RT-PCR Mediated Identification of SARS-CoV-2 Patients from Particular Regions of Bangladesh and the Multi-factorial Analysis Considering Their Pre and Post Infection Health Conditions

Main Article Content

Kazi Mahmuda Akter
Tanjum Tushi
Sabrina Jahan Mily
Rashenda Aziz Mohona
Samin Anis
Adittya Kishor Chakraborty
Elmee Tabassum
Tahmid Ul Islam
Ozifatun Jannat Akhi
Israt Sultana Nishe
Badrun Nahar Laxy
Sanjida Sultana Zerin
Abdiqani Jama Roble
Md. Imran Hossain
Sharmin Ahmed
Salauddin Al Azad

Abstract

Background: SARS-CoV-2 is a type of coronavirus shows bizarre features with fatality rates at 34.4%. The clinical and non-clinical features of COVID-19 might be causative factors for more rapid community spreading compared to MERS and SARS-CoV-1.

Objectives: To study the efficacy of RT-PCR based detection of SARS-CoV-2 patients. Besides, the patients' pre and post-infection health conditions depending on selective clinical and nonclinical parameters were analyzed.

Materials and Methods:  Clinical and non- clinical data were collected from 205 randomly selected COVID-19 patients, identified through RT-PCR from different areas of Bangladesh. The data were analyzed using statistical and analytical tools to illustrate the impact of the pandemic situation on the sufferers. 

Results: Molecular identification of the patients through RT-PCR has been observed as the most efficient option for detecting SARS-CoV-2 patients. Patients with the smoking habit have been reported to be more prone to the COVID-19 infection; surprisingly the non-smoker female was the worse suffers. The patients aged 60-69 years were the worst sufferers with every adverse health conditions mentioned. Professionally, 28% self-employed male and 8.19% female were infected. The most infected individuals were house wife (32.029%), as next to the health care workers (22.1%). With the increased age group, a decreased number of smokers were found.               Nebulization of 5% home and 12% hospital treated patients were provided, with Oxygen for 26% of hospitalized patients. After recovery, combined physical and psychological complications were observed in 19% of male and 11% female. The socioeconomic, environmental and geographical annotations exposed a clear relationship with the rate of infection as revealed from the nonclinical data analysis.

Conclusion: RT-PCR proved its specialty in COVID-19 detection. In addition, impacts of different clinical and nonclinical factors on the physical conditions of the nCoV patients were found significant in the research.

Keywords:
SARS-CoV-2, RT-PCR mediated identification, Bangladesh, multi-factorial analysis, pre and post infection health conditions

Article Details

How to Cite
Akter, K. M., Tushi, T., Jahan Mily, S., Mohona, R. A., Anis, S., Chakraborty, A. K., Tabassum, E., Islam, T. U., Akhi, O. J., Nishe, I. S., Laxy, B. N., Zerin, S. S., Roble, A. J., Hossain, M. I., Ahmed, S., & Azad, S. A. (2020). RT-PCR Mediated Identification of SARS-CoV-2 Patients from Particular Regions of Bangladesh and the Multi-factorial Analysis Considering Their Pre and Post Infection Health Conditions. Biotechnology Journal International, 24(6), 43-56. https://doi.org/10.9734/bji/2020/v24i630121
Section
Original Research Article

References

Kim JM, Chung YS, Jo HJ, Lee NJ, Kim MS, Woo SH, Park S, Kim JW, Kim HM, Han MG. Identification of Coronavirus Isolated from a Patient in Korea with COVID-19. Osong Public Health Res Perspect. 2020;11(1):3.

Available:https://doi.org/10.24171/j.phrp.2020.11.1.02

Zhang J, Litvinova M, Wang W, Wang Y, Deng X, Chen X, Li M, Zheng W, Yi L, Chen X, Wu Q. Evolving epidemiology and transmission dynamics of coronavirus disease 2019 outside Hubei province, China: A descriptive and modelling study. Lancet Infect Dis. 2020;20:793-802.

Available:https://doi.org/10.1016/S1473-3099(20)30230-9

Alcoba-Florez J, González-Montelongo R, Íñigo-Campos A, de Artola DG, Gil-Campesino H, Team TM, Ciuffreda L, Valenzuela-Fernández A, Flores C. Fast SARS-CoV-2 detection by RT-qPCR in preheated nasopharyngeal swab samples. Int J Infect Dis. 2020;97:66-68.

Available:https://doi.org/10.1016/j.ijid.2020.05.099

Riccò M, Ferraro P, Gualerzi G, Ranzieri S, Henry BM, Said YB, Pyatigorskaya NV, Nevolina E, Wu J, Bragazzi NL, Signorelli C. Point-of-Care Diagnostic Tests for Detecting SARS-CoV-2 Antibodies: A Systematic Review and Meta-Analysis of Real-World Data. J Clin Med. 2020;9(5): 1515.

Available:https://doi.org/10.3390/jcm9051515

Ai T, Yang Z, Hou H, Zhan C, Chen C, Lv W, Tao Q, Sun Z, Xia L. Correlation of chest CT and RT-PCR testing in coronavirus disease 2019 (COVID-19) in China: A report of 1014 cases. Radiology 2020;296(2):E32-E40.

Available:https://doi.org/10.1148/radiol.2020200642

Martin A, Markhvida M, Hallegatte S, Walsh B. Socio-economic impacts of COVID-19 on household consumption and poverty. Economics of Disasters and Climate Change. 2020;23:1-27.

Available:https://doi.org/10.1007/s41885-020-00070-3

Buheji M, da Costa Cunha K, Beka G, Mavric B, de Souza YL, da Costa Silva SS, Hanafi M, Yein TC. The extent of covid-19 pandemic socio-economic impact on global poverty. A global integrative multidisciplinary review. Am J Econ. 2020; 10(4):213-24.

DOI: 10.5923/j.economics.20201004.02

Davies NG, Klepac P, Liu Y, Prem K, Jit M, Eggo RM, CMMID COVID-19 working group. Age-dependent effects in the transmission and control of COVID-19 epidemics. Nat Med. 2020;26:1205– 1211.

Available:https://doi.org/10.1038/s41591-020-0962-9

Conti P, Younes A. Coronavirus COV-19/SARS-CoV-2 affects women less than men: Clinical response to viral infection. J Biol Regul Homeost Agents. 2020;34(2): 71.

DOI: 10.23812/Editorial-Conti-3

Berlin I, Thomas D, Le Faou AL, Cornuz J. COVID-19 and smoking. Nicotine & Tobacco Research 2020;22(9):1650-1652.

Available:https://doi.org/10.1093/ntr/ntaa059

Grundy EJ, Suddek T, Filippidis FT, Majeed A, Coronini-Cronberg S. Smoking, SARS-CoV-2 and COVID-19: A review of reviews considering implications for public health policy and practice. Tob Induc Dis. 2020;18.

Available:https://doi.org/10.18332/tid/124788

Akbari A, Emami A, Javanmardi F, Pirbonyeh N, Fadakar N. Early epidemiological analysis of CoVID-19: first report from South of Iran.

Available:https://doi.org/10.21203/rs.3.rs-19915/v1

Lee J, Kim M. Estimating the number of Korean workers at high risk of COVID-19 infection. Epidemiology and Health. 2020; 42:e2020051.

Available:https://doi.org/10.4178/epih.e2020051

Balachandar V, Mahalaxmi I, Devi SM, Kaavya J, Kumar NS, Laldinmawii G, Arul N, Reddy SJ, Sivaprakash P, Kanchana S, Vivekanandhan G. Follow-up studies in COVID-19 recovered patients-is it mandatory? Science of the Total Environment. 2020;139021.

Available:https://doi.org/10.1016/j.scitotenv.2020.139021

Dom NC, Latif ZA, Ahmad AH, Ismail R, Pradhan B. Manifestation of GIS Tools for Spatial Pattern Distribution Analysis of Dengue Fever Epidemic in the City of Subang Jaya, Malaysia. Environment Asia. 2012;5(2).

Franch-Pardo I, Napoletano BM, Rosete-Verges F, Billa L. Spatial analysis and GIS in the study of COVID-19. A review. Science of the Total Environment. 2020; 140033.

Available:https://doi.org/10.1016/j.scitotenv.2020.140033

Mollalo A, Vahedi B, Rivera KM. GIS-based spatial modeling of COVID-19 incidence rate in the continental United States. Science of The Total Environment. 2020;138884.

Available:https://doi.org/10.1016/j.scitotenv.2020.138884

Grillo M, Margolis FL. Use of reverse transcriptase polymerase chain reaction to monitor expression of intronless genes. Biotechniques. 1990;9(3):262-4.

Yip CC, Ho CC, Chan JF, To KK, Chan HS, Wong SC, Leung KH, Fung AY, Ng AC, Zou Z, Tam AR. Development of a novel, genome subtraction-derived, SARS-CoV-2-specific COVID-19-nsp2 real-time RT-PCR assay and its evaluation using clinical specimens. Int J Mol Sci. 2020; 21(7):2574.

Available:https://doi.org/10.3390/ijms21072574

Corman VM, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu DK, Bleicker T, Brünink S, Schneider J, Schmidt ML, Mulders DG. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Eurosurveillance. 2020;25(3): 2000045.

Available:https://doi.org/10.2807/1560-7917.ES.2020.25.3.2000045

Emery SL, Erdman DD, Bowen MD, Newton BR, Winchell JM, Meyer RF, Tong S, Cook BT, Holloway BP, McCaustland KA, Rota PA. Real-time reverse transcription–polymerase chain reaction assay for SARS-associated coronavirus. Emerg Infect Dis. 2004;10(2):311.

Available:https://dx.doi.org/10.3201/eid1002.030759.

Kim H, Hong H, Yoon SH. Diagnostic performance of CT and reverse transcriptase-polymerase chain reaction for coronavirus disease 2019: A meta-analysis. Radiology. 2020;201343.

Available:https://doi.org/10.1148/radiol.2020201343

D'Cruz RJ, Currier AW, Sampson VB. Laboratory testing methods for novel severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). Frontiers in cell and developmental biology. 2020;8.

Available:https://doi.org/10.3389/fcell.2020.00468

Atkins JL, Masoli JA, Delgado J, Pilling LC, Kuo CL, Kuchel GA, Melzer D. Preexisting comorbidities predicting COVID-19 and mortality in the UK Biobank community cohort. The Journals of Gerontology: Series A; 2020.

Available:https://doi.org/10.1093/gerona/glaa183

Du Y, Tu L, Zhu P, Mu M, Wang R, Yang P, Wang X, Hu C, Ping R, Hu P, Li T. Clinical features of 85 fatal cases of COVID-19 from Wuhan. A retrospective observational study. Am J Respir Crit Care Med. 2020;201(11):1372-9.

Available:https://doi.org/10.1164/rccm.202003-0543OC

Baradaran A, Ebrahimzadeh MH, Baradaran A, Kachooei AR. Prevalence of comorbidities in COVID-19 patients: A systematic review and meta-analysis. Archives of Bone and Joint Surgery. 2020; 8(Suppl 1):247.

DOI: 10.22038/abjs.2020.47754.2346

Pei G, Zhang Z, Peng J, Liu L, Zhang C, Yu C, Ma Z, Huang Y, Liu W, Yao Y, Zeng R. Renal involvement and early prognosis in patients with COVID-19 pneumonia. J Am Soc Nephrol. 2020;31(6):1157-65.

Available:https://doi.org/10.1681/ASN.2020030276

Yang X, Yu Y, Xu J, Shu H, Liu H, Wu Y, Zhang L, Yu Z, Fang M, Yu T, Wang Y. Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: A single-centered, retrospective, observational study. Lancet Respir Med; 2020.

Available:https://doi.org/10.1016/S2213-2600(20)30079-5

Wang L, Li X, Chen H, Yan S, Li Y, Li D, Gong Z. SARS-CoV-2 infection does not significantly cause acute renal injury: An analysis of 116 hospitalized patients with COVID-19 in a single hospital, Wuhan, China. Wuhan, China (2/17/2020); 2020.

Available:https://doi.org/10.1101/2020.02.19.20025288

Patanavanich R, Glantz SA. Smoking is associated with COVID-19 progression: a meta-analysis. Nicotine & Tobacco Research; 2020.

DOI: 10.1093/ntr/ntaa082

Reddy RK, Charles WN, Sklavounos A, Dutt A, Seed PT, Khajuria A. The effect of smoking on COVID-19 severity: A systematic review and meta-analysis. J Med Virol; 2020.

Available:https://doi.org/10.1002/jmv.26389

Lippi G, Henry BM. Active smoking is not associated with severity of coronavirus disease 2019 (COVID-19). Eur J Intern Med; 2020.

DOI: 10.1016/j.ejim.2020.03.014

Wan S, Xiang Y, Fang W, Zheng Y, Li B, Hu Y, Lang C, Huang D, Sun Q, Xiong Y, Huang X. Clinical features and treatment of COVID-19 patients in northeast Chongqing. J Med Virol; 2020.

Available:https://doi.org/10.1002/jmv.25783

Gautret P, Lagier JC, Parola P, Meddeb L, Mailhe M, Doudier B, Courjon J, Giordanengo V, Vieira VE, Dupont HT, Honoré S. Hydroxychloroquine and azithromycin as a treatment of COVID-19: results of an open-label non-randomized clinical trial. Int J Antimicrob Agents. 2020; 105949.

Available:https://doi.org/10.1016/j.ijantimicag.2020.105949

James M, Marguerite L, Tomasz Z, James B. Pharmacologic treatments for coronavirus disease 2019 (COVID-19). JAMA. 2020;323(18):1824-36.

DOI: 10.1001/jama.2020.6019

Benge CD, Barwise JA. Aerosolization of COVID-19 and Contamination Risks During Respiratory Treatments. Federal Practitioner. 2020;37(4): 160.

Horie S, McNicholas B, Rezoagli E, Pham T, Curley G, McAuley D, O’Kane C, Nichol A, Dos Santos C, Rocco PR, Bellani G. Emerging pharmacological therapies for ARDS: COVID-19 and beyond. Intensive Care Med. 2020;1-9.

Available:https://doi.org/10.1007/s00134-020-06141-z

Shen C, Yue X, Wang J, Shi C, Li W. Nocturnal oxygen therapy as an option for early COVID-19. Int J Infect Dis. 2020;98: 176-9. Available:https://doi.org/10.1016/j.ijid.2020.06.080

De Maio A, Hightower LE. COVID-19, acute respiratory distress syndrome (ARDS), and hyperbaric oxygen therapy (HBOT): what is the link?. Cell Stress & Chaperones. 2020;1.

Available:https://doi.org/10.1007/s12192-020-01121-0

Carfora V, Spiniello G, Ricciolino R, Di Mauro M, Migliaccio MG, Mottola FF, Verde N, Coppola N. Anticoagulant treatment in COVID-19: A narrative review. J Thromb Thrombolysis. 2020;1-7.

Available:https://doi.org/10.1007/s11239-020-02242-0

Ribes A, Vardon-Bounes F, Mémier V, Poette M, Au-Duong J, Garcia C, Minville V, Sié P, Bura-Rivière A, Voisin S, Payrastre B. Thromboembolic events and Covid-19. Advances in Biological Regulation. 2020;77:100735.

Available:https://doi.org/10.1016/j.jbior.2020.100735

Tritschler T, Mathieu ME, Skeith L, Rodger M, Middeldorp S, Brighton T, Sandset PM, Kahn SR, Angus DC, Blondon M, Bonten MJ. Anticoagulant interventions in hospitalized patients with COVID-19: A scoping review of randomized controlled trials and call for international collaboration. J Thromb Haemost; 2020.

Available:https://doi.org/10.1111/jth.15094

Jayawardena R, Sooriyaarachchi P, Chourdakis M, Jeewandara C, Ranasinghe P. Enhancing immunity in viral infections, with special emphasis on COVID-19: A review. Diabetes & Metabolic Syndrome: Clinical Research & Reviews; 2020.

Available:https://doi.org/10.1016/j.dsx.2020.04.015

Lehtoranta L, Pitkäranta A, Korpela R. Probiotics in respiratory virus infections. Eur J Clin Microbiol Infect Dis. 2014;33(8): 1289-302.

DOI: 10.1007/s10096-014-2086-y

Abdullah-Al-Mamun M, Hasan MJ, Al Azad S, Uddin MG, Shahriyar S, Mondal KJ. Evaluation of potential probiotic characteristics of isolated lactic acid bacteria from goat milk. Biotechnology Journal International. 2016;1-7.

Available:https://doi.org/10.9734/BBJ/2016/26397

Al Azad S, Moazzem Hossain K, Rahman SM, Al Mazid MF, Barai P, Gazi MS. In ovo inoculation of duck embryos with different strains of Bacillus cereus to analyse their synergistic post-hatch anti-allergic potentialities. Vet Med Sci; 2020.

Available:https://doi.org/10.1002/vms3.279

Rocha-Ramírez LM, Pérez-Solano RA, Castañón-Alonso SL, Moreno Guerrero SS, Ramírez Pacheco A, García Garibay M, Eslava C. Probiotic Lactobacillus strains stimulate the inflammatory response and activate human macrophages. Journal of Immunology Research; 2017.

Available:https://doi.org/10.1155/2017/4607491

Al Azad S, Shahriyar S, Mondal KJ. Opsonin and its mechanism of action in secondary immune. Journal of Molecular Studies and Medicine Research. 2016; 1(02):48-56.

Available:https://doi.org/10.18801/jmsmr.010216.06

Bong CL, Brasher C, Chikumba E, McDougall R, Mellin-Olsen J, Enright A. The COVID-19 Pandemic: Effects on Low-and Middle-Income Countries. Anesth Analg; 2020.

DOI: 10.1213/ANE.0000000000004846

Zar HJ, Dawa J, Fischer GB, Castro-Rodriguez JA. Challenges of COVID-19 in children in low-and middle-income countries. Paediatr Respir Rev; 2020.

Available:https://doi.org/10.1016/j.prrv.2020.06.016

Lee SS, Wong NS. The clustering and transmission dynamics of pandemic influenza A (H1N1) 2009 cases in Hong Kong. Journal of Infection. 2011;63(4): 274-80.

Available:https://doi.org/10.1016/j.jinf.2011.03.011

Mutambudzi M, Niedzwiedz CL, Macdonald EB, Leyland AH, Mair FS, Anderson JJ, Celis-Morales CA, Cleland J, Forbes J, Gill JM, Hastie C. Occupation and risk of COVID-19: prospective cohort study of 120, 621 UK Biobank participants. MedRxiv; 2020.

Xu Y, Xu Z, Liu X, Cai L, Zheng H, Huang Y, Zhou L, Huang L, Lin Y, Deng L, Li J. Clinical findings in critical ill patients infected with SARS-Cov-2 in Guangdong Province, China: A multi-center, retrospective, observational study. MedRxiv; 2020.

Available:https://doi.org/10.1101/2020.03.03.20030668

Raphael B. Overview of the development of psychological support in emergencies. Advances in Disaster Mental Health and Psychological Support. 2006;6.

DOI: 10.1056/NEJMp2008017

Zhou Z, Chen P, Peng H. Are healthy smokers really healthy? Tob Induc Dis. 2016;14(1):35.

DOI: 10.1186/s12971-016-0101-z

Available:https://www.medpagetoday.com/infectiousdisease/covid19/86556

Yang L, Yu Z, Xu Y, Liu W, Liu L, Mao H. Mental status of patients with chronic insomnia in China during COVID-19 epidemic. Int J Soc Psychiatry. 2020; 66(8):821-6.

Available:https://doi.org/10.1177/0020764020937716

Iqbal Y, Jahan R, Yesmin S, Selim A, Siddique SN. COVID-19-related issues on tele-counseling helpline in Bangladesh. Asia-Pacific Psychiatry. 2020;e12407.

Available:https://doi.org/10.1111/appy.12407

Romero-Blanco C, Rodríguez-Almagro J, Onieva-Zafra MD, Parra-Fernández ML, Prado-Laguna MD, Hernández-Martínez A. Sleep Pattern Changes in Nursing Students during the COVID-19 Lockdown. Int J Environ Res Public Health. 2020; 17(14):5222.

Available:https://doi.org/10.3390/ijerph17145222

Varshney M, Parel JT, Raizada N, Sarin SK. Initial psychological impact of COVID-19 and its correlates in Indian Community: An online (FEEL-COVID) survey. Plos One. 2020;15(5):e0233874.

Available:https://doi.org/10.1371/journal.pone.0233874

Mamun MA, Griffiths MD. First COVID-19 suicide case in Bangladesh due to fear of COVID-19 and xenophobia: Possible suicide prevention strategies. Asian J Psychiatr. 2020;51:102073.

DOI: 10.1016/j.ajp.2020.102073

Lee SS, Wong NS. The clustering and transmission dynamics of pandemic influenza A (H1N1) 2009 cases in Hong Kong. Journal of Infection. 2011;63(4): 274-80.

Available:https://doi.org/10.1016/j.jinf.2011.03.011

Stier A, Berman M, Bettencourt L. COVID-19 attack rate increases with city size. Mansueto Institute for Urban Innovation Research Paper Forthcoming; 2020.

Available:https://doi.org/10.1101/2020.03.22.20041004

Xie J, Zhu Y. Association between ambient temperature and COVID-19 infection in 122 cities from China. Science of the Total Environment. 2020;724:138201.

Available:https://doi.org/10.1016/j.scitotenv.2020.138704

Fattorini D, Regoli F. Role of the chronic air pollution levels in the Covid-19 outbreak risk in Italy. Environmental Pollution. 2020; 114732. Available:https://doi.org/10.1016/j.envpol.2020.114732

Contini D, Costabile F. Does Air Pollution Influence COVID-19 Outbreaks?
Available:https://doi.org/10.3390/atmos11040377

Available:https://ruralopioids.soc.iastate.edu/wp-content/uploads/sites/210/2020/04/STR1059_covid19.pdf