CRISPR Technology in Infectious Disease Management: Principles, Applications, and Future Challenges with Emphasis on SARS-CoV-2, HIV, and HBV

Yuxing Han; Tianyou Yan; Chujing Zhang; Junwen Zhang

doi:10.54097/09vggj25

Authors

Yuxing Han
Tianyou Yan
Chujing Zhang
Junwen Zhang

DOI:

https://doi.org/10.54097/09vggj25

Keywords:

CRISPR-Cas; COVID-19; HIV/AIDS; HBV.

Abstract

Retroviruses and double-stranded DNA (dsDNA) viruses enter cells by integrating their genetic materials into host DNA. During this period, the virus stays dormant and can escape host immune surveillance, which is difficult to detect and kill clinically. Thus, viral diseases, especially those caused by RNA viruses, pose a huge threat to public health. Currently, more research shows that clearing the genome of the virus has become a direct and effective way to treat viral diseases. However, viral diseases such as SARS-CoV-2 exhibit significant genetic diversity, with over 300000 mutants discovered, covering the entire genome of the virus, which greatly limits the traditional gene editing techniques for diagnosing and clearing the virus sequence. CRISPR-Cas can target multiple regions, exhibiting stronger catalytic activity compared to other gene editing methods. At present, it has been widely used in the diagnosis and treatment of viral diseases. Therefore, understanding the principles of CRISPR-Cas technologies and identifying their potential applications in viral diseases is of great significance. This paper reviews the principles of this technology and its current applications in three aspects, COVID-19, HIV, and HBV. Additionally, this paper summarizes the difficulty in applying CRISPR-Cas technology and future expectations.

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References

Li J, Xu R, Qin R, et al. Genome editing mediated by SpCas9 variants with broad non-canonical PAM compatibility in plants. Molecular Plant, 2021, 14(2): 352–360.

Shmakov S, Abudayyeh Omar O, Makarova Kira S, et al. Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems. Molecular Cell, 2015, 60(3): 385–397.

Gootenberg J S, Abudayyeh O O, Lee J W, et al. Nucleic acid detection with CRISPR-Cas13a/C2c2. Science, 2017, 356(6336): 438–442.

Barrangou R, Fremaux C, Deveau H, et al. CRISPR provides acquired resistance against viruses in prokaryotes. Science (New York, N.Y.), United States: 2007, 315(5819): 1709–12.

Garneau J E, Dupuis M-È, Villion M, et al. The CRISPR-Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature, 2010, 468(7320): 67–71.

Jinek M, Chylinski K, Fonfara I, et al. A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity. Science, 2012, 337(6096): 816–821.

Abudayyeh O O, Gootenberg J S, Konermann S, et al. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science, 2016, 353(6299): aaf5573.

Abbott T R, Dhamdhere G, Liu Y, et al. Development of CRISPR as an Antiviral Strategy to Combat SARS-CoV-2 and Influenza. Cell, 2020, 181(4): 865-876.e12.

Safari F, Afarid M, Rastegari B, et al. CRISPR systems: Novel approaches for detection and combating COVID-19. Virus Research, 2021, 294: 198282.

Kannan S, Altae-Tran H, Jin X, et al. Compact RNA editors with small Cas13 proteins. Nature Biotechnology, 2021, 40(2): 194–197.

Nguyen T M, Zhang Y, Pandolfi P P. Virus against virus: a potential treatment for 2019-nCov (SARS-CoV-2) and other RNA viruses. Cell Research, 2020, 30(3): 189–190.

Lino C A, Harper J C, Carney J P, et al. Delivering CRISPR: a review of the challenges and approaches. Drug Delivery, 2018, 25(1): 1234–1257.

Blanchard E L, Vanover D, Bawage S S, et al. Treatment of influenza and SARS-CoV-2 infections via mRNA-encoded Cas13a in rodents. Nature Biotechnology, 2021: 1–10.

Fareh M, Zhao W, Hu W, et al. Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. Nature Communications, 2021, 12(1).

Pascarella G, Strumia A, Piliego C, et al. COVID‐19 diagnosis and management: a comprehensive review. Journal of Internal Medicine, 2020, 288(2).

Ravi N, Cortade D L, Ng E, et al. Diagnostics for SARS-CoV-2 detection: A comprehensive review of the FDA-EUA COVID-19 testing landscape. Biosensors & Bioelectronics, 2020, 165: 112454.

Liu L, Li X, Wang J, et al. Two Distant Catalytic Sites Are Responsible for C2c2 RNase Activities. Cell, 2017, 168(1-2): 121-134.e12.

Palaz F, Kalkan A K, Can Ö, et al. CRISPR-Cas13 System as a Promising and Versatile Tool for Cancer Diagnosis, Therapy, and Research. ACS Synthetic Biology, 2021, 10(6): 1245–1267.

Chen J S, Ma E, Harrington L B, et al. CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity. Science, 2018, 360(6387): 436–439.

Joung J, Ladha A, Saito M, et al. Point-of-care testing for COVID-19 using SHERLOCK diagnostics. medRxiv, 2020.

Joung J, Ladha A, Saito M, et al. Detection of SARS-CoV-2 with SHERLOCK One-Pot Testing. New England Journal of Medicine, 2020, 383(15): 1492–1494.

Broughton J P, Deng X, Yu G, et al. CRISPR–Cas12-based detection of SARS-CoV-2. Nature Biotechnology, 2020, 38.

Fozouni P, Son S, Díaz de León Derby M, et al. Amplification-free detection of SARS-CoV-2 with CRISPR-Cas13a and mobile phone microscopy. Cell, 2020, 184(2).

The path that ends AIDS: UNAIDS Global AIDS Update 2023. www.unaids.org. https://www.unaids.org/en/resources/documents/2023/global-aids-update-2023.

Yu S, Yao Y, Xiao H, et al. Simultaneous Knockout of CXCR4 and CCR5 Genes in CD4+ T Cells via CRISPR-Cas9 Confers Resistance to Both X4- and R5-Tropic Human Immunodeficiency Virus Type 1 Infection. Human Gene Therapy, 2018, 29(1): 51–67.

Yin L, Hu S, Mei S, et al. CRISPR-Cas9 Inhibits Multiple Steps of HIV-1 Infection. Human Gene Therapy, 2018, 29(11): 1264–1276.

Darcis G, Binda C, Klaver B, et al. The Impact of HIV-1 Genetic Diversity on CRISPR-Cas9 Antiviral Activity and Viral Escape. Viruses, 2019, 11(3): 255.

Hartweger H, McGuire A T, Horning M, et al. HIV-specific humoral immune responses by CRISPR-Cas9-edited B cells. Journal of Experimental Medicine, 2019, 216(6): 1301–1310.

Lampi Y, Van Looveren D, Vranckx L S, et al. Targeted editing of the PSIP1 gene encoding LEDGF/p75 protects cells against HIV infection. Scientific Reports, 2019, 9(1).

Teng Y, Luo M, Yu T, et al. CRISPR-Cas9-mediated deletion of miR-146a enhances antiviral response in HIV-1 infected cells. Genes & Immunity, 2018.

Xiao Q, Chen S, Wang Q, et al. CCR5 editing by Staphylococcus aureus Cas9 in human primary CD4+ T cells and hematopoietic stem/progenitor cells promotes HIV-1 resistance and CD4+ T cell enrichment in humanized mice. Retrovirology, 2019, 16(1).

Xu Y. Characterization of HIV-1 drug resistance mutationsand a novel method for HIV-1 treatment using CRISPR-Cas9 technology. Zhejiang University: 2021.

Wang S, Li H, Kou Z, et al. Highly sensitive and specific detection of hepatitis B virus DNA and drug resistance mutations utilizing the PCR-based CRISPR-Cas13a system. Clinical Microbiology and Infection, 2021, 27(3): 443–450.

Lin S-R, Yang H-C, Kuo Y-T, et al. The CRISPR-Cas9 System Facilitates Clearance of the Intrahepatic HBV Templates In Vivo. Molecular Therapy - Nucleic Acids, 2014, 3: e186.

Dong C, Qu L, Wang H, et al. Targeting hepatitis B virus cccDNA by CRISPR-Cas9 nuclease efficiently inhibits viral replication. Antiviral Research, 2015, 118: 110–117.

Scott T, Moyo B, Nicholson S, et al. ssAAVs containing cassettes encoding SaCas9 and guides targeting hepatitis B virus inactivate replication of the virus in cultured cells. Scientific Reports, 2017, 7(1).