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ACADEMIA Letters National Molecular Surveillance of Recoveries/Mortalities Rate for COVID-19 in Pakistan-During First and Second Waves of Disease Adil Kalam Ayesha Sadiqa Javeria Samad Muhammad Usman Abstract The novel coronavirus disease (COVID-19) outbreak has caused significant global issues and challenged healthcare systems across the globe and in Pakistan as well. This infectious disease is found to be a pandemic and has massively impacted countries across the globe. The disease is still rapidly spreading and has caused many deaths in Pakistan, according to the world health organization; the Pakistan has ranked among the top 10 countries in the world reporting the highest number of new cases of COVID-19 per day during the first wave of the outbreak. The second wave of COVID-19 is relatively high on the first wave of disease in the current scenario of the pandemic in Pakistan. In Pakistan, the molecular technique real-time PCR is being applied for the qualitative confirmation of COVID-19 in the human nasopharyngeal swab samples according to WHO guidelines. Followed the extraction of COVID-19 nucleic acid, a probe-based real-time PCR assay is used for the detection of virus, mostly in all regions of country. The total of 416,499 confirmed cases are reported with the 2.0% death rate from Feb. to Dec.2020 in the first and second waves of disease. Academia Letters, July 2021 ©2021 by the authors — Open Access — Distributed under CC BY 4.0 Corresponding Author: Adil Kalam, adil.kalam@aku.edu Citation: Kalam, A., Sadiqa, A., Samad, J., Usman, M. (2021). National Molecular Surveillance of Recoveries/Mortalities Rate for COVID-19 in Pakistan-During First and Second Waves of Disease. Academia Letters, Article 1875. https://doi.org/10.20935/AL1875. 1 In Pakistan, cases of COVID-19 are rapidly increased on daily basis, Sindh and Punjab are the most affected provinces of Pakistan; however, Baluchistan, Khyber Pakhtunkhwa and other regions of Pakistan are less affected comparatively during both waves of Coronavirus disease. Keywords: Real-time PCR; COVID-19; Coronavirus; Pakistan; Primer and Probe Introduction The coronavirus disease outbreak-2019 has badly affected national and global populations. In the current scenario, Coronavirus (COVID-19) is a global pandemic that has caught the attention of many scholars. The number of daily COVID-19 cases rapidly increased during first and second waves. [1,2] As of Dec. 2020 so far 76,023,488 confirmed cases of COVID19 have been reported including 1,694,128 deaths globally (https://covid19.who.int/).[3] The first cases of COVID-19 in humans were reported by an official announcement from the Government of China in Wuhan City, in Dec. 2019 that caused 1,023 deaths in this part of China as of Feb. 2020. The healthcare workers are found to be at higher risks, as revealed by the result of the surveillance.[4] In Pakistan, the first positive case of the coronavirus (COVID-19) was identified in Karachi in a 22-year-old male with a “history of travel from Iran where he got an infection of COVID19 in Feb 2020.[5] Pakistan has the worst situation for the speedy rate of COVID-19 cases in the first wave of disease. As of March 15, 2020, due to the arrival of pilgrimages from Iran via the Taftan border, the number of confirmed cases had begun to increase rapidly. In addition, in less than a day the announcement and implementation of lockdown in Pakistan was made, generating chaos as migrants rushed to return to their hometowns, aggravating crowding and preventing impossible social distance.[6] In addition, cases jumped from 53 to 10788 from March 15-25, 2020 (DAWN, 2020). Since then, cases in all provinces of the country have been rising exponentially day by day.[6] The World Health Organization has confirmed COVID-19 as a “pandemic” in March 2020.[6] On October 28, 2020, the government of Pakistan has officially announced, the second spell of COVID-19 in the country, with a daily surge in cases reaching 750 compared to 400 to 500 a few weeks earlier.[7] Sudden increases in active cases from 6,000 to 11,000 and hospital admissions were registered nationally with critical cases of 93 on ventilators across Pakistan.[7] Academia Letters, July 2021 ©2021 by the authors — Open Access — Distributed under CC BY 4.0 Corresponding Author: Adil Kalam, adil.kalam@aku.edu Citation: Kalam, A., Sadiqa, A., Samad, J., Usman, M. (2021). National Molecular Surveillance of Recoveries/Mortalities Rate for COVID-19 in Pakistan-During First and Second Waves of Disease. Academia Letters, Article 1875. https://doi.org/10.20935/AL1875. 2 The condition of the second wave of COVID-19 pandemic is getting worse due to the ignorance and irresponsibility of the public and community as the results are increasing the positive ratio of the virus after a gap of 70 days by more than 3% from the first wave of disease.[7] The spread of the disease can only be controlled if the public and the government work together and follow the guidelines strictly. Patients and Methods Currently, the real-time PCR is being used for a qualitative diagnostic of COVID-19 globally, which is an easy and rapid method. The ministry of National Health Service Pakistan also recommends the real-time PCR method. This diagnostic test is being applied to samples of patients, who are hospitalized and non-hospitalized in various healthcare settings of Pakistan. [8] shows how the real-time PCR testing for COVID-19 works. Polymerase chain reaction (PCR) is a common laboratory technique, used in the Molecular biology area for making multiple copies of a particular region of DNA/cDNA, through which pathogen can be detected precisely even if it is in small amounts. Firstly, the sample is collected from the back of the nose or mouth of patients. After sample collection, Viral RNA is extracted and converted to complementary DND (cDNA) for further testing. A short single-stranded specific nucleic acid sequence named as primers are bound with the specific target region of viral cDNA, this leads to the amplification process. Fluorescent markers (probe) successfully reveal the absence or presence of the COVID-19 virus. This process is repeated multiple times, with each cycle doubling the target region. When amplification occurs, a fluorescent signal is created, and once the signal reaches a threshold, the test is declared a positive result. When there is no viral sequence, amplification will not occur which will lead to a negative result.[8] The finding of this qualitative testing is revealed in the results section. (The datasets of confirmed cases are available online at http://www.covid.gov.pk/).[9] Results & Discussion As of Dec.-05-2020 total numbers of reported cases in Pakistan are 416,499, out of which 8,361 individuals have died so far, while total recoveries are 355,012.[9] describes the confirmed cases in provinces of Pakistan as of Dec.-05-2020. Academia Letters, July 2021 ©2021 by the authors — Open Access — Distributed under CC BY 4.0 Corresponding Author: Adil Kalam, adil.kalam@aku.edu Citation: Kalam, A., Sadiqa, A., Samad, J., Usman, M. (2021). National Molecular Surveillance of Recoveries/Mortalities Rate for COVID-19 in Pakistan-During First and Second Waves of Disease. Academia Letters, Article 1875. https://doi.org/10.20935/AL1875. 3 The current data shows that 43.8% (182,473) of confirmed cases are registered in the Sindh region which is the highest number of cases in all over the country, followed by the province of Punjab with 29.5% (122,955).[9] Table 1. Recoveries/Mortalities data in % of all regions of Pakistan as of Dec.-05- 2020. The current report analyzed the cases in Pakistan; it had been found that the high numbers of recovery cases were reported from Sindh and KPK in the first wave of disease. The highest recovery and mortality cases of the second wave are reported from Azad Kashmir respectively. A high mortality rate was found in Balochistan during the first wave of the disease. Comparatively the province of Punjab has a well-improved rate in both waves as well. Out of total cases in the second wave the recovery and death rate are increased in Gilgit Baltistan and Islamabad (ICT) separately. Conclusion The current analysis revealed the mortality and recovery surveillance rate of COVID-19 cases in a high burden of disease through real-time PCR testing to diagnose these cases in Pakistan. Real-time PCR molecular technique has substantially increased sensitivity and provided a higher resolution of pathogen detection. The COVID-19 is a global pandemic and has affected a high number of populations across the globe. The COVID-19 cases are increasing at a rapid pace. The results of the reported study that Pakistan has an extremely high number of patients diagnosed during the second wave of COVID-19 in 2020 and Karachi is the most affected city so far. The infection rate of COVID-19 was a little bit decreased in July, Aug. and Sept. 2020, but now the situation is worsening again from Oct. 2020 after the government decision of easing lockdown. Academia Letters, July 2021 ©2021 by the authors — Open Access — Distributed under CC BY 4.0 Corresponding Author: Adil Kalam, adil.kalam@aku.edu Citation: Kalam, A., Sadiqa, A., Samad, J., Usman, M. (2021). National Molecular Surveillance of Recoveries/Mortalities Rate for COVID-19 in Pakistan-During First and Second Waves of Disease. Academia Letters, Article 1875. https://doi.org/10.20935/AL1875. 4 References 1. WHO, (2020). Corona Virus. Overview. Accessed from: https://www.who.int/healthtopics/coronavirus#tab=tab_1 2. Casadevall A, Pirofski LA. The convalescent sera option for containing COVID-19. The Journal of clinical investigation. 2020 Apr 1;130(4):1545-8. 3. Novel CP. The epidemiological characteristics of an outbreak of 2019 novel coronavirus diseases (COVID-19) in China. Zhonghua liu xing bing xue za zhi= Zhonghua liuxingbingxue zazhi. 2020 Feb 17;41(2):145. 4. Geo news. https://www.geo.tv/latest/274482-pakistan-confirms-first, Accessed 4th Apr 2020 5. Shafi M, Liu J, Ren W. Impact of COVID-19 pandemic on micro, small, and mediumsized Enterprises operating in Pakistan. Research in Globalization. 2020 Dec 1;2:100018. https://www.sciencedirect.com/science/article/pii/S2590051X20300071 6. Junaidi I. Second Covid wave under way in Pakistan. Dawn. 28 October 2020. https:// www.dawn.com/news/1587316 7. Hadaya J, Schumm M, Livingston EH. Testing individuals for coronavirus disease 2019 (COVID-19). Jama. 2020 May 19;323(19):1981-. https://jamanetwork.com/journals/ jama/fullarticle/2764238 8. COVID-19 cases status in PakistanAvailable: Government of Pakistan, http://covid.gov. pk/stats/pakistan (2020), Accessed Dec.-05- 2020. Academia Letters, July 2021 ©2021 by the authors — Open Access — Distributed under CC BY 4.0 Corresponding Author: Adil Kalam, adil.kalam@aku.edu Citation: Kalam, A., Sadiqa, A., Samad, J., Usman, M. (2021). National Molecular Surveillance of Recoveries/Mortalities Rate for COVID-19 in Pakistan-During First and Second Waves of Disease. Academia Letters, Article 1875. https://doi.org/10.20935/AL1875. 5