Genomic sequencing for epidemic and pandemic preparedness and response: EMRO's vision and strategic interventions.

Whole-genome sequencing (WGS) is an approach for studying and analysing the entire genomic sequence of pathogens. It provides the most comprehensive characterization of an organism's genetic make-up. In January 2020, scientists used next-generation sequencing (NGS) as one of several sequencing technologies to study severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and to reveal the first genetic makeup of this new virus only 11 days after the first cluster of cases due to the COVID-19 pandemic was reported. This crucial information was vital to the subsequent rapid development of test kits, vaccines and treatment regimens to respond to the pandemic. The sequencing information, later as the pandemic evolved, became essential for informing public health policies through monitoring and characterization of SARS-CoV-2 variants.

COVID-19 morbidity in Afghanistan: a nationwide, population-based seroepidemiological study.

OBJECTIVE: The primary objectives were to determine the magnitude of COVID-19 infections in the general population and age-specific cumulative incidence, as determined by seropositivity and clinical symptoms of COVID-19, and to determine the magnitude of asymptomatic or subclinical infections. DESIGN, SETTING AND PARTICIPANTS: We describe a population-based, cross-sectional, age-stratified seroepidemiological study conducted throughout Afghanistan during June/July 2020. Participants were interviewed to complete a questionnaire, and rapid diagnostic tests were used to test for SARS-CoV-2 antibodies. This national study was conducted in eight regions of Afghanistan plus Kabul province, considered a separate region. The total sample size was 9514, and the number of participants required in each region was estimated proportionally to the population size of each region. For each region, 31-44 enumeration areas (EAs) were randomly selected, and a total of 360 clusters and 16 households per EA were selected using random sampling. To adjust the seroprevalence for test sensitivity and specificity, and seroreversion, Bernoulli's model methodology was used to infer the population exposure in Afghanistan. OUTCOME MEASURES: The main outcome was to determine the prevalence of current or past COVID-19 infection. RESULTS: The survey revealed that, to July 2020, around 10 million people in Afghanistan (31.5% of the population) had either current or previous COVID-19 infection. By age group, COVID-19 seroprevalence was reported to be 35.1% and 25.3% among participants aged ≥18 and 5-17 years, respectively. This implies that most of the population remained at risk of infection. However, a large proportion of the population had been infected in some localities, for example, Kabul province, where more than half of the population had been infected with COVID-19. CONCLUSION: As most of the population remained at risk of infection at the time of the study, any lifting of public health and social measures needed to be considered gradually.

WHO's support for COVID-19 research and knowledge management in the Eastern Mediterranean Region.

Health research, innovation and knowledge management remain major priorities of the WHO's response to the COVID-19 pandemic. WHO's Eastern Mediterranean Regional Office (EMRO) supports priority research initiatives that address gaps in current knowledge regarding the COVID-19 pandemic. Through a specific call for proposals, 122 research proposals were received and reviewed in 2020, of which 17 were recommended for funding from eight countries. Ten countries in the region participated in the global solidarity trial to assess potential therapies for COVID-19. In addition, WHO advocated for early serological and epidemiological investigations ('COVID-19 Unity Studies') on the general population, healthcare workers, pregnant women and neonates, and extending technical, financial and material support for them.Starting in early 2020, scholarly articles on COVID-19 have been published in every issue of the Eastern Mediterranean Health Journal More than 6300 publications on COVID-19 were made available on the WHO knowledge management portal in the last year alone. WHO is also supporting countries in conducting studies to assess the field effectiveness of vaccines deployed nationally. To build and strengthen country capacities, regional webinars and intercountry meetings were conducted on research ethics, national health information systems and evidence-based health policy making. With support from WHO EMRO's new research and knowledge management pillar, countries in the region were well equipped to contribute to a global understanding of the novel virus's characteristics, as well as employ a national response based on informed evidence.

Influenza activity in the Eastern Mediterranean Region (EMR) in 2020-2021 amidst the COVID-19 pandemic.

INTRODUCTION: A global reduction in influenza virus activity during the COVID-19 pandemic has been observed, including in the Eastern Mediterranean Region (EMR). However, these changes have not been thoroughly evaluated scientifically in the EMR. OBJECTIVE: We aim to present data on seasonal influenza activity during the pre-pandemic period (2016-2019) and compare it to the pandemic period (2020-2021) in EM countries. METHODS: Epidemiological and virological influenza surveillance data were retrieved from both WHO FluNet and EMFLU networks. Four pre-pandemic analytical periods were used in the comparative analysis. We compiled and calculated weekly aggregated epidemiological data on the number of enrolled patients, number of tested specimens and number of positive influenza specimens. RESULTS: 19 out of the 22 countries of the EMR have functioning sentinel influenza surveillance systems, and these countries report the influenza data to WHO through FluNet and EMFLU. The number of enrolled patients and tested specimens increased gradually from 51 384 and 50 672, respectively, in 2016-2017 analytical period to 194 049 enrolled patients and 124 697 tested specimens in 2019-2020. A decrease has been witnessed in both enrolled patients and tested specimens in 2020-2021 'pandemic period' (166 576 and 44 764, respectively). By comparing influenza activity of analytical period 2020-2021 with that of 2016-2019 analytical periods, we found that there has been a decrease in influenza positivity rate in the EMR by 89%. CONCLUSION: The implementation of non-pharmaceutical interventions to control the COVID-19 pandemic may have also impacted the spread of influenza viruses. The low circulation of influenza viruses during 2020-2021 and the associated potential immunity gap may result in increased transmission and severity of post-pandemic influenza seasons. This necessitates high vigilance to continuous data and virus sharing to monitor circulating viruses in a timely fashion to reduce the intensity and severity of future influenza epidemics.

Transmission of SARS-CoV-2 in standardised first few X cases and household transmission investigations: A systematic review and meta-analysis.

We aimed to estimate the household secondary infection attack rate (hSAR) of SARS-CoV-2 in investigations aligned with the WHO Unity Studies Household Transmission Investigations (HHTI) protocol. We conducted a systematic review and meta-analysis according to PRISMA 2020 guidelines. We searched Medline, Embase, Web of Science, Scopus and medRxiv/bioRxiv for "Unity-aligned" First Few X cases (FFX) and HHTIs published 1 December 2019 to 26 July 2021. Standardised early results were shared by WHO Unity Studies collaborators (to 1 October 2021). We used a bespoke tool to assess investigation methodological quality. Values for hSAR and 95% confidence intervals (CIs) were extracted or calculated from crude data. Heterogeneity was assessed by visually inspecting overlap of CIs on forest plots and quantified in meta-analyses. Of 9988 records retrieved, 80 articles (64 from databases; 16 provided by Unity Studies collaborators) were retained in the systematic review; 62 were included in the primary meta-analysis. hSAR point estimates ranged from 2% to 90% (95% prediction interval: 3%-71%; I 2 = 99.7%); I 2 values remained >99% in subgroup analyses, indicating high, unexplained heterogeneity and leading to a decision not to report pooled hSAR estimates. FFX and HHTI remain critical epidemiological tools for early and ongoing characterisation of novel infectious pathogens. The large, unexplained variance in hSAR estimates emphasises the need to further support standardisation in planning, conduct and analysis, and for clear and comprehensive reporting of FFX and HHTIs in time and place, to guide evidence-based pandemic preparedness and response efforts for SARS-CoV-2, influenza and future novel respiratory viruses.

SARS-CoV-2 seroprevalence in Aden, Yemen: a population-based study.

BACKGROUND: In Yemen, initial surveillance of coronavirus disease 2019 (COVID-19) focused primarily on patients with symptoms or severe disease. The full spectrum of the disease remains unclear. To the best of the authors' knowledge, this is the first seroprevalence study performed in Yemen. METHODS: This cross-sectional investigation included 2001 participants from all age groups from four districts in Aden, southern Yemen. A multi-stage sampling method was used. Data were collected using a well-structured questionnaire, and blood samples were taken. Healgen COVID-19 IgG/IgM Rapid Diagnostic Test (RDT) Cassettes were used in all participants. All positive RDTs and 14% of negative RDTs underwent enzyme-linked immunosorbent assay (ELISA) testing (WANTAI SARS-CoV-2 Ab ELISA Kit) for confirmation. RESULTS: In total, 549 of 2001 participants were RDT positive and confirmed by ELISA, giving a prevalence of COVID-19 of 27.4%. The prevalence of immunoglobulin G was 25%. The prevalence of asymptomatic COVID-19 in the entire study group was 7.9%. The highest prevalence was observed in Al-Mansurah district (33.4%). Regarding sociodemographic factors, the prevalence of COVID-19 was significantly higher among females, housewives and subjects with a history of contact with a COVID-19 patient: 32%, 31% and 39%, respectively. CONCLUSION: This study found high prevalence of COVID-19 in the study population. Household transmission was common.