Background: The cytokine storm is a complication related to SARS-CoV-2 infection worldwide. This study aimed to address the level of three cytokines which were interleukin-1-beta (IL-1β), interleukin-6 (IL-6), and tumour necrosis factor-alpha (TNF-α), with different blood parameters to the formation of cytokine storm or any complication among COVID-19 patients. Method and material: A total of 104 serum samples were included for this purpose, and they were divided into three categories the healthy control group (n=30), mild COVID-19 patients (n=23), and severe cases of COVID-19 patients (n=51). The cytokine concentration was measured by enzyme-linked immunosorbent assays (ELISA). Serum ferritin, C-reactive protein (CRP) levels, and erythrocyte sedimentation rate were also evaluated and compared with the concentration of the proinflammatory cytokines. Result: The data analysis showed a significant relationship between the serum IL-6 level with serum ferritin and CRP and the progression to the severity of SARS-CoV-2 infection. The IL-6 level was increased in mild COVID-19 patients and was significantly elevated in severe COVID-19 patients. Patients in the severe group had significantly higher serum ferritin, CRP, and erythrocyte sedimentation rate levels than those in the mild and healthy groups. The IL-1β and TNF-α were not significantly different in the groups compared with the healthy control group. Conclusion: This study revealed that the proinflammatory cytokines and biochemical laboratory tests are promising biomarkers for detecting the severity of COVID-19 cases.

Acinetobacter baumannii is an aggressive opportunistic bacterial pathogen that causes severe nosocomial infections, especially among burn patients. An increasing number of hospitals-acquired infections have been reported all over the world. However, little attention has been paid to the relatedness between A. baumannii isolates from different hospital environments and patients. In this study, 27 isolates were collected from the Burn and Plastic Surgery Hospital of Al Sulaymaniyah City, Iraq, from January through December 2019 (11 from patients and 16 from the wards environment), identified to species level as A. baumannii using Vitek 2 system and molecular detection of 16S rRNA gene, and then confirmed by targeting the bla_OXA-51 gene. Moreover, the isolates were characterized by means of automated antimicrobial susceptibility assay, antimicrobial-resistant patterns, a phenotypic method using a combined disk test, and molecular methods for the detection of class A and C -lactamase genes, and finally, the genetic relatedness was classified. Antimicrobial susceptibility testing showed that 63% (17/27) of the retrieved A. baumannii isolates were extensively drug-resistant to 8/9 antimicrobial classes. Furthermore, 37% (10/27) of the isolates were classified as multidrug-resistant; 8 isolates exhibited similar resistant patterns and the other two isolates showed 2 different patterns, while resistance was greater in isolates from patients than from the ward environment. Combined disk test showed that two isolates contained extended-spectrum -lactamase. All isolates carried bla_TEM-1, and two copies of the bla_CTX-1 gene were indicated in one isolate, while bla_SHV was absent in all isolates. Twenty-four isolates carried the bla_AmpC gene; among them, 3 isolates harbored the insertion sequence ISAba-1 upstream to the gene. Using Enterobacterial Repetitive Intergenic Consensus PCR, the isolates were clustered into 6 distinct types; among them, two clusters, each of four strains, were classified to contain isolates from both patients and environments. The clusters of similar genotypes were found in inpatients as well as the environments of different wards during time periods, suggesting transmission within the hospital. Identification of possible infection sources and controlling the transmission of these aggressive resistance strains should be strictly conducted.

In order to achieve the commitment made by the World Health Organisation to eliminate viral hepatitis by 2030, it is essential that clinicians can obtain basic sequencing data for hepatitis B virus (HBV) infected patients. While accurate diagnosis of HBV is achievable in most clinical settings, genotyping and identification of resistance-associated substitutions (RAS) present a practical challenge in regions with limited healthcare and biotechnology infrastructure. Here we outline two workflows for generating clinically relevant HBV sequence data directly from dried serum spot (DSS) cards without DNA extraction using either Sanger, or the portable MinION sequencing platforms. Data obtained from the two platforms were highly consistent and allowed determination of HBV genotype and RAS. This is the first demonstration of MinION sequencing from DSS, illustrating the broad utility of this sequencing technology. We demonstrated the clinical application of this technology using sera sampled on DSS cards obtained from both Iraq and Brazil. The sample stability provided by DSS cards, combined with the rapid PCR and sequencing protocols will enable regional/national centres to provide information relevant to patient management. By providing viable workflows for both the Sanger and MinION sequencing platforms, which vary greatly in the infrastructure and expertise required, we demonstrate that MinION sequencing is a viable method for HBV genotyping in resource-limited settings. These workflows could also be applied to sequencing of other blood borne DNA viruses and bacterial pathogens.

The human cytomegalovirus (HCMV) UL24 and UL43 are tegument proteins that have recently been shown to interact with each other in a yeast two-hybrid system. By their overexpression in MRC5 cells, we demonstrate that these viral proteins interact with several important host proteins, especially Dicer and trans-activation response RNA binding protein. As these hots proteins are involved in regulating the production of cellular micro-RNAs, the cytomegalovirus (CMV) proteins could interfere with their actions to favor viral replication directly or through an immune escape mechanism. Double knockout of UL24 and UL43 does not show a remarkable effect on CMV entry or replication, but it significantly downregulates the expression of CMV-encoded miR-UL59, which is thought to regulate the expression of a downstream target UL16 binding protein 1 (ULBP1). Interestingly, the double knockout increases the expression of the ULBP1 recognized by the NKG2D activating receptor of natural killer cells. This study investigates the potential role of several proteins encoded by HCMV in regulating the host cellular environment to favor escape from immunity, and it also provides some basis for the future development of RNA-targeted small molecules to control HCMV infection.

Omicron variants have been classified as Variants of Concern (VOC) by the World Health Organization (WHO) ever since they first emerged as a result of a significant mutation in this variant, which showed to have an impact on transmissibility and virulence of the virus, as evidenced by the ongoing modifications in the SARS-CoV-2 virus. As a global pandemic, the Omicron variant also spread among the Kurdish population. This study aimed to analyze different strains from different cities of the Kurdistan region of Iraq to show the risk of infection and the impact of the various mutations on immune responses and vaccination. A total of 175 nasopharyngeal/oropharyngeal specimens were collected at West Erbil Emergency Hospital and confirmed for SARS-CoV-2 infection by RT-PCR. The genomes of the samples were sequenced using the Illumina COVID-Seq Method. The genome analysis was established based on previously published data in the GISAID database and compared to previously detected mutations in the Omicron variants, and that they belong to the BA.1 lineage and include most variations determined in other studies related to transmissibility, high infectivity and immune escape. Most of the mutations were found in the RBD (receptor binding domain), the region related to the escape from humoral immunity. Remarkably, these point mutations (G339D, S371L, S373P, S375F, T547K, D614G, H655Y, N679K and N969K) were also determined in this study, which were unique, and their impact should be addressed more. Overall, the Omicron variants were more contagious than other variants. However, the mortality rate was low, and most infectious cases were asymptomatic. The next step should address the potential of Omicron variants to develop the next-generation COVID-19 vaccine.