ABSTRACT
Background: In fall 2020 when schools in the Netherlands operated under a limited set of COVID-19 measures, we conducted outbreaks studies in four secondary schools to gain insight in the level of school transmission and the role of SARS-CoV-2 transmission via air and surfaces. Methods: Outbreak studies were performed between 11 November and 15 December 2020 when the wild-type variant of SARS-CoV-2 was dominant. Clusters of SARS-CoV-2 infections within schools were identified through a prospective school surveillance study. All school contacts of cluster cases, irrespective of symptoms, were invited for PCR testing twice within 48 hrs and 4-7 days later. Combined NTS and saliva samples were collected at each time point along with data on recent exposure and symptoms. Surface and active air samples were collected in the school environment. All samples were PCR-tested and sequenced when possible. Results: Out of 263 sampled school contacts, 24 tested SARS-CoV-2 positive (secondary attack rate 9.1%), of which 62% remained asymptomatic and 42% had a weakly positive test result. Phylogenetic analysis on 12 subjects from 2 schools indicated a cluster of 8 and 2 secondary cases, respectively, but also other distinct strains within outbreaks. Of 51 collected air and 53 surface samples, none were SARS-CoV-2 positive. Conclusion: Our study confirmed within school SARS-CoV-2 transmission and substantial silent circulation, but also multiple introductions in some cases. Absence of air or surface contamination suggests environmental contamination is not widespread during school outbreaks.
Subject(s)
COVID-19 , Severe Acute Respiratory SyndromeABSTRACT
In the first wave of the COVID-19 pandemic (April 2020), SARS-CoV-2 was detected in farmed minks and genomic sequencing was performed on mink farms and farm personnel. Here, we describe the outbreak and use sequence data with Bayesian phylodynamic methods to explore SARS-CoV-2 transmission in minks and related humans on farms. High number of farm infections (68/126) in minks and farm related personnel (>50% of farms) were detected, with limited spread to the general human population. Three of five initial introductions of SARS-CoV-2 lead to subsequent spread between mink farms until November 2020. The largest cluster acquired a mutation in the receptor binding domain of the Spike protein (position 486), evolved faster and spread more widely and longer. Movement of people and distance between farms were statistically significant predictors of virus dispersal between farms. Our study provides novel insights into SARS-CoV-2 transmission between mink farms and highlights the importance of combing genetic information with epidemiological information at the animal-human interface.
Subject(s)
COVID-19ABSTRACT
Background: The Dutch province of Limburg borders the German district of Heinsberg, which had a large cluster of COVID-19 cases linked to local carnival activities in February, before any cases were reported in the Netherlands. However, Heinsberg was not included as an area reporting local or community transmission per the national case definition at the time. In early March, two residents from a long-term care facility (LTCF) in Sittard, a Dutch town located in close vicinity to the district of Heinsberg, started experiencing respiratory symptoms and were admitted to the regional hospital at which they were tested for COVID-19. Introduction of the virus could have occurred following the carnival activities in the surrounding area by LTCF visitors or health care workers.Methods: Surveys and semi-structured oral interviews were conducted with all present residents by health care workers during regular points of care for information on new or unusual signs and symptoms of disease. Both throat and nasopharyngeal swabs were taken from residents suspect of COVID-19 for the detection of SARS-CoV-2 by Real-time Polymerase Chain Reaction and whole genome sequencing was performed using a SARS-CoV-2 specific amplicon-based Nanopore sequencing approach. Additionally, twelve random residents were sampled for possible asymptomatic infections.Results: Since the start of the outbreak, nineteen (19%) residents tested positive for COVID-19. Eleven samples were sequenced, along with three random samples from COVID-19 patients hospitalized in the regional hospital at the time of the LTCF outbreak. Conclusions: All samples were linked to COVID-19 cases from the cross-border region of Heinsberg, Germany. Symptoms were reported only in about two third of the cases, and tended to be generally mild. We therefore recommend low-level screening of HCWs and residents following a confirmed COVID-19 case, even in the absence of symptoms. Since the LTCF residents who tested positive did not meet the criteria for suspect cases of COVID-19 at the time, this highlights the importance of cooperation among cross-border partners in order to establish a coordinated implementation of infection control measures in the region on top of national guidelines to limit the spread of infectious diseases such as COVID-19.
Subject(s)
COVID-19 , Ataxia , Communicable DiseasesABSTRACT
The current SARS-CoV-2 pandemic has rapidly become a major global health problem for which public health surveillance is crucial to monitor virus spread. Given the presence of viral RNA in feces in around 40% of infected persons, wastewater-based epidemiology has been proposed as an addition to disease-based surveillance to assess the spread of the virus at the community level. Here we have explored the possibility of using next-generation sequencing (NGS) of sewage samples to evaluate the diversity of SARS-CoV-2 at the community level from routine wastewater testing, and compared these results with the virus diversity in patients from the Netherlands and Belgium. Phylogenetic analysis revealed the presence of viruses belonging to the most prevalent clades (19A, 20A and 20B) in both countries. Clades 19B and 20C were not identified, while they were present in clinical samples during the same period. Low frequency variant (LFV) analysis showed that some known LFVs can be associated with particular clusters within a clade, different to those of their consensus sequences, suggesting the presence of at least 2 clades within a single sewage sample. Additionally, combining genome consensus and LFV analyses we found a total of 57 unique mutations in the SARS-CoV-2 genome which have not been described before. In conclusion, this work illustrates how NGS analysis of wastewater can be used to approximate the diversity of SARS-CoV-2 viruses circulating in a community.
ABSTRACT
Background This study aimed to assess the contribution of asymptomatic and presymptomatic residents and staff in SARS-CoV-2 transmission during a large outbreak in a Dutch nursing home. Methods Observational study in a 185-bed nursing home with two consecutive testing strategies: testing of symptomatic cases only, and weekly facility-wide testing of staff and residents regardless of symptoms. Nasopharyngeal and oropharyngeal testing with RT-PCR for SARs-CoV-2 was conducted with a standardized symptom assessment. Positive samples with a cycle threshold (CT) value below 32 were selected for sequencing. Results 185 residents and 244 staff participated. Sequencing identified one cluster. In the symptom-based test strategy period 3/39 residents were presymptomatic versus 38/74 residents in the period of weekly facility-wide testing (p-value<0.001). In total, 51/59 (91.1%) of SARS-CoV-2 positive staff was symptomatic, with no difference between both testing strategies (p-value 0.763). Loss of smell and taste, sore throat, headache or myalga was hardly reported in residents compared to staff (p-value <0.001). Median Ct-value of presymptomatic residents was 21.3, which did not differ from symptomatic (20.8) or asymptomatic (20.5) residents (p-value 0.624). Conclusions The frequency of a/presymptomatic residents compared to staff suggests that a/presymptomatic residents could be unrecognized symptomatic cases. However, symptomatic and presymptomatic/unrecognized symptomatic residents both have the same potential for viral shedding. The high prevalence symptomatic staff found in facility-wide testing suggests that staff has difficulty attributing their symptoms to possible SARS-CoV-2 infection. Weekly testing was an effective strategy for early identification of SARS-Cov-2 cases, resulting in fast isolation and mitigation of this outbreak.
Subject(s)
COVID-19 , HeadacheABSTRACT
The zoonotic origin of the SARS-CoV-2 pandemic is still unknown. Animal experiments have shown that non-human primates, cats, ferrets, hamsters, rabbits and bats can be infected by 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 of outbreaks on 16 mink farms and humans living or working on these farms, using whole genome sequencing. We conclude that the virus was initially introduced from humans and has evolved, most likely reflecting widespread circulation among mink in the beginning of the infection period several weeks prior to detection. At the moment, despite enhanced biosecurity, early warning surveillance and immediate culling of infected farms, there is ongoing transmission between mink farms with three big transmission clusters with unknown modes of transmission. We also describe the first animal to human transmissions of SARS-CoV-2 in mink farms. One sentence summarySARS-CoV-2 transmission on mink farms.
ABSTRACT
BackgroundAn outbreak of COVID-19 in a nursing home in the Netherlands, following an on-site church service held on March 8, 2020, triggered an investigation to unravel sources and chain(s) of transmission.MethodsEpidemiological data were collected from registries and through a questionnaire among church visitors. Symptomatic residents and healthcare workers (HCWs) were tested for SARS-CoV-2 by RT-PCR and subjected to whole genome sequencing (WGS). Sequences from a selection of people from the same area were included as community reference.ResultsAfter the church service, 30 of 39 visitors (77%) developed symptoms; 14 were tested and were positive for COVID-19 (11 residents and 3 non-residents). In the following five weeks, 62 of 300 residents (21%) and 30 of 640 HCWs (5%) tested positive for COVID-19; 21 of 62 residents (34%) died. The outbreak was controlled through a cascade of measures. WGS of samples from residents and HCWs identified a diversity of sequence types, grouped into eight clusters. Seven resident church visitors all were infected with distinct viruses, four of which belonged to two larger clusters in the nursing home.ConclusionsAlthough initial investigation suggested the church service as source of the outbreak, detailed analysis showed a more complex picture, most consistent with widespread regional circulation of the virus in the weeks before the outbreak, and multiple introductions into the nursing home before the visitor ban. The findings underscore the importance of careful outbreak investigations to understand SARS-CoV-2 transmission to develop evidence-based mitigation measures.
Subject(s)
COVID-19 , Genomic InstabilityABSTRACT
In April 2020, respiratory disease and increased mortality were observed in farmed mink on two farms in the Netherlands. In both farms, at least one worker had been found positive for SARS-CoV-2. Necropsies of the mink revealed interstitial pneumonia, and organ and swab samples tested positive for SARS-CoV-2 RNA by qPCR. Variations in viral genomes point at between-mink transmission on the farms and lack of infection link between the farms. Inhalable dust in the mink houses contained viral RNA, indicating possible exposure of workers.
Subject(s)
Respiratory Tract Diseases , Lung Diseases, InterstitialABSTRACT
Background: Ten days after the first reported case of SARS-CoV-2 infection in the Netherlands, 3.9% of healthcare workers (HCWs) in nine hospitals located in the South of the Netherlands tested positive for SARS-CoV-2 RNA. The extent of nosocomial transmission that contributed to the HCW infections was unknown. Methods: We combined epidemiological data, collected by means of structured interviews of HCWs, with whole genome sequencing (WGS) of SARS-CoV-2 in clinical samples from HCWs and patients in three of nine hospitals that participated in the HCW screening, to perform an in-depth analysis of sources and modes of transmission of SARS -CoV-2 in HCWs and patients. Results: A total of 1,796 out of 12,022 HCWs (15%) of the three participating hospitals were screened, based on clinical symptoms, of whom 96 (5%) tested positive for SARS-CoV-2. We obtained complete genome sequences of 50 HCWs and 18 patients. Most sequences grouped in 3 clusters, with 2 clusters displaying local circulation within the region. The observed patterns are most consistent with multiple introductions into the hospitals through community acquired infections, and local amplification in the community. Conclusions: Although direct transmission in the hospitals cannot be ruled out, the data does not support widespread nosocomial transmission as source of infection in patients or healthcare workers.
Subject(s)
COVID-19 , InfectionsABSTRACT
SARS-CoV-2 is a novel coronavirus that has rapidly spread across the globe. In the Netherlands, the first case of SARS-CoV-2 has been notified on the 27th of February. Here, we describe the first three weeks of the SARS-CoV-2 outbreak in the Netherlands, which started with several different introductory events from Italy, Austria, Germany and France followed by local amplification in, and later also, outside the South of the Netherlands. The timely generation of whole genome sequences combined with epidemiological investigations facilitated early decision making in an attempt to control local transmission of SARS-CoV-2 in the Netherlands.