Identification of the novel HLA-C*04:495 allele by sequencing-based typing

The HLA-C*04:495 allele differs from HLA-C*04:01:01:31 by two nucleotide changes in the 5'UTR and exon 5.

Identification of the novel HLA-DQB1*03:483 allele by sequencing-based typing

A single nucleotide change in exon 1 of HLA-DQB1*03:01:01:03 results in the novel HLA-DQB1*03:483 allele. This article is protected by copyright. All rights reserved.

Kinetics of antibody response in critically ill patients with Middle East respiratory syndrome and association with mortality and viral clearance

The objective of this study is to examine the IgG antibody response in critically ill patients with the Middle East respiratory syndrome (MERS) and to examine the association of early antibody response with mortality and viral clearance. We collected blood samples from 40 consecutive real-time reverse transcription-polymerase chain reaction (rRT-PCR) confirmed critically ill MERS patients on ICU days 1, 3, 7, 14 and 28. MERS-CoV antibodies were detected by enzyme-linked immunosorbent assay (ELISA), using wells coated with MERS-CoV S1 antigen. Patients were admitted to ICU after a median (Q1, Q3) of 9 (4, 13) days from onset of symptoms with an admission Sequential Organ Failure Assessment (SOFA) score of 11 (6.5, 12). Among the study cohort, 38 patients (95%) received invasive ventilation, 35 (88%) vasopressors, 21 (53%) renal replacement therapy and 17 (43%) corticosteroids. Median (Q1,Q3) ELISA optical density (OD) ratio significantly increased with time (p < 0.001) from 0.11 (0.07, 1.43) on day 1; to 0.69 (0.11, 2.08) on day 3, 2.72 (1.84, 3.54) on day 7, 2.51 (0.35, 3.35) on day 14 and 3.77 (3.70, 3.84) on day 28. Early antibody response (day 1-3) was observed in 13/39 patients (33%) and was associated with lower mortality (hazard ratio: 0.31, 95% CI 0.10, 0.96, p = 0.04) but was not associated with faster clearance of MERS-CoV RNA. In conclusion, among critically ill patients with MERS, early antibody response was associated with lower mortality but not with faster clearance of MERS-CoV RNA. These findings have important implications for understanding pathogenesis and potential immunotherapy.

Characterization of the novel HLA-B*57:02:01:03 allele by sequencing-based typing

Two-nucleotide changes in the 3' UTR of HLA-B*57:02:01:01 result in the novel HLA-B*57:02:01:03 allele.

Characterization of the novel HLA-A*68:277 allele by sequencing-based typing

A single nucleotide change in exon 1 of HLA-A*68:01:01:02 results in the novel HLA-A*68:277 allele.

Characterization of the novel HLA-A*31:199 allele by sequencing-based typing

A single nucleotide change in exon 4 of HLA-A*31:01:02:31 results in the novel HLA-A*31:199 allele.

Identification of a novel HLA-A*31 variant, HLA-A*31:01:02:31, in a Saudi individual

A single nucleotide change in the 5' UTR of A*31:01:02:01 results in the novel HLA-A*31:01:02:31 allele.

Identification of a novel HLA-B*18 variant, HLA-B*18:01:01:52, in a Saudi individual

A single nucleotide change in the 3' UTR of HLA-B*18:01:01:01 results in the novel HLA-B*18:01:01:52 allele.

Novel HLA-B*81:02:02 allele identified in a Saudi individual

HLA-B*81:02:02 differs from HLA-B*81:02 by a synonymous substitution in exon 5.

The novel HLA-DQB1*06:03:01:06 allele identified in a Saudi individual

HLA-DQB1*06:03:01:06 differs from HLA-DQB1*06:03:01:01 by a single nucleotide substitution in intron 2.

Novel HLA-C*06:284 allele, identified by next-generation sequencing in a Saudi individual

HLA-C*06:284 differs from HLA-C*06:02:01:02 by two single nucleotide substitutions in codon 24 (Ser > Thr).

Novel HLA-DPB1*10:01:05 allele, identified by next-generation sequencing in a Saudi individual

HLA-DPB1*10:01:05 differs from HLA-DPB1*10:01:01:01 by a single synonymous nucleotide substitution in exon 2, 38 G>A.

Novel HLA-B*50:66 allele, identified by next-generation sequencing in a Saudi individual

HLA-B*50:66 differs from HLA-B*50:01:01:01 by a single nucleotide substitution (C>A) in codon 153.

Novel HLA-DPB1*14:01:11 allele, identified by next-generation sequencing in a Saudi individual

HLA-DPB1*14:01:11 differs from HLA-DPB1*14:01:01:01 by a single synonymous nucleotide substitution in codon 52.

The novel HLA-A*68:227 allele, identified by Next-Generation Sequencing in a Saudi individual

HLA-A*68:227 differs from HLA-A*68:84 by two single nucleotide substitutions in codon 10 and 90.

The novel HLA-DRB1*13:290 allele, identified by next-generation sequencing in a Saudi individual

HLA-DRB1*13:290 differs from HLA-DRB1*13:02:01:01 by a single nucleotide substitution in codon 86 (Gly > Ala).

The novel HLA-B*07:387 allele, identified by next-generation sequencing in a Saudi individual

HLA-B*07:387 differs from HLA-B*07:05:01:01 by a single nucleotide substitution in codon 91 (Glycine to Tryptophan).

The novel HLA-DRB3*03:39 allele, identified by next-generation sequencing in a Saudi individual

HLA-DRB3*03:39 differs from HLA-DRB3*03:01:01 by a single nucleotide substitution in codon 22 (Glutamic acid to Lysine).

The novel HLA-DQB1*06:358 allele, identified by Next-Generation Sequencing in a Saudi individual

HLA-DQB1*06:358 differs from HLA-DQB1*06:09:01:01 by two single nucleotide substitutions: 2949 C>T and 3001 A>T.

A novel HLA-C null allele, HLA-C*12:299N, identified by next-generation sequencing in a Saudi individual

A single nucleotide deletion in HLA-C*12:03:01:01 results in a novel null allele, HLA-C*12:299N.

A novel HLA-B allele, HLA-B*08:242, identified by next-generation sequencing in a Saudi individual

HLA-B*08:242 differs from HLA-B*08:01:01:01 in codons 33 and 36 of exon 2.

Identification of the novel HLA-B*35:01:01:16 allele in a Saudi individual

HLA-B*35:01:01:16 differs from HLA-B*35:01:01:01 by a single nucleotide substitution (C → A) at position 3941.

Identification of the novel HLA-C*04:01:01:31 allele in a Saudi individual

HLA-C*04:01:01:31 differs from HLA-C*04:01:01:01 by a single nucleotide substitution (G → T) at position 72.

Identification of the novel HLA-A*30:02:01:04 allele in a Saudi individual

HLA-A*30:02:01:04 differs from HLA-A*30:02:01:01 by a single nucleotide substitution (G ➔ C) at position 3222.

Identification of the novel HLA-B*18:01:01:17 allele in a Saudi individual

HLA-B*18:01:01:17 differs from HLA-B*18:01:01:01 by a single nucleotide substitution (A➔T) at position 3956.

Identification of the novel HLA-A*32:01:01:08 allele in a Saudi individual

HLA-A*32:01:01:08 differs from HLA-A*32:01:01:01 by a single nucleotide substitution (G → A) at position 2200.

Identification of the novel HLA-B*51:230 allele in a Saudi individual

One nucleotide replacement at codon 349 of HLA-B*51:01:01:01 results in a new allele, HLA-B*51:230.

Feasibility of Using Convalescent Plasma Immunotherapy for MERS-CoV Infection, Saudi Arabia

Efficacy testing will be challenging because of the small pool of donors with sufficiently high antibody titers.

We explored the feasibility of collecting convalescent plasma for passive immunotherapy of Middle East respiratory syndrome coronavirus (MERS-CoV) infection by using ELISA to screen serum samples from 443 potential plasma donors: 196 patients with suspected or laboratory-confirmed MERS-CoV infection, 230 healthcare workers, and 17 household contacts exposed to MERS-CoV. ELISA-reactive samples were further tested by indirect fluorescent antibody and microneutralization assays. Of the 443 tested samples, 12 (2.7%) had a reactive ELISA result, and 9 of the 12 had reactive indirect fluorescent antibody and microneutralization assay titers. Undertaking clinical trials of convalescent plasma for passive immunotherapy of MERS-CoV infection may be feasible, but such trials would be challenging because of the small pool of potential donors with sufficiently high antibody titers. Alternative strategies to identify convalescent plasma donors with adequate antibody titers should be explored, including the sampling of serum from patients with more severe disease and sampling at earlier points during illness.

HLA class II polymorphism in Saudi patients with multiple sclerosis

Several studies have investigated the association of different HLA antigens with multiple sclerosis (MS). However, only few studies have considered the association of high-resolution HLA type and MS with none yet from Saudi Arabia. The aim of this study was to investigate the association of HLA class II alleles with MS in the Saudi population. We used next-generation sequencing to investigate HLA association with MS. This study was conducted at King Abdulaziz Medical City in Riyadh, Saudi Arabia. We found that several HLA-DRB1 and DQB1 alleles were associated with MS. These alleles included HLA-DRB1*15:01 (odds ratio [OR]: 3.01; 95%, confidence interval [CI]: 1.68-5.54; P = .0001), HLA-DQB1*02:01 (OR: 1.76; 95% CI: 1.20-2.58; P = .0022), HLA-DQB1*06:02 (OR: 3.52; 95% CI: 1.87-6.86; P < .0001), and HLA-DQB1*06:03 (OR: 2.42; 95% CI: 1.16-5.25; P = 0.01). Interestingly, HLA-DRB1*15:01 was associated with increased risk of previous relapses. In addition, HLA-DRB1*15:01 and HLA-DQB1*06:02 were found to be associated with lower vitamin D levels. This study provides insights on the association of different HLA alleles with clinical characteristics and outcome of MS among Saudis. These insights can have future implications for the clinical management of MS based on the patient genetic profile.

Histopathology of Middle East respiratory syndrome coronovirus (MERS-CoV) infection - clinicopathological and ultrastructural study

Aims

The pathogenesis, viral localization and histopathological features of Middle East respiratory syndrome – coronavirus (MERS‐CoV) in humans are not described sufficiently. The aims of this study were to explore and define the spectrum of histological and ultrastructural pathological changes affecting various organs in a patient with MERS‐CoV infection and represent a base of MERS‐CoV histopathology.

Methods and results

We analysed the post‐mortem histopathological findings and investigated localisation of viral particles in the pulmonary and extrapulmonary tissue by transmission electron microscopic examination in a 33‐year‐old male patient of T cell lymphoma, who acquired MERS‐CoV infection. Tissue needle biopsies were obtained from brain, heart, lung, liver, kidney and skeletal muscle. All samples were collected within 45 min from death to reduce tissue decomposition and artefact. Histopathological examination showed necrotising pneumonia, pulmonary diffuse alveolar damage, acute kidney injury, portal and lobular hepatitis and myositis with muscle atrophic changes. The brain and heart were histologically unremarkable. Ultrastructurally, viral particles were localised in the pneumocytes, pulmonary macrophages, renal proximal tubular epithelial cells and macrophages infiltrating the skeletal muscles.

Conclusion

The results highlight the pulmonary and extrapulmonary pathological changes of MERS‐CoV infection and provide the first evidence of the viral presence in human renal tissue, which suggests tissue trophism for MERS‐CoV in kidney.

Middle East Respiratory Syndrome

Between September 2012 and January 20, 2017, the World Health Organization (WHO) received reports from 27 countries of 1879 laboratory-confirmed cases in humans of the Middle East respiratory syndrome (MERS) caused by infection with the MERS coronavirus (MERS-CoV) and at least 659 related deaths. Cases of MERS-CoV infection continue to occur, including sporadic zoonotic infections in humans across the Arabian Peninsula, occasional importations and associated clusters in other regions, and outbreaks of nonsustained human-to-human transmission in health care settings. Dromedary camels are considered to be the most likely source of animal-to-human transmission. MERS-CoV enters host cells after binding the dipeptidyl peptidase 4 (DPP-4) receptor and the carcinoembryonic antigen–related cell-adhesion molecule 5 (CEACAM5) cofactor ligand, and it replicates efficiently in the human respiratory epithelium. Illness begins after an incubation period of 2 to 14 days and frequently results in hypoxemic respiratory failure and the need for multiorgan support. However, asymptomatic and mild cases also occur. Real-time reverse-transcription–polymerase-chain-reaction (RT-PCR) testing of respiratory secretions is the mainstay for diagnosis, and samples from the lower respiratory tract have the greatest yield among seriously ill patients. There is no antiviral therapy of proven efficacy, and thus treatment remains largely supportive; potential vaccines are at an early developmental stage. There are multiple gaps in knowledge regarding the evolution and transmission of the virus, disease pathogenesis, treatment, and prospects for a vaccine. The ongoing occurrence of MERS in humans and the associated high mortality call for a continued collaborative approach toward gaining a better understanding of the infection both in humans and in animals. MERS-CoV was first identified in September 2012 in a patient from Saudi Arabia who had hypoxemic respiratory failure and multiorgan illness. Subsequent cases have included infections in humans across the Arabian Peninsula, occasional importations and associated clusters in other regions, and outbreaks of nonsustained human-to-human transmission in health care settings (Fig. 1).

Organ trade using social networks

Organ transplantation is recognized worldwide as an effective treatment for organ failure. However, due to the increase in the number of patients requiring a transplant, a shortage of suitable organs for transplantation has become a global problem. Human organ trade is an illegal practice of buying or selling organs and is universally sentenced. The aim of this study was to search social network for organ trade and offerings in Saudi Arabia. The study was conducted from June 22, 2015 to February 19, 2016. The search was conducted on Twitter, Google answers, and Facebook using the following terms: kidney for sale, kidneys for sale, liver for sale, kidney wanted, liver wanted, kidney donor, and liver donor. We found a total of 557 adverts on organ trade, 165 (30%) from donors or sellers, and 392 (70%) from recipients or buyers. On Twitter, we found 472 (85%) adverts, on Google answers 61 (11%), and on Facebook 24 (4%). Organ trade is a global problem, and yet it is increasingly seen in many countries. Although the Saudi Center for Organ Transplantation by-laws specifically prohibits and monitors any form of commercial transplantation, it is still essential to enforce guidelines for medical professionals to detect and prevent such criminal acts.

Association of human leukocyte antigen class II alleles with severe Middle East respiratory syndrome-coronavirus infection

BACKGROUND:

Middle East Respiratory Syndrome (MERS) is a disease of the lower respiratory tract and is characterized by high mortality. It is caused by a beta coronavirus (CoV) referred to as MERS-CoV. Majority of MERS-CoV cases have been reported from Saudi Arabia.

AIM:

We investigated the human leukocyte antigen (HLA) Class II alleles in patients with severe MERS who were admitted in our Intensive Care Unit.

METHODS:

A total of 23 Saudi patients with severe MERS-CoV infection were typed for HLA class II, results were compared with those of 161 healthy controls.

RESULTS:

Two HLA class II alleles were associated with the disease; HLA-DRB1*11:01 and DQB1*02:02, but not with the disease outcome.

CONCLUSIONS:

Our results suggest that the HLA-DRB1*11:01 and DQB1*02:02 may be associated with susceptibility to MERS.

C1q-binding anti-HLA antibody assay: A test dilemma

Detection of donor-specific anti-HLA antibodies in patients with kidney graft, or awaiting kidney graft, acts as a predictor for antibody mediated rejection. Several methods are in practice for the detection of anti-HLA antibodies; including the latest introduction of C1q-binding anti-HLA antibody method. This method depends on detecting complement fixing anti-HLA antibodies on single antigen beads using C1q as the marker for the presence of those antibodies. Here we discuss recent data on this method and present a working hypothesis for explaining the inability of this method to detect low titer anti-HLA antibodies.

MERS-CoV diagnosis: An update

Diagnosis of MERS-Cov still a major concern in most of daignostic laboratories. To date the Real-time Polymerase Chain reaction (RT-PCR) is the mainstay for diagnosis of MERS-CoV. RT-PCR has limitations, including a long turnaround time and lack of common measurements and correlations with Viral Load (VL). It is recommended to screen for MERS-CoV using RT-PCR of the upstream of envelope gene (upE) followed by confirmation of the presence of one of the following genes; open reading frame 1A, 1B genes or nucleocapsid (N) gene. Scientists are looking to implement viral sequencing on all negative samples by RT-PCR and they beleive that can be exposed to another level of testing using sequencing of the RNA-dependent RNA polymerase (RdRp) gene or N gene and in this case a positive result is diagnostic. It is also very important to maintain a contineous and random sequencing for MERS-Cov samples to be able to pick early viral mutations. Serological assays still not widely or routinely performed, and a lot of studies looking to implement such method in routine patient's testings.

Feasibility, safety, clinical, and laboratory effects of convalescent plasma therapy for patients with Middle East respiratory syndrome coronavirus infection: a study protocol

As of September 30, 2015, a total of 1589 laboratory-confirmed cases of infection with the Middle East respiratory syndrome coronavirus (MERS-CoV) have been reported to the World Health Organization (WHO). At present there is no effective specific therapy against MERS-CoV. The use of convalescent plasma (CP) has been suggested as a potential therapy based on existing evidence from other viral infections. We aim to study the feasibility of CP therapy as well as its safety and clinical and laboratory effects in critically ill patients with MERS-CoV infection. We will also examine the pharmacokinetics of the MERS-CoV antibody response and viral load over the course of MERS-CoV infection. This study will inform a future randomized controlled trial that will examine the efficacy of CP therapy for MERS-CoV infection. In the CP collection phase, potential donors will be tested by the enzyme linked immunosorbent assay (ELISA) and the indirect fluorescent antibody (IFA) techniques for the presence of anti-MERS-CoV antibodies. Subjects with anti-MERS-CoV IFA titer of ≥1:160 and no clinical or laboratory evidence of MERS-CoV infection will be screened for eligibility for plasma donation according to standard donation criteria. In the CP therapy phase, 20 consecutive critically ill patients admitted to intensive care unit with laboratory-confirmed MERS-CoV infection will be enrolled and each will receive 2 units of CP. Post enrollment, patients will be followed for clinical and laboratory outcomes that include anti-MERS-CoV antibodies and viral load. This protocol was developed collaboratively by King Abdullah International Medical Research Center (KAIMRC), Gulf Cooperation Council (GCC) Infection Control Center Group and the World Health Organization—International Severe Acute Respiratory and Emerging Infection Consortium (ISARIC-WHO) MERS-CoV Working Group. It was approved in June 2014 by the Ministry of the National Guard Health Affairs Institutional Review Board (IRB). A data safety monitoring board (DSMB) was formulated. The study is registered at http://www.clinicaltrials.gov (NCT02190799).

Stem cell research and regenerative medicine at King Abdullah International Medical Research Center

Translation of stem cell research from bench to bedside opens up exciting new therapeutic options for patients. Although stem cell research has progressed rapidly, its clinical applications have not kept pace. We report on the establishment of a stem cell research and regenerative medicine program at King Abdullah International Medical Research Center (KAIMRC). The purpose of this unit is to coordinate advanced stem cell research and translational outcomes with the goal of treating chronic human diseases, such as cancer, diabetes, cardiovascular, neurological, immunological, and liver diseases. Our first step in achieving this goal was to integrate the stem cells and regenerative medicine unit with our umbilical cord blood bank and bone marrow registry. This organizational structure will provide different sources for stem cells for research and clinical purposes, and facilitate our stem cell research and stem cell transplantation program. We are at an early and exciting stage in our program, but we believe that our progress to the international stage will be rapid and have a significant impact.

Three new HLA-C alleles (HLA-C*14:02:13, HLA-C*15:72 and HLA-C*15:74) in Saudi bone marrow donors

Three new HLA-C alleles were identified by sequence-based typing method (SBT) in donors for the Saudi Bone Marrow Donor Registry (SBMDR). HLA-C*14:02:13 differs from HLA-C*14:02:01 by a silent G to A substitution at nucleotide position 400 in exon 2, where lysine at position 66 remains unchanged. HLA-C*15:72 differs from HLA-C*15:22 by a nonsynonymous C to A substitution at nucleotide position 796 in exon 3, resulting in an amino acid change from phenylalanine to leucine at position 116. HLA-C*15:74 differs from HLA-C*15:08 by a nonsynonymous C to T substitution at nucleotide position 914 in exon 3, resulting in an amino acid change from arginine to tryptophan at position 156.