Characteristics of cases infected by severe acute respiratory syndrome coronavirus 2 of different genotypes_West China Medical Journal

Authors：

LI Jiao ¹ , MAO Yi ¹ , CHEN Heng ^2,3 , YANG Ming ⁴ , ZHANG Renqing ¹ ,  JIANG Liangshuang ¹ , PU Ping ¹ , LIU Liangqian ¹ , XIAO Yan ^5,6 , WANG Ying ⁵ , DANG Shengyuan ⁵ , REN Lili ^5,6

1. Emergency Department, Chengdu Public Health Clinical Medical Center, Chengdu, Sichuan 610061, P. R. China;
2. Chengdu Workstation of Emerging Infectious Diseases, Chinese Academy of Medical Sciences, Chengdu, Sichuan 610041, P. R. China;
3. Chengdu Center for Disease Control and Prevention, Chengdu, Sichuan 610041, P. R. China;
4. Tuberculosis Department, Chengdu Public Health Clinical Medical Center, Chengdu, Sichuan 610061, P. R. China;
5. National Health Commission of the People’s Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, P. R. China;
6. Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, P. R. China;

Corresponding author：

JIANG Liangshuang, Email: 502830704@qq.com

Keywords：

Severe acute respiratory syndrome coronavirus 2; genotype; clinical features

DOI：

10.7507/1002-0179.202108050

Video：

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Objective To explore the clinical characteristics of patients who were infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) of different genotypes. Methods A retrospective study was conducted on 111 SARS-CoV-2 infected cases at home and abroad admitted to Chengdu Public Health Clinical Medical Center between January and September 2020. The basic information, gene sequencing results (Pangolin typing method), clinical typing, first laboratory examinations 24 hours after admission, and whether repositive after discharge were collected. According to Pangolin typing, patients were divided into five groups: A, B, B.X, B.1.X and B.1.1.X. The basic information (age, sex, and origin), laboratory test results (lymphocyte count, C-reactive protein, serum amyloid A, CD3⁺ T lymphocytes, CD4⁺ T lymphocytes, and CD8⁺ T lymphocytes), clinical classification and whether repositive were compared among different genotype infected patients. Results Among the 111 infected patients, 54 (48.6%) were males and 57 (51.4%) were females. Their ages ranged from 16 to 87 years, with a median age of 49 years. In terms of clinical classification, there were 10 asymptomatic cases (9.0%), 10 mild cases (9.0%), 64 ordinary cases (57.7%), 13 severe cases (11.7%), and 14 critical cases (12.6%). There were 75 domestic cases (67.6%) and 36 imported cases (32.4%). Eighty cases (72.1%) did not return to positive, and 31 cases (27.9%) returned to positive. There were 8 cases infected by type A virus, 18 cases infected by type B virus, 26 cases infected by type B.X virus, 5 cases infected by type B.1.X virus, and 54 cases infected by type B.1.1.X virus. Among patients infected by different genotype viruses, no statistically significant difference was found in sex, age, clinical type, laboratory examination, or whether repositive (P>0.05), but there was statistically significant difference in the distribution of domestic and imported cases (P=0.016). Type B virus infected patients were mostly domestic cases, while type B.X virus infected patients were mostly imported cases. Conclusion The distribution of domestic and imported cases is different among SARS-CoV-2 of different genotypes.

Citation： LI Jiao, MAO Yi, CHEN Heng, YANG Ming, ZHANG Renqing, JIANG Liangshuang, PU Ping, LIU Liangqian, XIAO Yan, WANG Ying, DANG Shengyuan, REN Lili. Characteristics of cases infected by severe acute respiratory syndrome coronavirus 2 of different genotypes. West China Medical Journal, 2022, 37(2): 171-175. doi: 10.7507/1002-0179.202108050 Copy

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15.	Laamarti M, Alouane T, Kartti S, et al. Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geo-distribution and a rich genetic variations of hotspots mutations. PLoS One, 2020, 15(11): e0240345.
16.	Pan B, Ji Z, Sakkiah S, et al. Identification of epidemiological traits by analysis of SARS-CoV-2 sequences. Viruses, 2021, 13(5): 764.
17.	Goyal M, De Bruyne K, van Belkum A, et al. Different SARS-CoV-2 haplotypes associate with geographic origin and case fatality rates of COVID-19 patients. Infect Genet Evol, 2021, 90: 104730.
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19.	Loconsole D, Centrone F, Morcavallo C, et al. Rapid spread of the SARS-CoV-2 variant of concern 202012/01 in Southern Italy (December 2020-March 2021). Int J Environ Res Public Health, 2021, 18(9): 4766.
20.	Galloway SE, Paul P, Maccannell DR, et al. Emergence of SARS-CoV-2 B. 11.7 Lineage-United States, December 29, 2020-January 12, 2021. MMWR Morb Mortal Wkly Rep, 2021, 70(3): 95-99.
21.	Liu CY, Huang LJ, Lai CH, et al. Clinical characteristics, management and prognostic factors in patients with probable severe acute respiratory syndrome (SARS) in a SARS center in Taiwan. J Chin Med Assoc, 2005, 68(3): 110-117.
22.	邹莉萍, 毛毅, 罗海霞, 等. 成都市新型冠状病毒感染境外输入患者与相关本土患者的临床分析. 中国胸心血管外科临床杂志, 2021(9): 1021-1028.
23.	中华医学会呼吸病学分会, 中国医师协会呼吸医师分会. 中国成人 2019 冠状病毒病的诊治与防控指南. 中华医学杂志, 2021, 101(18): 1293-1356.
24.	Yan N, Wang W, Gao Y, et al. Medium term follow-up of 337 patients with coronavirus disease 2019 (COVID-19) in a Fangcang shelter hospital in Wuhan, China. Front Med (Lausanne), 2020, 7: 373.
25.	Gao Z, Xu Y, Guo Y, et al. A systematic review of re-detectable positive virus nucleic acid among COVID-19 patients in recovery phase. Infect Genet Evol, 2020, 85: 104494.
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27.	Yao MQ, Zheng QX, Xu J, et al. Factors associated with a SARS-CoV-2 recurrence after hospital discharge among patients with COVID-19: systematic review and meta-analysis. J Zhejiang Univ Sci B, 2020, 21(12): 940-947.
28.	Hong LX, Liu L, Lin A, et al. Risk factors for SARS-CoV-2 re-positivity in COVID-19 patients after discharge. Int Immunopharmacol, 2021, 95: 107579.
29.	Gao C, Zhu L, Jin CC, et al. Prevalence and impact factors of recurrent positive SARS-CoV-2 detection in 599 hospitalized COVID-19 patients. Clin Microbiol Infect, 2021, 27(5): 785.e1-785.e7.

1. Zhu N, Zhang DY, Wang WL, et al. A novel coronavirus from patients with pneumonia in China, 2019. N Engl J Med, 2020, 382(8): 727-733.
2. 世界卫生组织. 2019 冠状病毒病（COVID-19）疫情. [2021-06-07]. https://www.who.int/zh/emergencies/diseases/novel-coronavirus-2019.
3. Dumonteil E, Fusco D, Drouin A, et al. Genomic signatures of SARS-CoV-2 associated with patient mortality. Viruses, 2021, 13(2): 227.
4. Toyoshima Y, Nemoto K, Matsumoto S, et al. SARS-CoV-2 genomic variations associated with mortality rate of COVID-19. J Hum Genet, 2020, 65(12): 1075-1082.
5. Zhao S, Lou J, Cao L, et al. An early assessment of a case fatality risk associated with P.1 SARS-CoV-2 lineage in Brazil: an ecological study. J Travel Med, 2021, 28(7): taab078.
6. Yamamoto N, Bauer G. Apparent difference in fatalities between Central Europe and East Asia due to SARS-COV-2 and COVID-19: four hypotheses for possible explanation. Med Hypotheses, 2020, 144: 110160.
7. 宋洋, 许文波. 新型冠状病毒基因组序列的网络平台与基因分型. 病毒学报, 2021, 37(1): 181-190.
8. 中华人民共和国国家卫生健康委员会办公厅, 国家中医药管理局办公室. 新型冠状病毒肺炎诊疗方案(试行第八版). 中国医药, 2020, 15(10): 1494-1499.
9. 国务院应对新型冠状病毒肺炎疫情联防联控机制综合组. 新型冠状病毒肺炎防控方案(第七版). 中国感染控制杂志, 2020, 19(11): 1042-1048.
10. O’Toole Á, Scher E, Underwood A, et al. Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool. Virus Evol, 2021, 7(2): veab064.
11. Rambaut A, Holmes EC, O’Toole Á, et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol, 2020, 5(11): 1403-1407.
12. Tang XL, Wu CC, Xiang L, et al. On the origin and continuing evolution of SARS-CoV-2. Natl Sci Rev, 2020, 7(6): 1012-1023.
13. Grubaugh ND, Petrone ME, Holmes EC. We shouldn’t worry when a virus mutates during disease outbreaks. Nat Microbiol, 2020, 5(4): 529-530.
14. Day T, Gandon S, Lion S, et al. On the evolutionary epidemiology of SARS-CoV-2. Curr Biol, 2020, 30(15): R849-R857.
15. Laamarti M, Alouane T, Kartti S, et al. Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geo-distribution and a rich genetic variations of hotspots mutations. PLoS One, 2020, 15(11): e0240345.
16. Pan B, Ji Z, Sakkiah S, et al. Identification of epidemiological traits by analysis of SARS-CoV-2 sequences. Viruses, 2021, 13(5): 764.
17. Goyal M, De Bruyne K, van Belkum A, et al. Different SARS-CoV-2 haplotypes associate with geographic origin and case fatality rates of COVID-19 patients. Infect Genet Evol, 2021, 90: 104730.
18. Feder KA, Pearlowitz M, Goode A, et al. Linked clusters of SARS-CoV-2 variant B.1.351 - Maryland, January-February 2021. MMWR Morb Mortal Wkly Rep, 2021, 70(17): 627-631.
19. Loconsole D, Centrone F, Morcavallo C, et al. Rapid spread of the SARS-CoV-2 variant of concern 202012/01 in Southern Italy (December 2020-March 2021). Int J Environ Res Public Health, 2021, 18(9): 4766.
20. Galloway SE, Paul P, Maccannell DR, et al. Emergence of SARS-CoV-2 B. 11.7 Lineage-United States, December 29, 2020-January 12, 2021. MMWR Morb Mortal Wkly Rep, 2021, 70(3): 95-99.
21. Liu CY, Huang LJ, Lai CH, et al. Clinical characteristics, management and prognostic factors in patients with probable severe acute respiratory syndrome (SARS) in a SARS center in Taiwan. J Chin Med Assoc, 2005, 68(3): 110-117.
22. 邹莉萍, 毛毅, 罗海霞, 等. 成都市新型冠状病毒感染境外输入患者与相关本土患者的临床分析. 中国胸心血管外科临床杂志, 2021(9): 1021-1028.
23. 中华医学会呼吸病学分会, 中国医师协会呼吸医师分会. 中国成人 2019 冠状病毒病的诊治与防控指南. 中华医学杂志, 2021, 101(18): 1293-1356.
24. Yan N, Wang W, Gao Y, et al. Medium term follow-up of 337 patients with coronavirus disease 2019 (COVID-19) in a Fangcang shelter hospital in Wuhan, China. Front Med (Lausanne), 2020, 7: 373.
25. Gao Z, Xu Y, Guo Y, et al. A systematic review of re-detectable positive virus nucleic acid among COVID-19 patients in recovery phase. Infect Genet Evol, 2020, 85: 104494.
26. Azam M, Sulistiana R, Ratnawati M, et al. Recurrent SARS-CoV-2 RNA positivity after COVID-19: a systematic review and meta-analysis. Sci Rep, 2020, 10(1): 20692.
27. Yao MQ, Zheng QX, Xu J, et al. Factors associated with a SARS-CoV-2 recurrence after hospital discharge among patients with COVID-19: systematic review and meta-analysis. J Zhejiang Univ Sci B, 2020, 21(12): 940-947.
28. Hong LX, Liu L, Lin A, et al. Risk factors for SARS-CoV-2 re-positivity in COVID-19 patients after discharge. Int Immunopharmacol, 2021, 95: 107579.
29. Gao C, Zhu L, Jin CC, et al. Prevalence and impact factors of recurrent positive SARS-CoV-2 detection in 599 hospitalized COVID-19 patients. Clin Microbiol Infect, 2021, 27(5): 785.e1-785.e7.

West China Medical Journal

Characteristics of cases infected by severe acute respiratory syndrome coronavirus 2 of different genotypes

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