Close origin to SARS-CoV-2 in Pangolins
New pneumonia associated with SARS-CoV-2 causing COVID-19 pandemic was associated with animal reservoirs like pangolins (mammalian order Pholidota), these are mammals distributed in the southeast-Asian region (1). They live in the forest and his ecosystem is endangered by the wildlife traffic because they are used in foods and traditional medicine (Figure1). In the past, a genomic study from lung pangolin samples detected coronaviruses(2). Pangolin-CoV is the second closest relative of SARS-CoV-2 behind RaTG13 (sequence in bats) with 91.02% identical to SARS-CoV-2 at the whole-genome (3). The specie related to SARS-CoV-2 is in Malayan pangolin (Manis javanica) (4). The sequences of new coronavirus have been submitted to GISAID (https://www.gisaid.org/). The most related samples collected are pangolin/Guandong/1/2020 (accession EPI_ISL_410721) and pangolin/Guangdong/P2S/2019 (accession EPI_ISL_410544). The other who are parented are pangolin/Guangxi/P5E/2017 (accession EPI_ISL_410541), pangolin/Guangxi/P4L/2017 (accession EPI_ISL_410538), pangolin/Guangxi/P5L/2017 (accession EPI_ISL_410540), pangolin/Guangxi/P1E/2017 (accession EPI_ISL_410539) (Figure 2), those SARS-like pangolin viruses of this sequences are parented with the first sample sequence in humans WH-Human_1 (accession MN908947). This information suggests that pangolins should be considered as zoonotic hosts and intermediate before bats for this virus. The government may ban the sale and buy of this species for human consumption; therefore, this species needs to be monitoring for preventing a new outbreak in the future.
Figure 1. Distribution of species of the Manidae family in the world(inaturalist.com).
Figure 2. Phylogeny of SARS-like beta coronaviruses including novel coronavirus SARS-CoV-2 (nextstrain.com).
References
1. Challender D, Willcox DHA, Panjang E, Lim N, Nash H, Heinrich S, et al. Manis javanica (Sunda Pangolin) [Internet]. The IUCN Red List of Threatened Species 2019. 2019 [citado 5 de mayo de 2020]. Disponible en: https://www.iucnredlist.org/species/12763/123584856
2. Liu P, Chen W, Chen J-P. Viral Metagenomics Revealed Sendai Virus and Coronavirus Infection of Malayan Pangolins (Manis javanica). Viruses [Internet]. 24 de octubre de 2019 [citado 5 de mayo de 2020];11(11):979. Disponible en: https://www.mdpi.com/1999-4915/11/11/979
3. Zhang T, Wu Q, Zhang Z. Probable Pangolin Origin of SARS-CoV-2 Associated with the COVID-19 Outbreak. Curr Biol. 6 de abril de 2020;30(7):1346–1351.e2.
4. Lam TTY, Shum MHH, Zhu HC, Tong YG, Ni XB, Liao YS, et al. Identifying SARS-CoV-2 related coronaviruses in Malayan pangolins. Nature. 26 de marzo de 2020;1–6.