key: cord-319351-hcxbkvgd authors: Benrahma, H.; Diawara, I.; Smyej, I.; Rahoui, J.; Meskaouni, N.; Benmessaoud, R.; Arouro, K.; Jaras, K.; Adam, Z.; Nahir, S.; Aouzal, Z.; Elguazzar, H.; Jeddane, L.; Ousti, F.; Elbakkouri, J.; Nejjari, C. title: Epidemiological description and analysis of RdRp, E and N genes dynamic by RT-PCR of SARS-CoV-2 in Moroccan population: Experience of the National Reference Laboratory (LNR)-UM6SS date: 2020-06-20 journal: nan DOI: 10.1101/2020.06.18.20135137 sha: doc_id: 319351 cord_uid: hcxbkvgd The coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a new infectious disease that first emerged in Hubei province, China, in December 2019. On 2 March 2020, the Moroccan Ministry of Health confirmed the first COVID-19 case in Morocco. The new virus SARS-CoV-2 was identified in the sample of a Moroccan expatriate residing in Italy. Without a therapeutic vaccine or specific antiviral drugs, early detection and isolation become essential against novel Coronavirus. This study aims to analyze the epidemiological profile of the SARS-CoV-2 in Moroccan cases and to investigate the dynamic of RdRp gene, N gene, and E gene in patients from diagnosis until the recovery. Among 859 Covid-19 RT-PCR tests realized for 285 patients, 133 cases had positive results Covid-19. 9 % of these cases present the 3 genes RdRp, N, and E, 47% only the RdRp gene, 2% with RdRp and N gene, 26% cases are positives with N gene, and 16 % with N and E gene. The analysis of the Covid-19 genes (RdRp, N, and E) dynamic reveal that more than 6% stay positive with detection of the N and E gene, and 14% with the N gene after 12 days of treatment. The median period from positive to the first negative Covid-19 RT-PCR tests was 6.8{+/-}2.24 days for 44% cases, 14.31 {+/-} 2.4 days for 30%, and 22.67 {+/-} 1.21 days for 4%. This a first description of the Moroccan COVID-19 cases and the analysis of the dynamic of the 3 genes RdRp, N, and E. The analysis of our population can help to involved in the care of patients. According to the World Health Organization (WHO), the WHO China Country Office was 61 informed of cases of pneumonia of unknown etiology in Wuhan City, Hubei Province, on 62 December 31, 2019 [1] . 63 The investigations identified a new virus that was closely related to severe acute respiratory In acute respiratory infection, RT-PCR is routinely used to detect causative viruses from 84 respiratory secretions. For ensuring the diagnostic of Covid-19, the LNR has been equipped 85 with different platforms to performed real-time RT-PCR testing for three targets in the virus: 86 the envelope (E), the RNA dependent RNA polymerase (RdRp) and the nucleocapsid (N). The coronavirus SARS-CoV-2 genome consists of a leader sequence, ORF1ab encoding 88 proteins for RNA replication, and genes for non-structural proteins (nps) and structural 89 proteins [8] . Like other betacoronaviruses, the SARS-CoV-2 genome encodes four major 90 All rights reserved. No reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted June 20, 2020. . https://doi.org/10.1101/2020.06.18.20135137 doi: medRxiv preprint structural proteins. The structural proteins are involved in various viral processes, including 91 virus particle formation. The structural proteins include spike (S), envelope (E), membrane 92 protein (M), and nucleoprotein (N), which are common to all coronaviruses [9, 10]. To date, no studies exploring the variation of RdRp, N and E genes expression of SARS-CoV-94 2 in the patient's specimen. In this study, in first time, we analyses the epidemiological profile The LNR provide a RT-PCR to clinically suspected COVID-19 patients when they were (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted June 20, 2020. . https://doi.org/10.1101/2020.06.18.20135137 doi: medRxiv preprint The result interpretation was performed according to the manufacturer's protocol (table 1) 136 All rights reserved. No reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted June 20, 2020. The analysis of these families showed that 71% included 2 cases, 21% included 3 cases, 4% 155 included 4 cases, and 4% included 5 cases, 166 All rights reserved. No reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted June 20, 2020. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted June 20, 2020. The current SARS-CoV-2 outbreak is the third epidemic attributed to coronavirus in the 21st 183 century, and incredibly the number of confirmed SARS-CoV-2 infection has surpassed SARS 184 and MERS in world wild [1, 11] . The SARS-Cov-2 share similar sequencing characteristics with SARS-CoV and MERS-CoV, 208 but the analysis of different case series showed that the shedding pattern of the viral nucleic 209 All rights reserved. No reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted June 20, 2020. . https://doi.org/10.1101/2020.06.18.20135137 doi: medRxiv preprint acid of patients infected with SARS-CoV-2 is different from SARS-CoV. In the early stage, 210 the SARS-CoV had a modest viral load peaked approximately 10 days after symptoms onset. For the SARS-CoV-2, the median duration of the virus in the respiratory sample was 18 days, 212 and from symptom onset, the peak viral shedding in respiratory specimens of positive cases 213 occurred after about 10 to days for the SARS-CoV [18, 19] . In our study, we found that the 214 duration of virus shedding in lower respiratory tract samples was longer than 14 days for 30% 215 of cases, and peak viral shedding occurred after about two weeks from symptom onset. If we analyze the Coronavirus life cycle, we found that the initial attachment of the virion to 240 the host cell is initiated by interactions between the S protein and its receptor. Following 241 All rights reserved. No reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted June 20, 2020. . https://doi.org/10.1101/2020.06.18.20135137 doi: medRxiv preprint receptor binding, the virus must next gain access to the host cell cytosol. This is generally (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted June 20, 2020. World Health Organization (WHO) A pneumonia outbreak associated with a new 280 coronavirus of probable 388 bat origin The species Severe acute respiratory 282 syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 Naming the WHO,2020 " naming-the-coronavirus-disease-(covid-2019)-and-the-virus-that-causes-287 it siRNA targeting the leader sequence of SARS-CoV 293 inhibits virus replication Comparative full-length genome sequence 297 analysis of 14 SARS coronavirus isolates and common mutations associated with 298 putative origins of infection The epidemiology and clinical information about 300 COVID-19 Epidemiological and clinical characteristics of 99 302 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Dynamic profile of RT-PCR findings from COVID-19 patients in Wuhan, China: A descriptive study Prevalence of comorbidities in the Middle East respiratory 308 syndrome coronavirus (MERS-CoV): a systematic review and meta-analysis Clinical features of patients infected with 2019 novel 311 coronavirus in Wuhan No reuse allowed without permission. 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The copyright holder for this preprint this version posted Asians Do Not Exhibit Elevated Expression or Unique 313 Genetic Polymorphisms for ACE2, the Cell-Entry Receptor of SARS-CoV-2 Presumed asymptomatic carrier transmission of COVID-316 19 Viral loads in clinical specimens and SARS 318 manifestations Antagonism of the interferon-induced OASRNase L 320 pathway by murine coronavirus ns2 protein is required for virus replication and liver 321 pathology COVID-19 Outbreak: An Overview Detection of 2019 novel coronavirus (2019-325 nCoV) by real-time RT-PCR SARS-CoV-2 Viral Load in Upper Respiratory 327 Specimens of Infected Patients Coronaviruses: An Overview of Their Replication and 329 The Coronavirus Nucleocapsid Is a 332 Multifunctional Protein Severe Acute Respiratory Syndrome Coronavirus An overview of viral structure and host response All rights reserved. No reuse allowed without permission.(which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint this version posted June 20, 2020. . https://doi.org/10.1101/2020.06.18.20135137 doi: medRxiv preprint