31 research outputs found
Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example
Whole genome sequencing can be used to characterize and to trace viral outbreaks. Nanopore-based whole genome sequencing protocols have been described for several different viruses. These approaches utilize an overlapping amplicon-based approach which can be used to target a specific virus or group of genetically related viruses. In addition to confirmation of the virus presence, sequencing can be used for genomic epidemiology studies, to track viruses and unravel origins, reservoirs and modes of transmission. For such applications, it is crucial to understand possible effects of the error rate associated with the platform used. Routine application in clinical and public health settings require that this is documented with every important change in the protocol. Previously, a protocol for whole genome Usutu virus sequencing on the nanopore sequencing platform was validated (R9.4 flowcell) by direct comparison to Illumina sequencing. Here, we describe the method used to determine the required read coverage, using the comparison between the R1
Global status of Middle East respiratory syndrome coronavirus in dromedary camels: a systematic review
Dromedary camels have been shown to be the main reservoir for human Middle East respiratory syndrome (MERS) infections. This systematic review aims to compile and analyse all
published data on MERS-coronavirus (CoV) in the global camel population to provide an
overview of current knowledge on the distribution, spread and risk factors of infections in
dromedary camels. We included original research articles containing laboratory evidence of
MERS-CoV infections in dromedary camels in the field from 2013 to April 2018. In general,
camels only show minor clinical signs of disease after being infected with MERS-CoV.
Serological evidence of MERS-CoV in camels has been found in 20 countries, with molecular
evidence for virus circulation in 13 countries. The seroprevalence of MERS-CoV antibodies
increases with age in camels, while the prevalence of viral shedding as determined by
MERS-CoV RNA detection in nasal swabs decreases. In several studies, camels that were
sampled at animal markets or quarantine facilities were seropositive more often than camels
at farms as well as imported camels vs. locally bred camels. Some studies show a relatively
higher seroprevalence and viral detection during the cooler winter months. Knowledge of
the animal reservoir of MERS-CoV is essential to develop intervention and control measures
to prevent human infections
Landscape level associations between birds, mosquitoes and microclimates: possible consequences for disease transmission?
oai:scholarlypublications.universiteitleiden.nl:item_3731020Environmental Biolog
Drivers of MERS-CoV Emergence in Qatar
MERS-CoV (Middle East respiratory syndrome corona virus) antibodies were detected
in camels since 1983, but the first human case was only detected in 2012. This study sought to
identify and quantify possible drivers for the MERS-CoV emergence and spillover to humans. A list
of potential human, animal and environmental drivers for disease emergence were identified from
literature. Trends in possible drivers were analyzed from national and international databases,
and through structured interviews with experts in Qatar. The discovery and exploitation of oil
and gas led to a 5-fold increase in Qatar GDP coupled with a 7-fold population growth in the
past 30 years. The lifestyle gradually transformed from Bedouin life to urban sedentary life,
along with a sharp increase in obesity and other comorbidities. Owing to substantial governmental
support, camel husbandry and competitions flourished, exacerbating the already rapidly occurring
desertification that forced banning of free grazing in 2005. Consequently, camels were housed in
compact barns alongside their workers. The transition in husbandry leading to high density camel
farming along with increased exposure to humans, combined with the increase of camel movement for
the racing and breeding industry, have led to a convergence of factors driving spillover of MERS-CoV
from camels to humans
Qatar experience on One Health approach for middle-east respiratory syndrome coronavirus, 2012-2017: A viewpoint
The emergence of the Middle East Respiratory Syndrome Corona Virus (MERS-CoV) in the Middle East in 2012
was associated with an overwhelming uncertainty about its epidemiological and clinical characteristics. Once
dromedary camels (Camelus dromedarius) was found to be the natural reservoir of the virus, the public health
systems across the Arabian Peninsula encountered an unprecedented pressure to control its transmission. This
view point describes how the One Health approach was used in Qatar to manage the MERS-CoV outbreak during
the period 2012–2017.
One Health focuses on the association between the human, animals and environment sectors for total health
and wellbeing of these three sectors. To manage the MERS outbreak in Qatar through a One Health approach, the
Qatar National Outbreak Control Taskforce (OCT) was reactivated in November 2012. The animal health sector
was invited to join the OCT. Later on, technical expertise was requested from the WHO, FAO, CDC, EMC, and
PHE. Subsequently, a comprehensive One Health roadmap was delivered through leadership and coordination;
surveillance and investigation; epidemiological studies and increase of local diagnostic capacity.
The joint OCT, once trained had easy access to allocated resources and high risk areas to provide more
evidence on the potential source of the virus and to investigate all reported cases within 24–48 h. Lack of
sufficient technical guidance on veterinary surveillance and poor risk perception among the vulnerable population constituted major obstacles to maintain systematic One Health performance
First molecular analysis of rabies virus in Qatar and clinical cases imported into Qatar, a case report
Identifying the origin of the rabies virus (RABV) infection may have significant implications for control measures. Here, we identified the source of a RABV infection of two Nepalese migrants in Qatar by comparing their RABV genomes with RABV genomes isolated from the brains of a RABV infected camel and fox from Qatar
SARS-CoV-2 infection in farmed minks, the Netherlands, April and May 2020
Respiratory disease and increased mortality occurred in minks on two farms in the Netherlands, with interstitial pneumonia and SARS-CoV-2 RNA in organ and swab samples. On both farms, at least one worker had coronavirus disease-associated symptoms before the outbreak. Variations in mink-derived viral genomes showed between-mink transmission and no infection link between the farms. Inhalable dust contained viral RNA, indicating possible exposure of workers. One worker is assumed to have attracted the virus from mink
Transmission of SARS-CoV-2 on mink farms between humans and mink and back to humans
Animal experiments have shown that nonhuman primates, cats, ferrets, hamsters, rabbits, and bats can be infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In addition, SARS-CoV-2 RNA has been detected in felids, mink, and dogs in the field. Here, we describe an in-depth investigation using whole-genome sequencing of outbreaks on 16 mink farms and the humans living or working on these farms. We conclude that the virus was initially introduced by humans and has since evolved, most likely reflecting widespread circulation among mink in the beginning of the infection period, several weeks before detection. Despite enhanced biosecurity, early warning surveillance, and immediate culling of animals in affected farms, transmission occurred between mink farms in three large transmission clusters with unknown modes of transmission. Of the tested mink farm residents, employees, and/or individuals with whom they had been in contact, 68% had evidence of SARS-CoV-2 infection. Individuals for which whole genomes were available were shown to have been infected with strains with an animal sequence signature, providing evidence of animal-to-human transmission of SARS-CoV-2 within mink farms
COVID-19 in health-care workers in three hospitals in the south of the Netherlands: a cross-sectional study
Background: 10 days after the first reported case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in the Netherlands (on Feb 27, 2020), 55 (4%) of 1497 health-care workers in nine hospitals located in the south of the Netherlands had tested positive for SARS-CoV-2 RNA. We aimed to gain insight in possible sources of infection in health-care workers. Methods: We did a cross-sectional study at three of the nine hospitals located in the south of the Netherlands. We screened health-care workers at the participating hospitals for SARS-CoV-2 infection, based on clinical symptoms (fever or mild respiratory symptoms) in the 10 days before screening. We obtained epidemiological data through structured interviews with health-care workers and combined this information with data from whole-genome sequencing of SARS-CoV-2 in clinical samples taken from health-care workers and patients. We did an in-depth analysis of sources and modes of transmission of SARS-CoV-2 in health-care workers and patients. Findings: Between March 2 and March 12, 2020, 1796 (15%) of 12 022 health-care workers were screened, of whom 96 (5%) tested positive for SARS-CoV-2. We obtained complete and near-complete genome sequences from 50 health-care workers and ten patients. Most sequences were grouped in three clusters, with two clusters showing local circulation within the region. The noted patterns were consistent with multiple introductions into the hospitals through community-acquired infections and local amplification in the community. Interpretation: Although direct transmission in the hospitals cannot be ruled out, our data do not support widespread nosocomial transmission as the source of infection in patients or health-care workers. Funding: EU Horizon 2020 (RECoVer, VEO, and the European Joint Programme One Health METASTAVA), and the National Institute of Allergy and Infectious Diseases, National Institutes of Health
Weighing serological evidence of human exposure to animal influenza viruses − A literature review
Assessing influenza A virus strains circulating in animals and their potential to cross the species barrier and cause human infections is important to improve human influenza surveillance and preparedness. We reviewed studies describing serological evidence of human exposure to animal influenza viruses. Comparing serological data is difficult due to a lack of standardisation in study designs and in laboratory methods used in published reports. Therefore, we designed a scoring system to assess and weigh specificity of obtained serology results in the selected articles. Many studies report reliable evidence of antibodies to swine influenza viruses among persons occupationally exposed to pigs. Most avian influenza studies target H5, H7 and H9 subtypes and most serological evidence of human exposure to avian influenza viruses is reported for these subtypes. Avian influenza studies receiving a low grade in this review often reported higher seroprevalences in humans compared with studies with a high grade. Official surveillance systems mainly focus on avian H5 and H7 viruses. Swine influenza viruses and avian subtypes other than H5 and H7 (emphasising H9) should be additionally included in official surveillance systems. Surveillance efforts should also be directed towards understudied geographical areas, such as Africa and South America