scholarly journals Genome Sequencing of SARS-CoV-2 Allows Monitoring of Variants of Concern through Wastewater

Water ◽  
2021 ◽  
Vol 13 (21) ◽  
pp. 3018
Author(s):  
Malte Herold ◽  
Aymeric Fouquier d′Hérouël ◽  
Patrick May ◽  
Francesco Delogu ◽  
Anke Wienecke-Baldacchino ◽  
...  
Keyword(s):  
Genetic Material ◽  
Population Based ◽  
Epidemiological Surveillance ◽  
Clinical Samples ◽  
Short Read ◽  
Regional Clusters ◽  
Subsequent Time ◽  
Infection Dynamics ◽  
Time Period ◽  
Wastewater Samples

Monitoring SARS-CoV-2 in wastewater has shown to be an effective tool for epidemiological surveillance. More specifically, RNA levels determined with RT-qPCR have been shown to track with the infection dynamics within the population. However, the surveillance of individual lineages circulating in the population based on genomic sequencing of wastewater samples is challenging, as the genetic material constitutes a mixture of different viral haplotypes. Here, we identify specific signature mutations from individual SARS-CoV-2 lineages in wastewater samples to estimate lineages circulating in Luxembourg. We compare circulating lineages and mutations to those detected in clinical samples amongst infected individuals. We show that especially for dominant lineages, the allele frequencies of signature mutations correspond to the occurrence of particular lineages in the population. In addition, we provide evidence that regional clusters can also be discerned. We focused on the time period between November 2020 and March 2021 in which several variants of concern emerged and specifically traced the lineage B.1.1.7, which became dominant in Luxembourg during that time. During the subsequent time points, we were able to reconstruct short haplotypes, highlighting the co-occurrence of several signature mutations. Our results highlight the potential of genomic surveillance in wastewater samples based on amplicon short-read data. By extension, our work provides the basis for the early detection of novel SARS-CoV-2 variants.

scholarly journals Efficient whole genome sequencing of influenza A viruses

2019 ◽  
Author(s):  
Marina Escalera-Zamudio ◽  
Ana Georgina Cobián-Güemes ◽  
Blanca Taboada ◽  
Irma López-Martínez ◽  
Joel Armando Vázquez-Pérez ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Influenza A Virus ◽  
Genome Sequencing ◽  
Influenza A ◽  
Genetic Material ◽  
Influenza Viruses ◽  
Epidemiological Surveillance ◽  
Clinical Samples ◽  
Whole Genome ◽  
Influenza A Viruses

ABSTRACTThe constant threat of emergence for novel pathogenic influenza A viruses with pandemic potential, makes full-genome characterization of circulating influenza viral strains a high priority, allowing detection of novel and re-assorting variants. Sequencing the full-length genome of influenza A virus traditionally required multiple amplification rounds, followed by the subsequent sequencing of individual PCR products. The introduction of high-throughput sequencing technologies has made whole genome sequencing easier and faster. We present a simple protocol to obtain whole genome sequences of hypothetically any influenza A virus, even with low quantities of starting genetic material. The complete genomes of influenza A viruses of different subtypes and from distinct sources (clinical samples of pdmH1N1, tissue culture-adapted H3N2 viruses, or avian influenza viruses from cloacal swabs) were amplified with a single multisegment reverse transcription-PCR reaction and sequenced using Illumina sequencing platform. Samples with low quantity of genetic material after initial PCR amplification were re-amplified by an additional PCR using random primers. Whole genome sequencing was successful for 66% of the samples, whilst the most relevant genome segments for epidemiological surveillance (corresponding to the hemagglutinin and neuraminidase) were sequenced with at least 93% coverage (and a minimum 10x) for 98% of the samples. Low coverage for some samples is likely due to an initial low viral RNA concentration in the original sample. The proposed methodology is especially suitable for sequencing a large number of samples, when genetic data is urgently required for strains characterization, and may also be useful for variant analysis.

scholarly journals Role of children in the transmission of the COVID-19 pandemic: a rapid scoping review

2020 ◽  
Vol 4 (1) ◽  
pp. e000722 ◽  
Author(s):  
Luis Rajmil
Keyword(s):  
Scoping Review ◽  
Population Based ◽  
Epidemiological Surveillance ◽  
Igg Antibody ◽  
Population Based Study ◽  
Time Period ◽  
Spanish Study ◽  
Childhood Population ◽  
Transmission Studies

BackgroundAs a response to the COVID-19 pandemic, most countries have adopted measures of social distance, with the childhood population being one of the main focus of attention in these measures.MethodsA rapid scoping review was carried out by searching PubMed to know if children are more contagious than adults, and the proportion of asymptomatic cases in children. Google Scholar and MedRxiv/bioRxiv were also searched. The time period was restricted from 1 December 2019 until 28 May 2020. Only studies published in English, Italian, French or Spanish were included.ResultsFourteen out of 1099 identified articles were finally included. Studies included cases from China (n=9 to 2143), China and Taiwan (n=536), Korea (n=1), Vietnam (n=1), Australia (n=9), Geneva (n=40), the Netherlands (n=116), Ireland (n=3) and Spain (population-based study of IgG, n=8243). Although no complete data were available, between 15% and 55%–60% were asymptomatic, and 75%–100% of cases were from family transmission. Studies analysing school transmission showed children as not a driver of transmission. Prevalence of COVID-19 IgG antibody in children <15 years was lower than the general population in the Spanish study.ConclusionsChildren are not transmitters to a greater extent than adults. There is a need to improve the validity of epidemiological surveillance to solve current uncertainties, and to take into account social determinants and child health inequalities during and after the current pandemic.

scholarly journals Understanding SARS-CoV-2 Infection and Dynamics with Long Term Wastewater based Epidemiological Surveillance

2021 ◽  
Author(s):  
Athmakuri Tharak ◽  
Harishankar Kopperi ◽  
Manupati Hemalatha ◽  
Uday Kiran ◽  
C. G. Gokulan ◽  
...  
Keyword(s):  
Total Population ◽  
Genetic Material ◽  
Population Level ◽  
Warning Signal ◽  
Domestic Sewage ◽  
Epidemiological Surveillance ◽  
Viral Spread ◽  
Infection Dynamics ◽  
Longitudinal Sampling

Wastewater-based epidemiology (WBE) of SARS-CoV-2 emerged as an advantageous method to study the infection dynamics at substantial population level A temporal glimpse at sewage viral genome helps as diagnostic tool to understand the viral spread at community level. In this study for the long-term epidemiological surveillance we monitored the SARS-CoV-2 genetic material in domestic sewage by adopting the longitudinal sampling to represent a selected community (~1.8 lakhs population which occupies 1.79% of the total population of Hyderabad city) to understand the dynamics of infection Dynamics and spread of COVID-19 outbreak within the selected community were achieved by studying the longitudinal sampling for a specific period of time WBE also promotes clinical scrutiny along with disease detection and management in contrast to an advance warning signal to anticipate outbreaks

scholarly journals COVID-19 infection dynamics revealed by SARS-CoV-2 wastewater sequencing analysis and deconvolution

2021 ◽  
Author(s):  
Vic-Fabienne Schumann ◽  
Rafael Cuadrat ◽  
Emanuel Wyler ◽  
Ricardo Wurmus ◽  
Aylina Deter ◽  
...  
Keyword(s):  
Continuous Monitoring ◽  
Sequencing Analysis ◽  
Sequencing Data ◽  
Actual Case ◽  
Symptomatic Disease ◽  
Infection Dynamics ◽  
Time Period ◽  
Clinical Detection ◽  
Wastewater Samples ◽  
New Mutations

The use of RNA sequencing from wastewater samples is proven to be a valuable way for estimating infection dynamics and circulating lineages of SARS-CoV-2. This approach has the advantage of being independent from patient population testing and symptomatic disease courses. However, it is equally important to develop easily accessible and scalable tools which can highlight critical changes in infection rates and dynamics over time across different locations given the sequencing data from the wastewater. Here we provide the first analysis of variant dynamics in Germany using wastewater sequencing and present PiGx SARS-CoV-2, a bit-by-bit reproducible end-to-end pipeline with comprehensive reports. To our knowledge, this is the first pipeline that includes all steps from raw-data to shareable reports, additional taxonomic analysis, deconvolution and geospatial time series analysis. Using our pipeline on a dataset of wastewater samples, from different locations across Berlin, over the time period from February 2021 to June 2021, we could reconstruct the dynamic of the Variant of Concern (VoC) B.1.1.7 (alpha). Additionally, we detected the unique signature mutation M:T26767C for the VoC B.1.617.2 (delta) and its raise in early June. We also show that SARS-CoV-2 mutation load measured from wastewater sequencing is correlated with actual case numbers and it has potential to be used in a predictive manner. All in all, our study provides additional evidence that systematic wastewater analysis using sequencing and computational methods can be used for modeling the infection dynamics of SARS-CoV-2. In addition, the results show that our tool can be used to tease out new mutations and to detect any emerging new lineages of concern before clinical detection. Our approach can support efforts for establishing continuous monitoring and early-warning projects for COVID-19 or any other infectious disease.

scholarly journals A.07 Characterizing the epidemiology of epilepsy in Saskatchewan, Canada

2018 ◽  
Vol 45 (s2) ◽  
pp. S11-S11
Author(s):  
L Hernandez Ronquillo ◽  
L Thorpe ◽  
P Pahwa ◽  
J Tellez Zenteno
Keyword(s):  
Cohort Study ◽  
Age Groups ◽  
Population Based ◽  
Secular Trends ◽  
Health Administrative Data ◽  
Time Period ◽  
Canadian Population ◽  
Incidence And Mortality ◽  
All Cause Mortality ◽  
Icd Codes

Background: There is no available estimate of the incidence and mortality of epilepsy in all age groups in the Canadian population. This study aimed to measure the incidence, prevalence, mortality and the secular trends for epilepsy in Saskatchewan between 2005 and 2010. Methods: A population-based cohort study was established from Saskatchewan’s provincial health administrative data. The population was followed until termination of coverage, death, or 31 December 2010. Individuals with epilepsy were identified based on ICD codes algorithms from 2005 to 2010. Results: The age-standardized incidence of epilepsy was 62 per 100,000 person-year. The age-standardized incidence rate of epilepsy in self-declared Registered Indians was 122 per 100,000 person-year. There was a significant decrease in the incidence of epilepsy for all groups over the study period. The age-standardized prevalence of epilepsy was 9 per 1,000 people. There was a significant increase in the prevalence of epilepsy over this time period. The adjusted mortality rate was 0.023 per 1000 person-year, and the all-cause Standardized Mortality Ration for epilepsy was 2.45. The SMR remained constant over the six-year period of the study. Conclusions: This study is the first in Canada to measure the incidence and all-cause mortality of epilepsy in all age groups.

scholarly journals Evaluating the genetic variability of rubber hybrid progenies of the two crosses PB260 x RO44/71 and PB260 x RO62/54 by RAPD technique

2019 ◽  
Vol 2 (3) ◽  
pp. 36-43
Author(s):  
Thien Minh Nguyen ◽  
Tien Thi My Pham
Keyword(s):  
Genetic Variation ◽  
Genetic Variability ◽  
Genetic Similarity ◽  
Field Experiments ◽  
Agronomic Traits ◽  
Genetic Relationships ◽  
Genetic Material ◽  
Population Based ◽  
Shannon Index ◽  
Polymorphic Bands

The agronomic values of this population have been evaluated in the field experiments based on their phenotypic performance of agronomic traits, but the genetic variability of this population needs to be evaluated via techniques based on genetic material - DNA. In this study, the genetic variability in the investigated population of 71 hybrids and their parents was evaluated by RAPD technique, using eight selected arbitrarily primers; Genetic parameters and dendrogram expressing the genetic relationships among the investigated population were analyzed by GenALEx 6.1, Popgene 1.31 and NTSYSpc 2.1 softwares. Eight primers were used to generate the amplify products on each individual in the investigated population. From 74 genotypes, a total of 109 fragments were generated, among which, there were 89 polymorphic bands representing 81.65% with an average of 11 polymorphic bands/primer. Genetic similarity coefficient among the investigated population, based on DICE coefficient, ranged from 0.560 (LH05/0822 and PB260) to 0.991 (LH05/0781 and LH05/0841) with an average of 0,796, meaning that the genetic distance among ranged from 0.009 to 0.440 with an average of 0.231. The Shannon index and mean heterozygosity values were 0.328 and 0,176, respectively. This indicated that the progenies of the two investigated crosses possessed a relatively high range of genetic variability. The analysis of molecular variance (AMOVA) showed that genetic variation within population represented 62%, while genetic variation among two different crosses contributes 38% to the total genetic variability. Dendrogram based on DICE’s genetic similarity using UPGMA method showed that the hybrids divide into two major genetic groups (0.75), but the crosses were scattered independently of the hybrid.

scholarly journals Firework-related injuries treated at emergency departments in the United States during the COVID-19 pandemic in 2020 compared to 2018–2019

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Nathan Maassel ◽  
Abbie Saccary ◽  
Daniel Solomon ◽  
David Stitelman ◽  
Yunshan Xu ◽  
...  
Keyword(s):  
United States ◽  
Census Data ◽  
The United States ◽  
Population Based ◽  
Emergency Department Visits ◽  
Consumer Product Safety Commission ◽  
Injury Surveillance System ◽  
Time Period ◽  
National Estimates ◽  
Us Census

Abstract Background Despite a national decrease in emergency department visits in the United States during the first 10 months of the pandemic, preliminary Consumer Product Safety Commission data indicate increased firework-related injuries. We hypothesized an increase in firework-related injuries during 2020 compared to years prior related to a corresponding increase in consumer firework sales. Methods The National Electronic Injury Surveillance System (NEISS) was queried from 2018 to 2020 for cases with product codes 1313 (firework injury) and narratives containing “fireworks”. Population-based national estimates were calculated using US Census data, then compared across the three years of study inclusion. Patient demographic and available injury information was also tracked and compared across the three years. Firework sales data obtained from the American Pyrotechnics Association were determined for the same time period to examine trends in consumption. Results There were 935 firework-related injuries reported to the NEISS from 2018 to 2020, 47% of which occurred during 2020. National estimates for monthly injuries per million were 1.6 times greater in 2020 compared to 2019 (p < 0.0001) with no difference between 2018 and 2019 (p = 0.38). The same results were found when the month of July was excluded. Firework consumption in 2020 was 1.5 times greater than 2019 or 2018, with a 55% increase in consumer fireworks and 22% decrease in professional fireworks sales. Conclusions Firework-related injures saw a substantial increase in 2020 compared to the two years prior, corroborated by a proportional increase in consumer firework sales. Increased incidence of firework-related injuries was detected even with the exclusion of the month of July, suggesting that the COVID-19 pandemic may have impacted firework epidemiology more broadly than US Independence Day celebrations.

scholarly journals Fuzzy set intersection based paired-end short-read alignment

2021 ◽  
Author(s):  
William J Bolosky ◽  
Arun Subramaniyan ◽  
Matei Zaharia ◽  
Ravi Pandya ◽  
Taylor Sittler ◽  
...  
Keyword(s):  
Fuzzy Set ◽  
Genetic Material ◽  
Genomic Data ◽  
Short Read ◽  
Read Alignment ◽  
Short Read Alignment ◽  
Set Intersection

Much genomic data comes in the form of paired-end reads: two reads that represent genetic material with a small gap between. We present a new algorithm for aligning both reads in a pair simultaneously by fuzzily intersecting the sets of candidate alignment locations for each read. This algorithm is often much faster and produces alignments that result in variant calls having roughly the same concordance as the best competing aligners.

scholarly journals Variant abundance estimation for SARS-CoV-2 in wastewater using RNA-Seq quantification

2021 ◽  
Author(s):  
Jasmijn A. Baaijens ◽  
Alessandro Zulli ◽  
Isabel M. Ott ◽  
Mary E. Petrone ◽  
Tara Alpert ◽  
...  
Keyword(s):  
Temporal Dynamics ◽  
The United States ◽  
Population Surveillance ◽  
High Variability ◽  
Clinical Samples ◽  
Abundance Estimation ◽  
Computational Techniques ◽  
Rna Seq ◽  
Clinical Sequencing ◽  
Wastewater Samples

Effectively monitoring the spread of SARS-CoV-2 variants is essential to efforts to counter the ongoing pandemic. Wastewater monitoring of SARS-CoV-2 RNA has proven an effective and efficient technique to approximate COVID-19 case rates in the population. Predicting variant abundances from wastewater, however, is technically challenging. Here we show that by sequencing SARS-CoV-2 RNA in wastewater and applying computational techniques initially used for RNA-Seq quantification, we can estimate the abundance of variants in wastewater samples. We show by sequencing samples from wastewater and clinical isolates in Connecticut U.S.A. between January and April 2021 that the temporal dynamics of variant strains broadly correspond. We further show that this technique can be used with other wastewater sequencing techniques by expanding to samples taken across the United States in a similar timeframe. We find high variability in signal among individual samples, and limited ability to detect the presence of variants with clinical frequencies <10%; nevertheless, the overall trends match what we observed from sequencing clinical samples. Thus, while clinical sequencing remains a more sensitive technique for population surveillance, wastewater sequencing can be used to monitor trends in variant prevalence in situations where clinical sequencing is unavailable or impractical.

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