Polymorphism of the TMPRSS2 gene relating to COVID-19 subceptibility in Vietnamese population

Authors

  • Nguyen Dang Ton V1. Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam 2. Graduate University of Science and Technology, Vietnam Academy of Science and Technology https://orcid.org/0000-0003-0182-8996
  • Vu Phuong Nhung 1. Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
  • Duong Thu Trang Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
  • Nguyen Thi Thanh Hoa 1. Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
  • Nguyen Hoai Nam 1. Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
  • Hoang Thi Thuan Graduate University of Science and Technology, Vietnam Academy of Science and Technology
  • Ho Anh Son Vietnam Military Medical University
  • Nguyen Thi Thanh Hai National Hospital for Tropical Diseases & Hanoi Medical University
  • Pham Ngoc Thach National Hospital for Tropical Diseases
  • Nong Van Hai 1. Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam 2. Graduate University of Science and Technology, Vietnam Academy of Science and Technology
  • Nguyen Hai Ha 1. Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam 2. Graduate University of Science and Technology, Vietnam Academy of Science and Technology https://orcid.org/0000-0002-5431-5935

DOI:

https://doi.org/10.15625/2615-9023/15829

Keywords:

SARS-CoV-2, human TMPRSS2, genetic polymorphism

Abstract

Recently, a contagious lung disease named coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), rapidly spread worldwide and has many serious consequences for human health. Human genetic polymorphisms may contribute to the variation of incidence, mortality as well as severity of COVID-19. To date, this factor in the Vietnamese population remains unknown. A cellular protease termed transmembrane protease serine 2 (TMPRSS2) was found to play a vital role in the entry of SARS-CoV-2 into host cells. In this study, we investigated polymorphisms in the TMPRSS2 gene from 270 whole exome sequencing data of Vietnamese peoples. We also employed bioinformatics tools including SIFT, Polyphen-2, and PROVEAN to predict the possible function of missense variants. A total of 34 TMPRSS2 variants were identified, of which, 29 were in non-coding regions and 14 were in coding regions. Variants found in exons included seven synonymous and seven non-synonymous point mutations, one of which was novel mutation (c.A1336C/p.R446R). Mutation c.G589A/p.V197M (rs12329760) possesses the highest frequency and was predicted to have the ability to damage protein by SIFT and Polyphen-2. In addition, the damaging possibility was also found in c.T244G/p.Y82D and c.C896T/p.A299V variants. This study contributes to the understanding of Vietnamese genetic variation databases relating to susceptibility to COVID-19.

 

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References

Asselta R., Paraboschi E. M., Mantovani A., Duga S., 2020. ACE2 and TMPRSS2 variants and expression as candidates to sex and country differences in COVID-19 severity in Italy. Aging (Albany. NY)., 12(11): 10087–10098.

Baughn L. B., Sharma N., Elhaik E., Sekulic A., Bryce A. H., Fonseca R., 2020. Targeting TMPRSS2 in SARS-CoV-2 Infection. Mayo Clin. Proc., 95(9): 1989–1999.

Chan J. F.-W., Yuan S., Kok K.-H., To K. K.-W., Chu H., Yang J., Xing F., Liu J., Yip C. C.-Y., Poon R. W.-S., Tsoi H.-W., Lo S. K.-F., Chan K.-H., Poon V. K.-M., Chan W.-M., Ip J. D., Cai J.-P., Cheng V. C.-C., Chen H., Hui C. K.-M., Yuen K.-Y., 2020. A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster. Lancet, 395(10223): 514–523.

Crackower M. A., Sarao R., Oliveira-dos-Santos A. J., Da Costa J., Zhang L., 2002. Angiotensin-converting enzyme 2 is an essential regulator of heart function. Nature, 417(6891): 822–828.

De Almeida-Pititto B., Dualib P. M., Zajdenverg L., Dantas J. R., De Souza F. D., Rodacki M., Bertoluci M. C., 2020. Severity and mortality of COVID 19 in patients with diabetes, hypertension and cardiovascular disease: A meta-analysis. Diabetol. Metab. Syndr., 12(1): 75.

Dong Y., Dong Y., Mo X., Hu Y., Qi X., Jiang F., Jiang Z., Jiang Z., Tong S., Tong S., Tong S., 2020. Epidemiology of COVID-19 among children in China. Pediatrics. https://doi.org/10.1542/peds. 2020-0702

FitzGerald L. M., Agalliu I., Johnson K., Miller M. A., Kwon E. M., Hurtado-Coll A., Fazli L., Rajput A. B., Gleave M. E., Cox M. E., Ostrander E. A., Stanford J. L., Huntsman D. G., 2008. Association of TMPRSS2-ERG gene fusion with clinical characteristics and outcomes: Results from a population-based study of prostate cancer. BMC Cancer, 8. https://doi.org/10.1186/1471-2407-8-230

Gorbalenya A., Baker S., Baric R., de Groot R., Drosten C., Gulyaeva A., Haagmans B., Lauber C., Leontovich A., Neuman B., Penzar D., Perlman S., Poon L., Samborskiy D., Sidorov I., Sola I., Ziebuhr J., 2020. Severe acute respiratory syndrome-related coronavirus : The species and its viruses – a statement of the Coronavirus Study Group. Nat. Microbiol., https://doi.org/10.1101/2020. 02.07.937862

Gross C. P., Essien U. R., Pasha S., Gross J. R., Wang S. yi, Nunez-Smith M., 2020. Racial and Ethnic Disparities in Population-Level Covid-19 Mortality. J. Gen. Intern. Med., 35(10): 3097–3099.

Hatcher S. M., Agnew-Brune C., Anderson M., Zambrano L. D., Rose C. E., Jim M. A., Baugher A., Liu G. S., Patel S. V., Evans M. E., Pindyck T., Dubray C. L., Rainey J. J., Chen J., Sadowski C., Winglee K., Penman-Aguilar A., Dixit A., Claw E., Parshall C., Provost E., Ayala A., Gonzalez G., Ritchey J., Davis J., Warren-Mears V., Joshi S., Weiser T., Echo-Hawk A., Dominguez A., Poel A., Duke C., Ransby I., Apostolou A., McCollum J., 2020. COVID-19 Among American Indian and Alaska Native Persons - 23 States, January 31–July 3, 2020. MMWR. Morb. Mortal. Wkly. Rep., 69(34): 1166–1169.

Hoffmann M., Kleine-Weber H., Schroeder S., Krüger N., Herrler T., Erichsen S., Schiergens T. S., Herrler G., Wu N. H., Nitsche A., Müller M. A., Drosten C., Pöhlmann S., 2020. SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor. Cell, 181(2): 271−280.e8.

Hou Y., Zhao J., Martin W., Kallianpur A., Chung M. K., Jehi L., Sharifi N., Erzurum S., Eng C., Cheng F., 2020. New insights into genetic susceptibility of COVID-19: An ACE2 and TMPRSS2 polymorphism analysis. BMC Med., 18(1).

Kim T. S., Heinlein C., Hackman R. C., Nelson P. S., 2006. Phenotypic Analysis of Mice Lacking the Tmprss2-Encoded Protease. Mol. Cell. Biol., 26(3): 965–975.

Kuhn J. H., Li W., Choe H., Farzan M., 2004., November Angiotensin-converting enzyme 2: A functional receptor for SARS coronavirus. Cell. Mol. Life Sci. https://doi.org/10.1007/s00018-004-4242-5

Kyte J., Doolittle R. F., 1982. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol., 157(1): 105–132.

Li W., Moore M. J., Vasllieva N., Sui J., Wong S. K., Berne M. A., Somasundaran M., Sullivan J. L., Luzuriaga K., Greeneugh T. C., Choe H., Farzan M., 2003. Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus. Nature, 426(6965): 450–454.

Shulla A., Heald-Sargent T., Subramanya G., Zhao J., Perlman S., Gallagher T., 2011. A Transmembrane Serine Protease Is Linked to the Severe Acute Respiratory Syndrome Coronavirus Receptor and Activates Virus Entry. J. Virol., 85(2): 873–882.

Simmons G., Gosalia D. N., Rennekamp A. J., Reeves J. D., Diamond S. L., Bates P., 2005. Inhibitors of cathepsin L prevent severe acute respiratory syndrome coronavirus entry. Proc. Natl. Acad. Sci. U. S. A., 102(33): 11876–11881.

Torre-Fuentes L., Matías-Guiu J., Hernández-Lorenzo L., Montero-Escribano P., Pytel V., Porta-Etessam J., Gómez-Pinedo U., Matías-Guiu J. A., 2020. ACE2, TMPRSS2, and Furin variants and SARS-CoV-2 infection in Madrid, Spain. J. Med. Virol., 93(2): 863–869.

Walls A. C., Park Y. J., Tortorici M. A., Wall A., McGuire A. T., Veesler D., 2020. Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein. Cell, 181(2): 281−292.e6.

Wang C., Horby P. W., Hayden F. G., Gao G. F., 2020. A novel coronavirus outbreak of global health concern. Lancet., https://doi.org/10.1016/S0140-6736(20)30 185−9

WHO Director-General’s remarks at the media briefing on 2019-nCoV on 11 February 2020. https://www.who.int/dg/speeches/detail/who-director-general-s-remarks-at-the-media-briefing-on-2019-ncov-on-11-february-2020 (accessed 4 December 2020)

Wu C., Zheng M., Yang Y., Gu X., Yang K., Li M., Liu Y., Zhang Q., Zhang P., Wang Y., Wang Q., Xu Y., Zhou Y., Zhang Y., Chen L., Li H., 2020. Furin: A Potential Therapeutic Target for COVID-19. IScience, 23(10): 101642.

Zhu N., Zhang D., Wang W., Li X., Yang B., Song J., Zhao X., Huang B., Shi W., Lu R., Niu P., Zhan F., Ma X., Wang D., Xu W., Wu G., Gao G. F., Tan W., 2020. A Novel Coronavirus from Patients with Pneumonia in China, 2019. N. Engl. J. Med., 382(8): 727–733.

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Published

31-03-2021

How to Cite

Ton, N. D., Nhung, V. P., Trang, D. T., Hoa, N. T. T., Nam, N. H., Thuan, H. T., Son, H. A., Hai, N. T. T., Thach, P. N., Hai, N. V., & Ha, N. H. (2021). Polymorphism of the TMPRSS2 gene relating to COVID-19 subceptibility in Vietnamese population. Academia Journal of Biology, 43(1). https://doi.org/10.15625/2615-9023/15829

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