scholarly journals Phylogenomics reveals viral sources, transmission, and potential superinfection in early-stage COVID-19 patients in Ontario, Canada

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Calvin P. Sjaarda ◽  
Nazneen Rustom ◽  
Gerald A. Evans ◽  
David Huang ◽  
Santiago Perez-Patrigeon ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Disease Surveillance ◽  
Early Stage ◽  
Emerging Diseases ◽  
Contact Tracing ◽  
Travel History ◽  
Infectious Disease Surveillance ◽  
Viral Genomes ◽  
Heterozygous Variant ◽  
Sequencing Platforms

AbstractThe emergence and rapid global spread of SARS-CoV-2 demonstrates the importance of infectious disease surveillance, particularly during the early stages. Viral genomes can provide key insights into transmission chains and pathogenicity. Nasopharyngeal swabs were obtained from thirty-two of the first SARS-CoV-2 positive cases (March 18–30) in Kingston Ontario, Canada. Viral genomes were sequenced using Ion Torrent (n = 24) and MinION (n = 27) sequencing platforms. SARS-CoV-2 genomes carried forty-six polymorphic sites including two missense and three synonymous variants in the spike protein gene. The D614G point mutation was the predominate viral strain in our cohort (92.6%). A heterozygous variant (C9994A) was detected by both sequencing platforms but filtered by the ARTIC network bioinformatic pipeline suggesting that heterozygous variants may be underreported in the SARS-CoV-2 literature. Phylogenetic analysis with 87,738 genomes in the GISAID database identified global origins and transmission events including multiple, international introductions as well as community spread. Reported travel history validated viral introduction and transmission inferred by phylogenetic analysis. Molecular epidemiology and evolutionary phylogenetics may complement contact tracing and help reconstruct transmission chains of emerging diseases. Earlier detection and screening in this way could improve the effectiveness of regional public health interventions to limit future pandemics.

Chasing the origin of SARS-CoV-2 in Canada’s COVID-19 cases: A genomics study

2020 ◽  
Author(s):  
Calvin P Sjaarda ◽  
Nazneen Rustom ◽  
David Huang ◽  
Santiago Perez-Patrigeon ◽  
Melissa L Hudson ◽  
...  
Keyword(s):  
Disease Surveillance ◽  
Early Stage ◽  
Protein A ◽  
Emerging Diseases ◽  
Economic Consequences ◽  
Local Health ◽  
Gene Encoding ◽  
Viral Origin ◽  
Viral Genomes ◽  
The Usa

AbstractThe emergence and global spread of SARS-CoV-2 has had profound social and economic consequences and has shed light on the importance of continued and additional investment in global health and infectious disease surveillance. Identifying changes in viral genomes provides key insights into viral diversity, how viruses spread within populations, and viral strategies for evasion of host immune systems. Here we report twenty-five SARS-CoV-2 genome sequences collected from some of the first COVID-19 cases in eastern Ontario, Canada (March 18-30, 2020). The reported genomes belong to the S-clade (n=2) and G-clade (n=23) of SARS-CoV-2 and contain 45 polymorphic sites including one shared missense and three unique synonymous variants in the gene encoding the spike protein. A phylogenetic analysis enabled the tracing of viral origin and potential transmission into and within Canada. There may be as many as sixteen unique infection events represented in these samples, including at least three that were likely introduced from Europe and seven from the USA. In addition, four separate genomes are each shared by multiple patients, suggesting a common origin or community spread even during this early stage of infection. These results demonstrate how molecular epidemiology and evolutionary phylogenetics can help local health units track origins and vectors of spread for emerging diseases like SARS-CoV-2. Earlier detection and screening in this way could improve the effectiveness of regional public health interventions to prevent future pandemics.

scholarly journals Detection of epidemics in their early stage through infectious disease surveillance

2000 ◽  
Vol 29 (5) ◽  
pp. 905-910 ◽  
Author(s):  
Shuji Hashimoto ◽  
Yoshitaka Murakami ◽  
Kiyosu Taniguchi ◽  
Masaki Nagai
Keyword(s):  
Infectious Disease ◽  
Disease Surveillance ◽  
Early Stage ◽  
Infectious Disease Surveillance

scholarly journals A review of infectious disease surveillance to inform public health action against the novel coronavirus SARS-CoV-2

2020 ◽  
Author(s):  
David Larsen ◽  
Rachel E. Dinero ◽  
Elizabeth Asiago-Reddy ◽  
Hyatt Green ◽  
Sandra Lane ◽  
...  
Keyword(s):  
Public Health ◽  
Infectious Disease ◽  
Disease Surveillance ◽  
Behavioral Interventions ◽  
Contact Tracing ◽  
Public Health Action ◽  
Infectious Disease Surveillance ◽  
Genetic Sequencing ◽  
Social Distancing ◽  
Infected People

The SARS-CoV-2 pandemic exposed the inadequacy of infectious disease surveillance throughout the US and other countries. Isolation and contact tracing to identify all infected people are key public health interventions necessary to control infectious disease outbreaks. However, these activities are dependent upon the surveillance platform to identify infections quickly. A robust surveillance platform can also reinforce community adherence to behavioral interventions such as social distancing. In situations where contact tracing is feasible, all suspected cases and contacts of confirmed cases must be tested for a SARS-CoV-2 infection and effectively isolated. At the community level wastewater surveillance can identify areas where transmission is or is not occurring, and genetic sequencing of SARS-CoV-2 can help to elucidate the intensity of transmission independent of the number of known cases and hospitalizations. State and county public health departments should improve the infectious disease surveillance platform whilst the public is practicing social distancing. These enhanced surveillance activities are necessary to contain the epidemic once the curve has been sufficiently flattened in highly burdened areas, and to prevent escalation in areas where transmission is minimal.

scholarly journals Eurosurveillance comes of age and moves to ECDC

2007 ◽  
Vol 12 (2) ◽  
pp. 1-2 ◽  
Author(s):  
H Therre ◽  
J C Desenclos ◽  
E Hoile ◽  
N Gill ◽  
J B Brunet
Keyword(s):  
Infectious Disease ◽  
Disease Surveillance ◽  
Prevention And Control ◽  
Early Stage ◽  
Scientific Information ◽  
Large Network ◽  
Public Health Community ◽  
Infectious Disease Surveillance ◽  
Health Community ◽  
And Control

Eurosurveillance was created in 1995 to support exchange and dissemination of authoritative scientific information within the part of public health community involved in the field of infectious disease surveillance and control, at a time when European surveillance networks were at an early stage of growth. Now part of a large network, the publication is entering a new stage: the editorial function will now be hosted at the European Centre for Disease Prevention and Control (ECDC) in Stockholm. This will strengthen the platform for the next stage in Eurosurveillance’s development as the major home of peer-reviewed European information on infectious disease surveillance and control.

scholarly journals Epidemiological and Genomic Analysis of SARS-CoV-2 in Ten Patients from a Mid-sized City outside of Hubei, China

2020 ◽  
Author(s):  
Jinkun Chen ◽  
Evann E. Hilt ◽  
Huan Wu ◽  
Zhuojing Jiang ◽  
QinChao Zhang ◽  
...  
Keyword(s):  
Mutation Rate ◽  
Nucleotide Substitution ◽  
Vaccine Development ◽  
Early Stage ◽  
Genomic Analysis ◽  
Dynamic Nature ◽  
Travel History ◽  
Viral Genomes ◽  
Living Together ◽  
Novel Coronavirus

ABSTRACTA novel coronavirus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the ongoing COVID-19 pandemic. In this study, we performed a comprehensive epidemiological and genomic analysis of SARS-CoV-2 genomes from ten patients in Shaoxing, a mid-sized city outside of the epicenter Hubei province, China, during the early stage of the outbreak (late January to early February, 2020). We obtained viral genomes with > 99% coverage and a mean depth of 296X demonstrating that viral genomic analysis is feasible via metagenomics sequencing directly on nasopharyngeal samples with SARS-CoV-2 Real-time PCR Ct values less than 28. We found that a cluster of 4 patients with travel history to Hubei shared the exact same virus with patients from Wuhan, Taiwan, Belgium and Australia, highlighting how quickly this virus spread to the globe. The virus from another cluster of two family members living together without travel history but with a sick contact of a confirmed case from another city outside of Hubei accumulated significantly more mutations (9 SNPs vs average 4 SNPs), suggesting a complex and dynamic nature of this outbreak. We also found 70% patients in this study had the S genotype, consistent with an early study showing a higher prevalence of genotype out of Hubei than that inside Hubei. We calculated an average mutation rate of 1.37×10−3 nucleotide substitution per site per year, which is similar to that of other coronaviruses. Our findings add to the growing knowledge of the epidemiological and genomic characteristics of SARS-CoV-2 that are important for guiding outbreak containment and vaccine development. The moderate mutation rate of this virus also lends hope that development of an effective, long-lasting vaccine may be possible.

scholarly journals Estimating the transmissibility of SARS-CoV-2 VOC 202012/01 in Japan using travel history information

2022 ◽  
Vol 19 (3) ◽  
pp. 2750-2761
Author(s):  
Taishi Kayano ◽  
◽  
Hiroshi Nishiura
Keyword(s):  
Generation Time ◽  
Early Stage ◽  
Time Estimation ◽  
Right Censoring ◽  
Contact Tracing ◽  
Baseline Scenario ◽  
Primary Case ◽  
Travel History ◽  
Short Period ◽  
History Information

<abstract> <p>Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has rapidly spread across the globe. The variant of concern (VOC) 202012/01 (B.1.1.7, also known as the alpha variant) bearing the N501Y mutation emerged in late 2020. VOC 202012/01 was more transmissible than existing SARS-CoV-2 variants and swiftly became dominant in many regions. More than 150 cases of VOC 202012/01 were reported in Japan by 26 February 2021. During the very early stage of introduction, only a subset arose from domestic transmission. If the reproduction number <italic>R</italic> (i.e., the average number of secondary transmission events caused by a single primary case) is greater than 1, the corresponding proportion should converge to 1 in a short period of time, and thus it is critical to understand the transmissibility of VOC 202012/01 based on travel history information. The present study aimed to estimate <italic>R</italic> of VOC 202012/01 using overseas travel history information. A mathematical model was developed to capture the relationship between travel history and <italic>R</italic>. We obtained travel history data for each confirmed case of VOC 202012/01 infection from 26 December 2020 to 26 February 2021. Maximum likelihood estimation was used to estimate <italic>R</italic>, accounting for right censoring during real-time estimation. In the baseline scenario, <italic>R</italic> was estimated at 2.11 (95% confidence interval: 1.63, 2.94). By 26 February 2021, an average of nine generations had elapsed since the first imported case. If the generation time of VOC 202012/01 was assumed to be longer, <italic>R</italic> was increased, consistent with estimates of <italic>R</italic> from case data. The estimated <italic>R</italic> of VOC 202012/01 in Japan exceeded 1 on 26 February 2021, suggesting that domestic transmission events caused a major epidemic. Moreover, because our estimate of <italic>R</italic> was dependent on generation time and ascertainment biases, continuous monitoring of contact tracing data is crucial to decipher the mechanisms of increased VOC 202012/01 transmissibility.</p> </abstract>

scholarly journals Lost and found: applying network analysis to public health contact tracing for HIV

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Dana K. Pasquale ◽  
Irene A. Doherty ◽  
Peter A. Leone ◽  
Ann M. Dennis ◽  
Erika Samoff ◽  
...  
Keyword(s):  
North Carolina ◽  
Network Analysis ◽  
Disease Surveillance ◽  
Time Window ◽  
Temporal Trends ◽  
Contact Tracing ◽  
Infectious Disease Surveillance ◽  
Hiv Epidemic ◽  
Lost And Found ◽  
Network Component

AbstractInfectious disease surveillance is often case-based, focused on people diagnosed and their contacts in a predefined time window, and treated as independent across infections. Network analysis of partners and contacts joining multiple investigations and infections can reveal social or temporal trends, providing opportunities for epidemic control within broader networks. We constructed a sociosexual network of all HIV and early syphilis cases and contacts investigated among residents of 11 contiguous counties in North Carolina over a two-year period (2012–2013). We anchored the analysis on new HIV diagnoses (“indexes”), but also included nodes and edges from syphilis investigations that were within the same network component as any new HIV index. After adding syphilis investigations and deduplicating people included in multiple investigations (entity resolution), the final network comprised 1470 people: 569 HIV indexes, 700 contacts to HIV indexes who were not also new cases themselves, and 201 people who were either indexes or contacts in eligible syphilis investigations. Among HIV indexes, nearly half (48%; n = 273) had no located contacts during single-investigation contact tracing, though 25 (9%) of these were identified by other network members and thus not isolated in the final multiple investigation network. Constructing a sociosexual network from cases and contacts across multiple investigations mitigated some effects of unobserved partnerships underlying the HIV epidemic and demonstrated the HIV and syphilis overlap in these networks.

An Epidemiological Analysis of COVID-19 Confirmed Cases, Reported at National Institute of Health, Pakistan (Preprint)

2020 ◽  
Author(s):  
Ambreen Chaudhry
Keyword(s):  
Age Groups ◽  
Target Population ◽  
Control Measures ◽  
Contact Tracing ◽  
Bivariate Analysis ◽  
Travel History ◽  
Disease Epidemiology ◽  
Hygiene Practices ◽  
Multi Center Study ◽  
Epidemiological Characteristics

BACKGROUND Coronavirus disease (Covid-19) is a zoonotic disease of novel origin that posed a continuous threat to health worldwide after taking the shape of the pandemic. An understanding of disease epidemiology is supportive in timely preventive and control measures as well as contact tracing and curbing surveillance activities. OBJECTIVE The objective of our study was to determine the epidemiological characteristics of COVID-19 confirmed cases reported at the National Institute of Health Pakistan and elements of its spread in Pakistan. METHODS A retrospective record review was conducted at the National Institute of Health (NIH) Islamabad, Pakistan from January 25 to April 4, 2020. Univariate and bivariate analysis was done with 95% CI and p<0.05. RESULTS A total of 14,422 samples of suspected COVID-19 cases were received with a positivity rate of 9% (n=1348). Among all 70% (n=939) were male. The median age was 41years of age (range: 01-99Years). Among all, 19% were from 30-39 years old followed by 50-59 years old (17%). Children remained the least affected by 3% (n=35). Of the total reported cases, 55% (n=735) have reported the travel history within the last 14 days. Among these travelers’ international travelers were 23% (n=166) and domestic travelers were 77% (n=569). Travel history including both international and domestic remained significantly associated with the different age groups and Young adults remained more vulnerable to COVID-19 (P=0.03). Fever, SOB, and Cough remained the most significantly associated (P<0.05) in all age groups. CONCLUSIONS A higher incidence of COVID-19 among elderly men suggests robust quarantine measures for this target population. An escalating incidence of local transmission needs strict social distancing and hygiene practices to help flatten the curve. An extensive multi-center study is also recommended for a full understanding of disease dynamics.

scholarly journals Symptom and Age Homophilies in SARS-CoV-2 Transmission Networks during the Early Phase of the Pandemic in Japan

Biology ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 499
Author(s):  
Ali Andalibi ◽  
Naoru Koizumi ◽  
Meng-Hao Li ◽  
Abu Bakkar Siddique
Keyword(s):  
Early Stage ◽  
Graph Model ◽  
Initial Response ◽  
Contact Tracing ◽  
Pcr Analysis ◽  
Exponential Random Graph Model ◽  
Transmission Networks ◽  
Random Graph Model ◽  
Healthcare Settings ◽  
Exponential Random Graph

Kanagawa and Hokkaido were affected by COVID-19 in the early stage of the pandemic. Japan’s initial response included contact tracing and PCR analysis on anyone who was suspected of having been exposed to SARS-CoV-2. In this retrospective study, we analyzed publicly available COVID-19 registry data from Kanagawa and Hokkaido (n = 4392). Exponential random graph model (ERGM) network analysis was performed to examine demographic and symptomological homophilies. Age, symptomatic, and asymptomatic status homophilies were seen in both prefectures. Symptom homophilies suggest that nuanced genetic differences in the virus may affect its epithelial cell type range and can result in the diversity of symptoms seen in individuals infected by SARS-CoV-2. Environmental variables such as temperature and humidity may also play a role in the overall pathogenesis of the virus. A higher level of asymptomatic transmission was observed in Kanagawa. Moreover, patients who contracted the virus through secondary or tertiary contacts were shown to be asymptomatic more frequently than those who contracted it from primary cases. Additionally, most of the transmissions stopped at the primary and secondary levels. As expected, significant viral transmission was seen in healthcare settings.

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