SummaryBackgroundSince June, 2012, Middle East respiratory syndrome coronavirus (MERS-CoV) has, worldwide, caused 104 infections in people including 49 deaths, with 82 cases and 41 deaths reported from Saudi Arabia. In addition to confirming diagnosis, we generated the MERS-CoV genomic sequences obtained directly from patient samples to provide important information on MERS-CoV transmission, evolution, and origin.MethodsFull genome deep sequencing was done on nucleic acid extracted directly from PCR-confirmed clinical samples. Viral genomes were obtained from 21 MERS cases of which 13 had 100%, four 85–95%, and four 30–50% genome coverage. Phylogenetic analysis of the 21 sequences, combined with nine published MERS-CoV genomes, was done.FindingsThree distinct MERS-CoV genotypes were identified in Riyadh. Phylogeographic analyses suggest the MERS-CoV zoonotic reservoir is geographically disperse. Selection analysis of the MERS-CoV genomes reveals the expected accumulation of genetic diversity including changes in the S protein. The genetic diversity in the Al-Hasa cluster suggests that the hospital outbreak might have had more than one virus introduction.InterpretationWe present the largest number of MERS-CoV genomes (21) described so far. MERS-CoV full genome sequences provide greater detail in tracking transmission. Multiple introductions of MERS-CoV are identified and suggest lower R0 values. Transmission within Saudi Arabia is consistent with either movement of an animal reservoir, animal products, or movement of infected people. Further definition of the exposures responsible for the sporadic introductions of MERS-CoV into human populations is urgently needed.FundingSaudi Arabian Ministry of Health, Wellcome Trust, European Community, and National Institute of Health Research University College London Hospitals Biomedical Research Centre.

The Middle East respiratory syndrome coronavirus (MERS-CoV) was first documented in the Kingdom of Saudi Arabia (KSA) in 2012 and, to date, has been identified in 180 cases with 43% mortality. In this study, we have determined the MERS-CoV evolutionary rate, documented genetic variants of the virus and their distribution throughout the Arabian peninsula, and identified the genome positions under positive selection, important features for monitoring adaptation of MERS-CoV to human transmission and for identifying the source of infections. Respiratory samples from confirmed KSA MERS cases from May to September 2013 were subjected to whole-genome deep sequencing, and 32 complete or partial sequences (20 were ≥99% complete, 7 were 50 to 94% complete, and 5 were 27 to 50% complete) were obtained, bringing the total available MERS-CoV genomic sequences to 65. An evolutionary rate of 1.12 × 10−3 substitutions per site per year (95% credible interval [95% CI], 8.76 × 10−4; 1.37 × 10−3) was estimated, bringing the time to most recent common ancestor to March 2012 (95% CI, December 2011; June 2012). Only one MERS-CoV codon, spike 1020, located in a domain required for cell entry, is under strong positive selection. Four KSA MERS-CoV phylogenetic clades were found, with 3 clades apparently no longer contributing to current cases. The size of the population infected with MERS-CoV showed a gradual increase to June 2013, followed by a decline, possibly due to increased surveillance and infection control measures combined with a basic reproduction number (R0) for the virus that is less than 1.

The Saudi Arabian Ministry of Health implemented a pro-active surveillance programme for Middle East respiratory syndrome (MERS) coronavirus (MERS-CoV). We report MERS-CoV data from 5065 Kingdom of Saudi Arabia individuals who were screened for MERS-CoV over a 12-month period. From 1 October 2012 to 30 September 2013, demographic and clinical data were prospectively collected from all laboratory forms received at the Saudi Arabian Virology reference laboratory. Data were analysed by referral type, age, gender, and MERS-CoV real-time PCR test results. Five thousand and 65 individuals were screened for MER-CoV: hospitalized patients with suspected MERS-CoV infection (n = 2908, 57.4%), healthcare worker (HCW) contacts (n = 1695; 33.5%), and family contacts of laboratory-confirmed MERS cases (n = 462; 9.1%). Eleven per cent of persons tested were children (<17 years of age). There were 108 cases (99 adults and nine children) of MERS-CoV infection detected during the 12-month period (108/5065, 2% case detection rate). Of 108 cases, 45 were females (six children and 39 adults) and 63 were males (three children and 60 adults). Of the 99 adults with MERS-CoV infection, 70 were hospitalized patients, 19 were HCW contacts, and ten were family contacts. There were no significant increases in MERS-CoV detection rates over the 12-month period: 2.6% (19/731) in July 2013, 1.7% (19/1100) in August 2013, and 1.69% (21/1238) in September 2013. Male patients had a significantly higher MERS-CoV infection rate (63/2318, 2.7%) than females (45/2747, 1.6%) (p 0.013). MERS-CoV rates remain at low levels, with no significant increase over time. Pro-active surveillance for MERS-CoV in newly diagnosed patients and their contacts will continue.

MERS-CoV disease is not limited to adults. Most cases of childhood MERS-CoV infection were asymptomatic and tested positive during contact investigation of older patients. Severe disease can occur in children with underlying conditions.

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Influenza A H1N2 viruses, which emerged during 2001, are genetic reassortants between H1N1 and H3N2 subtype viruses which have cocirculated in the human population since 1977. They possess a H1 hemagglutinin antigenically and genetically similar to contemporary A/New Caledonia/20/99 (H1N1)-like viruses and seven genes closely related to those of recent A/Moscow/10/99 (H3N2)-like viruses. The viruses have spread to many regions of the world and have predominated over H1N1 viruses in several countries. Since half of the amino acid changes which accumulated in the HAs of H1N1 viruses since 1995 are in residues implicated in receptor binding, functional changes in the H1 HA may have facilitated its replacement of the H3 HA and may contribute to the future epidemiologic significance of these H1N2 viruses.

The Gulf Cooperation Council Center for Infection Control (GCC-IC) has placed the emergence of antimicrobial resistance (AMR) on the top of its agenda for the past four years. The board members have developed the initial draft for the GCC strategic plan for combating AMR in 2014. The strategic plan stems from the WHO mandate to combat AMR at all levels. The need for engaging a large number of stakeholders has prompted the GCC-IC to engage a wider core of professionals in finalizing the plan. A multi-disciplinary group of more than 40 experts were then identified. And a workshop was conducted in Riyadh January 2015 and included, for the first time, representation of relevant ministries and agencies as well as international experts in the field. Participants worked over a period of two and a half days in different groups. International experts shared the global experiences and challenges in addressing human, food, animal, and environmental aspects of controlling AMR. Participants were then divided into 4 groups each to address the human, animal, microbiological and diagnostic, or the environmental aspect of AMR. At the end of the workshop, the strategic plan was revised and endorsed by all participants. The GCC-IC board members then approved it as the strategic plan for AMR. The document produced here is the first GCC strategic plan addressing AMR, which shall be adopted by GCC countries to develop country-based plans and related key performance indicators (KPIs). It is now the role of each country to identify the body that will be accountable for implementing the plan at the country level.

The 2009 H1N1 influenza virus (formerly known as swine flu) first appeared in Mexico and the United States in March and April 2009 and has swept the globe with unprecedented speed as a result of airline travel. On June 11, 2009, the World Health Organization raised its pandemic level to the highest level, Phase 6, indicating widespread community transmission on at least two continents. The 2009 H1N1 virus contains a unique combination of gene segments from human, swine and avian influenza A viruses. Children and young adults appear to be the most affected, perhaps reflecting protection in the elderly owing to exposure to H1N1 strains before 1957. Most clinical disease is relatively mild but complications leading to hospitalization, with the need for intensive care, can occur, especially in very young children, during pregnancy, in morbid obesity, and in those with underlying medical conditions such as chronic lung and cardiac diseases, diabetes, and immunosuppression. Bacterial co-infection has played a significant role in fatal cases. The case of fatality has been estimated at around 0.4%. Mathematical modeling suggests that the effect of novel influenza virus can be reduced by immunization, but the question remains: can we produce enough H1N1 vaccine to beat the pandemic?