The COVID-19 pandemic is due to infection caused by the novel SARS-CoV-2 virus that impacts the lower respiratory tract. The spectrum of symptoms ranges from asymptomatic infections to mild respiratory symptoms to the lethal form of COVID-19 which is associated with severe pneumonia, acute respiratory distress, and fatality. To address this global crisis, up-to-date information on viral genomics and transcriptomics is crucial for understanding the origins and global dispersion of the virus, providing insights into viral pathogenicity, transmission, and epidemiology, and enabling strategies for therapeutic interventions, drug discovery, and vaccine development. Therefore, this review provides a comprehensive overview of COVID-19 epidemiology, genomic etiology, findings from recent transcriptomic map analysis, viral-human protein interactions, molecular diagnostics, and the current status of vaccine and novel therapeutic intervention development. Moreover, we provide an extensive list of resources that will help the scientific community access numerous types of databases related to SARS-CoV-2 OMICs and approaches to therapeutics related to COVID-19 treatment.

The COVID-19 pandemic is due to infection caused by the novel SARS-CoV-2 that impacts the lower respiratory tract. The spectrum of symptoms ranges from asymptomatic infections to mild respiratory symptoms to the lethal form of COVID-19 which is associated with severe pneumonia, acute respiratory distress and fatality. At present, the global case fatality rate of COVID-19 laboratory confirmed cases is ~4.7% ranging from ~0.3-0.4% in Chile and Israel to ~10.8% in Italy. To address this global crisis, up-to-date information on the viral genomics and transcriptomics is crucial for understanding the origins and global dispersal of the virus, providing insight into viral pathogenicity, transmission and epidemiology, and enabling strategies for therapeutic interventions, drug discovery and vaccine development. Therefore, this review provides a comprehensive overview of COVID-19 epidemiology, genomic etiology, findings from recent transcriptomic map analysis, viral-human protein interactions, molecular diagnostics, and the current status of vaccine and novel therapeutic intervention development. Moreover, we provide an extensive list of resources that will help the scientific community access numerous types of databases related to SARS-CoV-2 OMICs and approaches to therapeutics related to COVID-19 treatment.

With the easing of restriction measures, repeated community-based sampling for tracking new COVID-19 infections is anticipated for the next 6 to 12 months. A noninvasive, self-collected specimen like saliva will be useful for such public health surveillance. Investigations on the use of saliva for SARS-CoV-2 RT-PCR have largely been among COVID-19 in-pa\tients and symptomatic ambulatory patients with limited work in a community-based screening setting. This study was carried out to address this paucity of data and reported discrepancies in diagnostic accuracy for saliva samples. Patients and Methods: From 29th June to 14th July 2020, adults presenting for COVID-19 testing at a community-based screening facility in Dubai, United Arab Emirates were recruited. Clinical data, nasopharyngeal swab in universal transport media and drooling saliva in sterile containers were obtained. Reverse transcriptase PCR amplification of SARS-CoV-2 RdRp and N genes was used to detect the presence of the SARS-CoV-2 virus. Results: Of the 401 participants, 35 (8.7%) had viral detection in at least one specimen type and the majority (n=20/35; 57.1%) were asymptomatic. Both swab and saliva were positive in 19 (54.2%) patients, while 7 (20.0%) patients had swab positive/saliva negative results. There were 9 (25.7%) patients with saliva positive/swab negative result and this included 5 asymptomatic COVID-19 patients undergoing repeat screening. Using the swab as the reference gold standard, the sensitivity and specificity of saliva were 73.1% (95% CI 52.2-88.4%) and 97.6% (95% CI 95.5-98.9%) while the positive and negative predictive values were 67.9% (95% CI 51.5-80.8%) and 98.1% (95% CI 96.5-99.0%), respectively. Conclusion: The findings suggest good diagnostic accuracy for saliva and feasibility of utilization of specimen without transport media for SARS-CoV-2 RT-PCR. Saliva represents a potential specimen of choice in community settings and population-based screening.

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Objectives The high diagnostic accuracy indices for saliva SARS-CoV-2 reverse-transcriptase polymerase chain reaction (RT-PCR) reported in adults has not been demonstrated in children and adequately powered studies focused on the paediatric population are lacking. This study was carried out to determine the diagnostic accuracy of saliva for SARS-CoV-2 RT-PCR in ambulatory children. Methods From 1 st -23 rd October 2020, we recruited a population-based sample of children presenting for COVID-19 screening in Dubai, United Arab Emirates. Each child provided paired nasopharyngeal (NP) swab and saliva for SARS-CoV-2 RT-PCR N , E and RdRp genes detection. Results Paired NP swab and saliva samples were obtained from 476 children with mean (±SD) age of 10.8 years (±3.9) and 58.1% were male (n/N=277/476). Nine participants were sampled twice, hence 485 pairs of NP swab/saliva were tested. Viral detection in at least one specimen type was reported in 17.9% (n/N=87/485), with similar detection in NP swab (16.7%; n/N=81/485) and saliva (15.9%; n/N=77/485). Sensitivity and specificity of saliva RT-PCR was 87.7% (95% CI 78.5%-93.9%) and 98.5% (95% CI 96.8%-99.5%). The positive and negative predictive values were 92.2% (95% CI 84.2%-96.3%) and 97.6% (95% CI 95.7%-98.6%) with Kappa coefficient 0.879 (95% CI 0.821-0.937). Concordance of findings between NP swab and saliva did not differ by age (p=0.67) or gender (p=0.29). Cycle threshold (Ct) values were significantly higher in NP swab/saliva pairs with discordant findings compared to those with both specimens positive. Conclusion In light of these findings, we recommend saliva as a diagnostic specimen for COVID-19 screening in children.