Prognosis of COVID-19 in the middle eastern population, knowns and unknowns.

Since its emergence in China in 2019, the SARS-CoV-2 virus has affected all countries worldwide. The virus is easily transmitted from one person to another via infected aerosols or contaminated surfaces. Unlike its counterparts, the prognosis of COVID-19 ranges from asymptomatic to critical disease or death. Several factors play a role in determining the severity of the disease in infected patients. Among others, is the pre-existence of an underlying medical condition such as diabetes, cancer, and others. Furthermore, although children are less prone to the severe form of the COVID-19 disease, they require attention due to the report of many atypical presentations of the infection, post-asymptomatic exposure. In the Middle East, little is known about the prognosis of the SARS-CoV-2 infection in high-risk categories, notably patients with diabetes, cancer, and pregnant women. The aim of this review is to summarize the current knowledge about this group of population in the middle eastern region as well as to highlight the gap in the literature. We have found that the majority of the papers were from the Gulf countries. Although, few studies were conducted; high-risk patients appear to have an increased risk of morbidity and mortality from COVID-19 compared to their counterparts. Higher levels of inflammatory markers, C-reactive protein, erythrocyte sedimentation rate, D-dimer, and ferritin levels were also observed. Children are often asymptomatic or present with atypical presentations. More studies should be conducted to determine the clinical biomarkers of COVID-19 in high-risk categories to help in patient risk stratification and management in the middle eastern population.

Prognosis of COVID-19 in the middle eastern population, knowns and unknowns

Since its emergence in China in 2019, the SARS-CoV-2 virus has affected all countries worldwide. The virus is easily transmitted from one person to another via infected aerosols or contaminated surfaces. Unlike its counterparts, the prognosis of COVID-19 ranges from asymptomatic to critical disease or death. Several factors play a role in determining the severity of the disease in infected patients. Among others, is the pre-existence of an underlying medical condition such as diabetes, cancer, and others. Furthermore, although children are less prone to the severe form of the COVID-19 disease, they require attention due to the report of many atypical presentations of the infection, post-asymptomatic exposure. In the Middle East, little is known about the prognosis of the SARS-CoV-2 infection in high-risk categories, notably patients with diabetes, cancer, and pregnant women. The aim of this review is to summarize the current knowledge about this group of population in the middle eastern region as well as to highlight the gap in the literature. We have found that the majority of the papers were from the Gulf countries. Although, few studies were conducted;high-risk patients appear to have an increased risk of morbidity and mortality from COVID-19 compared to their counterparts. Higher levels of inflammatory markers, C-reactive protein, erythrocyte sedimentation rate, D-dimer, and ferritin levels were also observed. Children are often asymptomatic or present with atypical presentations. More studies should be conducted to determine the clinical biomarkers of COVID-19 in high-risk categories to help in patient risk stratification and management in the middle eastern population.

Evaluation of the Levels of Peripheral CD3+, CD4+, and CD8+ T Cells and IgG and IgM Antibodies in COVID-19 Patients at Different Stages of Infection.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection affects the stimulatory levels of cellular-mediated immunity, which plays an essential role in controlling SARS-CoV-2 infection. In fact, several studies have shown the association of lymphopenia with severe COVID-19 in patients. The aim of this study is to investigate the response of the immune system, including cell-mediated immunity and antibody production, during different stages of SARS-CoV-2 infection. Peripheral blood and serum samples were collected from patients with moderate infection, patients under medication (hospitalized), patients who had recovered, and healthy individuals (n = 80). Flow cytometry analysis was performed on peripheral blood samples to determine the cellular immunity profile of each patient. The data showed a significant reduction in the levels of CD3+, CD4+, and CD8+ T cells and CD45+ cells in the moderate and under-medication groups, suggesting lymphopenia in those patients. Also, enzyme-linked immunosorbent assay (ELISA) was conducted on the serum samples to measure the levels of antibodies, including IgM and IgG, in each patient. The results revealed a significant increase in the levels of IgM in the moderate infection and under-medication patients, thus indicating the production of IgM during the first week of infection. Furthermore, changes in the levels of IgG were significantly detected among recovered patients, indicating therefore a remarkable increase during the recovery stage of SARS-CoV-2 infection and thus a strong humoral-mediated immunity. In summary, the results of this study may help us to understand the main role of the cellular immune responses, including CD3+, CD4+, and CD8+ T cells, against SARS-CoV-2 infection. This understanding might support the development of SARS-CoV-2 treatments and vaccines in the near future. IMPORTANCE Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in late 2019 in China. This virus is a serious threat to people not only in China but also worldwide, where it has been detected in over 222 countries. It has been reported that ∼3.4% of SARS-CoV-2-infected patients have died. The significance of our study relies on the fact that an enzyme-linked immunosorbent assay and flow cytometry were used to measure the levels of antibodies and cellular immune response, respectively, from clinical samples of patients infected with SARS-CoV-2.

Amplicon and Metagenomic Analysis of Middle East Respiratory Syndrome (MERS) Coronavirus and the Microbiome in Patients with Severe MERS.

Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic infection that emerged in the Middle East in 2012. Symptoms range from mild to severe and include both respiratory and gastrointestinal illnesses. The virus is mainly present in camel populations with occasional zoonotic spill over into humans. The severity of infection in humans is influenced by numerous factors, and similar to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), underlying health complications can play a major role. Currently, MERS-CoV and SARS-CoV-2 are coincident in the Middle East and thus a rapid way of sequencing MERS-CoV to derive genotype information for molecular epidemiology is needed. Additionally, complicating factors in MERS-CoV infections are coinfections that require clinical management. The ability to rapidly characterize these infections would be advantageous. To rapidly sequence MERS-CoV, an amplicon-based approach was developed and coupled to Oxford Nanopore long read length sequencing. This and a metagenomic approach were evaluated with clinical samples from patients with MERS. The data illustrated that whole-genome or near-whole-genome information on MERS-CoV could be rapidly obtained. This approach provided data on both consensus genomes and the presence of minor variants, including deletion mutants. The metagenomic analysis provided information of the background microbiome. The advantage of this approach is that insertions and deletions can be identified, which are the major drivers of genotype change in coronaviruses. IMPORTANCE Middle East respiratory syndrome coronavirus (MERS-CoV) emerged in late 2012 in Saudi Arabia. The virus is a serious threat to people not only in the Middle East but also in the world and has been detected in over 27 countries. MERS-CoV is spreading in the Middle East and neighboring countries, and approximately 35% of reported patients with this virus have died. This is the most severe coronavirus infection so far described. Saudi Arabia is a destination for many millions of people in the world who visit for religious purposes (Umrah and Hajj), and so it is a very vulnerable area, which imposes unique challenges for effective control of this epidemic. The significance of our study is that clinical samples from patients with MERS were used for rapid in-depth sequencing and metagenomic analysis using long read length sequencing.

Amplicon-Based Detection and Sequencing of SARS-CoV-2 in Nasopharyngeal Swabs from Patients With COVID-19 and Identification of Deletions in the Viral Genome That Encode Proteins Involved in Interferon Antagonism.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). Sequencing the viral genome as the outbreak progresses is important, particularly in the identification of emerging isolates with different pathogenic potential and to identify whether nucleotide changes in the genome will impair clinical diagnostic tools such as real-time PCR assays. Although single nucleotide polymorphisms and point mutations occur during the replication of coronaviruses, one of the biggest drivers in genetic change is recombination. This can manifest itself in insertions and/or deletions in the viral genome. Therefore, sequencing strategies that underpin molecular epidemiology and inform virus biology in patients should take these factors into account. A long amplicon/read length-based RT-PCR sequencing approach focused on the Oxford Nanopore MinION/GridION platforms was developed to identify and sequence the SARS-CoV-2 genome in samples from patients with or suspected of COVID-19. The protocol, termed Rapid Sequencing Long Amplicons (RSLAs) used random primers to generate cDNA from RNA purified from a sample from a patient, followed by single or multiplex PCRs to generate longer amplicons of the viral genome. The base protocol was used to identify SARS-CoV-2 in a variety of clinical samples and proved sensitive in identifying viral RNA in samples from patients that had been declared negative using other nucleic acid-based assays (false negative). Sequencing the amplicons revealed that a number of patients had a proportion of viral genomes with deletions.

Unique challenges to control the spread of COVID-19 in the Middle East.

The COVID-19 pandemic is spreading at unprecedented pace among the Middle East and neighboring countries. This region is geographically, economically, politically, culturally and religiously a very sensitive area, which impose unique challenges for effective control of this epidemic. These challenges include compromised healthcare systems, prolonged regional conflicts and humanitarian crises, suboptimal levels of transparency and cooperation, and frequent religious gatherings. These factors are interrelated and collectively determine the response to the pandemic in this region. Here, we in-depth emphasize these challenges and take a glimpse of possible solutions towards mitigating the spread of COVID-19.