Letters

by S Gee, S Cotter, D O’Flanagan, on behalf of the national incident management tea

Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

We show the distribution of SARS-CoV-2 genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three available genomic nomenclature systems for SARS-CoV-2 to all sequence data from the WHO European Region available during the COVID-19 pandemic until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation. We provide a comparison of the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2.Peer reviewe

Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

We show the distribution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three genomic nomenclature systems to all sequence data from the World Health Organization European Region available until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation, compare the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2

Epidemiological data of Coxsackie and Echo viruses in N. Greece

<p>The circulation of Coxsackie and Echo viruses is investigated in a period of fourteen years. Clinical data were reported and IgM and IgG specific antibodies were detected by ELISA and IFA techniques for 6654 specimens (5368 for Coxsackie, 1286 for Echo) collected in hospitals of N. Greece. The results revealed 653 IgM positive and 2234 IgG positive specimens for Coxsackie as well as 98 IgM positive and 189 IgG positive specimens for Echo viruses. Coxsackie and Echo infections affected both genders and a statistically significant increase of IgM Coxsackie antibodies in females was found. Regarding the Coxsackie infections, 34.6% happened in spring, while Echo infections happened mainly in autumn and winter (62.2%). The infection rate generally decreased with age except for Echo viruses that infected the 19-60y individuals more than the 0-6y ones. Coxsackie viruses most often caused respiratory illness (IgM 19.9%) presenting statistically significant difference from the rest of clinical manifestations, while Echo mostly caused gastroenteritis (20.4%) though without total statistical significance. No statistically significant difference was observed for clinical manifestations between males and females.</p&gt

Evaluation of sample pooling in SARS-CoV-2 testing using the Taq- Path™ COVID-19 Combo Kit

<p>The worldwide spread of SARS-CoV-2 has led to a high demand for COVID-19 molecular testing. However, mass testing is causing heavy laboratory backlogs, reagent shortages and laboratory personnel burnouts. To overcome these difficulties, testing samples in pools has been shown to be an effective strategy for low COVID-19 prevalence regions. In the present study, we evaluated the effectiveness of pooled nasophryngeal specimens testing using the TaqPath COVID-19 Combo Kit. Four confirmed positive samples were tested individualy and also used as positive spike-ins for the pooling protocol. Each one was pooled with four different confirmed negatives to a total of five samples per pool. Five microliters of RNA were used for each reaction, whereas reactions with increased RNA input (10 and 15 ul) were performed to investigate probable effects on sensitivity and assay performance. All samples which were tested either individually or in pools resulted positive. Our results showed that testing in pools of five samples using the TaqPath COVID-19 Combo Kit is a reliable option for SARSCoV-2 detection, especially when mass testing is urgently needed.</p&gt

Kuzey Yunenistanda Pandemik H1N1 2009 Enfeksiyonun Epidemiyolojik Surveyans�

In response to the health emergency declared by the World Health Organization (WHO) in April 2009, Greece set up an enhanced surveillance system for pandemic H1N1 2009 by the 30th of April 2009. During the period of study (weeks 19-53), 3.903 suspected pharyngeal were examined at the National Influenza Centre for northern Greece. 1439 specimens were confirmed as pandemic H1N1 2009 (37.23%) infections. The hospitalization rate increased dramatically during November and December, while the death rate was 1.3%.Dünya sağlık örgütünün 2009 yılının Nisan ayında bildirmiş olduğu acil durumda Yunanistan pandemik H1N1 2009 enfeksiyonu için surveyans sistemini geliştirdi. Çalışma dönemi içinde (19-53 hafta) 3903 şüpheli faringeali Ulusal Kuzey Yunanistan İnfluenza Merkezinde tarandı. 1439 örnek pandemik H1N1 2009 olarak tespit edildi (%37.23). Hastaneye yatma oranı Kasım ve Aralık ayında dramatik olarak artmıştır. Ölüm oranı %1.3 idi

EUROPEAN CENTRE FOR DISEASE PREVENTION

A(H5N1): an overview of the current situation

Acute respiratory tract infections in SARS-CoV-2-negative children during the COVID-19 pandemic

<p>During the early stage of coronavirus disease 2019 (COVID-19) pandemic, detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was a priority; however, influenza viruses and RSV continued to cause seasonal epidemics complicating the diagnostic strategies. In the present study we estimated the proportion of SARS-CoV-2-negative pediatric cases attributed to respiratory syncytial virus (RSV) and influenza viruses during a 3-month period after the identification of the first COVID-19 case in Greece. Ninety SARS-CoV-2-negative children hospitalized with acute respiratory tract infection were included in the study. Following a SARS-CoV-2 negative result, the samples were tested by molecular methods for detection of RSV and influenza viruses. The positive samples were further tested for identification of the subtype of the viruses.</p><p>We detected RSV or influenza viruses in 22 (24.4%) samples. Influenza virus was detected in 13 (14.4%) patients (two of type A and 11 of type B), and RSV (all RSV-A) was detected in 9 (10%) patients.</p><p>In conclusion, a syndromic approach for simultaneous detection of at least influenza virus, SARS-CoV-2 and RSV will be beneficial for the prompt implementation of appropriate hospital management including antiviral treatment and isolation measures.</p&gt

Ιnfluenza A(H3N2) genetic variants in vaccinated patients in northern Greece

Background Influenza A(H3N2) viruses predominated during the influenza 2016/2017 season and showed extensive genetic diversification. A high vaccination failure rate was noticed during the 2016/17 season in Greece, especially among the elderly. Objectives The scope of the study was to investigate the genetic characteristics of A(H3N2) circulating viruses and viruses detected in vaccinated patients. Study design Virus samples originated from vaccinated and unvaccinated patients, obtained at the National Influenza Centre for northern Greece. Phylogenetic analysis and comparison of the haemagglutinin gene of the viruses to the vaccine virus A/Hong Kong/4801/2014 was performed. Results The majority of analysed viruses are clustering in the genetic clade 3C.2a, and in a newly emerged subclade, designated as 3C.2a1. The highest proportion of viruses detected in vaccinated patients fell into a distinct subcluster within the 3C.2a1 subclade, which is characterised by the amino acid substitutions N122D and T135 K in haemagglutinin. Conclusions Viruses that belong to the 3C.2a clade are generally considered to resemble antigenically to the northern hemisphere vaccine component A/Hong Kong/4801/2014 that was recommended by WHO to be included also into the 2017/18 vaccine. However, viruses belonging to a specific 3C.2a1 subcluster was extensively circulating in northern Greece and among vaccinated individuals. Both substitutions carried by this strain were located on antigenic sites and caused losses of N-linked glycosylation sites of the virus, which could potentially affect viral antigenicity. Further studies are needed to determine the antigenicity of this variant strain and its possible implication in vaccine effectiveness. © 201