangolins may be common, but whether animals become infected during transportation into China and whether pangolins served as intermediate hosts for SARS-CoV-2 or a progenitor virus is not clear.

Study design

Other

Study population and setting

The authors performed multiple PCR tests and sequencing of the nucleoprotein gene to confirm that virus RNA was present in samples. The presence of viral RNA was also confirmed in one of the deceased pangolin samples using metagenomic sequencing.

Summary of Main Findings

Three fecal samples from captive M. javanica individuals sampled in Dongguan, one lymph node from a deceased M. javanica confiscated in Guongzhou, and one intestine sample from a separate deceased confiscated M. javanica were positive for coronavirus RNA with multiple PCR tests. Phylogenetic analysis of the amplified nucleoprotein segments showed that all of the pangolins coronavirus sequences shared 98.13-100% sequence identity to each other and pangolin-CoV-MP789, the virus genome assembled from a subset of samples analyzed previously. The pangolin virus shared between 93.75-95.63% sequence identity with SARS-CoV-2 in the nucleoprotein gene segment. Quantitative analysis of ACE2 expression in pangolin organs showed the highest levels in kidney, lower levels in heart and spleen, and very low but detectable levels in lung, stomach, pancreas, and liver.

Study Strengths

The authors performed multiple PCR tests and sequencing of the nucleoprotein gene to confirm that virus RNA was present in samples. The presence of viral RNA was also confirmed in one of the deceased pangolin samples using metagenomic sequencing.

Limitations

It is unclear whether coronavirus infection was the cause of death in the 7 pangolins confiscated in Guangzhou. Other viruses were detected in the pangolins via metagenomic analysis, but animals may have died for other reasons besides viral infection. The very limited sample size from one captive group of animals is insufficient to conclude that the detected coronaviruses are circulating widely in pangolin populations. Furthermore, since these animals were rescued following importation into China at some unknown date prior to sampling, it is unclear whether animals became infected in the wild, during trafficking, or within the rescue facility.

Value added

Multiple studies have now found evidence of coronavirus infection in Malayan pangolins, although positives have only been found in trafficked animals after entering China through trade. Samples from this study were the first new pangolin samples from China since the start of the COVID-19 pandemic. These data suggest that transmission of coronaviruses related to SARS-CoV-2 continued in captive pangolins during 2020.

This review was posted on: 19 April 2021