scholarly journals A small number of early introductions seeded widespread transmission of SARS-CoV-2 in Québec, Canada

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Carmen Lía Murall ◽  
Eric Fournier ◽  
Jose Hector Galvez ◽  
Arnaud N’Guessan ◽  
Sarah J. Reiling ◽  
...  
Keyword(s):  
Epidemiological Data ◽  
Founder Effects ◽  
Canadian Province ◽  
Genomic Epidemiology ◽  
Spring Break ◽  
Health Measures ◽  
Travel Restrictions ◽  
Returning Travellers ◽  
Viral Lineage ◽  
Pandemic Wave

Abstract Background Québec was the Canadian province most impacted by COVID-19, with 401,462 cases as of September 24th, 2021, and 11,347 deaths due mostly to a very severe first pandemic wave. In April 2020, we assembled the Coronavirus Sequencing in Québec (CoVSeQ) consortium to sequence SARS-CoV-2 genomes in Québec to track viral introduction events and transmission within the province. Methods Using genomic epidemiology, we investigated the arrival of SARS-CoV-2 to Québec. We report 2921 high-quality SARS-CoV-2 genomes in the context of > 12,000 publicly available genomes sampled globally over the first pandemic wave (up to June 1st, 2020). By combining phylogenetic and phylodynamic analyses with epidemiological data, we quantify the number of introduction events into Québec, identify their origins, and characterize the spatiotemporal spread of the virus. Results Conservatively, we estimated approximately 600 independent introduction events, the majority of which happened from spring break until 2 weeks after the Canadian border closed for non-essential travel. Subsequent mass repatriations did not generate large transmission lineages (> 50 sequenced cases), likely due to mandatory quarantine measures in place at the time. Consistent with common spring break and “snowbird” destinations, most of the introductions were inferred to have originated from Europe via the Americas. Once introduced into Québec, viral lineage sizes were overdispersed, with a few lineages giving rise to most infections. Consistent with founder effects, the earliest lineages to arrive tended to spread most successfully. Fewer than 100 viral introductions arrived during spring break, of which 7–12 led to the largest transmission lineages of the first wave (accounting for 52–75% of all sequenced infections). These successful transmission lineages dispersed widely across the province. Transmission lineage size was greatly reduced after March 11th, when a quarantine order for returning travellers was enacted. While this suggests the effectiveness of early public health measures, the biggest transmission lineages had already been ignited prior to this order. Conclusions Combined, our results reinforce how, in the absence of tight travel restrictions or quarantine measures, fewer than 100 viral introductions in a week can ensure the establishment of extended transmission chains.

scholarly journals A small number of early introductions seeded widespread transmission of SARS-CoV-2 in Québec, Canada

2021 ◽  
Author(s):  
Carmen Lía Murall ◽  
Eric Fournier ◽  
Jose Hector Galvez ◽  
Arnaud N’Guessan ◽  
Sarah J. Reiling ◽  
...  
Keyword(s):  
Epidemiological Data ◽  
Founder Effects ◽  
Canadian Province ◽  
Genomic Epidemiology ◽  
Spring Break ◽  
Health Measures ◽  
Travel Restrictions ◽  
Spatio Temporal ◽  
Pandemic Wave ◽  
Temporal Spread

AbstractUsing genomic epidemiology, we investigated the arrival of SARS-CoV-2 to Québec, the Canadian province most impacted by COVID-19, with >280,000 positive cases and >10,000 deaths in a population of 8.5 million as of March 1st, 2021. We report 2,921 high-quality SARS-CoV-2 genomes in the context of >12,000 publicly available genomes sampled globally over the first pandemic wave (up to June 1st, 2020). By combining phylogenetic and phylodynamic analyses with epidemiological data, we quantify the number of introduction events into Québec, identify their origins, and characterize the spatio-temporal spread of the virus. Conservatively, we estimated at least 500 independent introduction events, the majority of which happened from spring break until two weeks after the Canadian border closed for non-essential travel. Subsequent mass repatriations did not generate large transmission lineages (>50 cases), likely due to mandatory quarantine measures in place at the time. Consistent with common spring break and ‘snowbird’ destinations, most of the introductions were inferred to have originated from Europe via the Americas. Fewer than 100 viral introductions arrived during spring break, of which 5-10 led to the largest transmission lineages of the first wave (accounting for 36-58% of all sequenced infections). These successful viral transmission lineages dispersed widely across the province, consistent with founder effects and superspreading dynamics. Transmission lineage size was greatly reduced after March 11th, when a quarantine order for returning travelers was enacted. While this suggests the effectiveness of early public health measures, the biggest transmission lineages had already been ignited prior to this order. Combined, our results reinforce how, in the absence of tight travel restrictions or quarantine measures, fewer than 100 viral introductions in a week can ensure the establishment of extended transmission chains.

scholarly journals State-wide Genomic Epidemiology Investigations of COVID-19 Infections in Healthcare Workers: Insights for Future Pandemic Preparedness

2021 ◽  
Author(s):  
Anne E Watt ◽  
Norelle L Sherry ◽  
Patiyan Andersson ◽  
Courtney R Lane ◽  
Sandra Johnson ◽  
...  
Keyword(s):  
Healthcare Workers ◽  
Genomic Analysis ◽  
Epidemiological Data ◽  
Pandemic Preparedness ◽  
Transmission Networks ◽  
Healthcare Facilities ◽  
Multiple Introductions ◽  
Genomic Epidemiology ◽  
Sequencing Coverage ◽  
Healthcare Settings

Background COVID-19 has resulted in many infections in healthcare workers (HCWs) globally. We performed state-wide SARS-CoV-2 genomic epidemiological investigations to identify HCW transmission dynamics and provide recommendations to optimise healthcare system preparedness for future outbreaks. Methods Genome sequencing was attempted on all COVID-19 cases in Victoria, Australia. We combined genomic and epidemiologic data to investigate the source of HCW infections across multiple healthcare facilities (HCFs) in the state. Phylogenetic analysis and fine-scale hierarchical clustering were performed for the entire Victorian dataset including community and healthcare cases. Facilities provided standardised epidemiological data and putative transmission links. Findings Between March and October 2020, approximately 1,240 HCW COVID-19 infection cases were identified; 765 are included here. Genomic sequencing was successful for 612 (80%) cases. Thirty-six investigations were undertaken across 12 HCFs. Genomic analysis revealed that multiple introductions of COVID-19 into facilities (31/36) were more common than single introductions (5/36). Major contributors to HCW acquisitions included mobility of staff and patients between wards and facilities, and characteristics and behaviours of individual patients including super-spreading events. Key limitations at the HCF level were identified. Interpretation Genomic epidemiological analyses enhanced understanding of HCW infections, revealing unsuspected clusters and transmission networks. Combined analysis of all HCWs and patients in a HCF should be conducted, supported by high rates of sequencing coverage for all cases in the population. Established systems for integrated genomic epidemiological investigations in healthcare settings will improve HCW safety in future pandemics.

scholarly journals Does incubation period of COVID-19 vary with age? A study of epidemiologically linked cases in Singapore

2020 ◽  
Vol 148 ◽  
Author(s):  
W. Y. T. Tan ◽  
L. Y. Wong ◽  
Y. S. Leo ◽  
M. P. H. S. Toh
Keyword(s):  
Public Health ◽  
Incubation Period ◽  
Elderly Person ◽  
Epidemiological Data ◽  
Positive Case ◽  
Epidemiological Investigation ◽  
Inclusion Criteria ◽  
Health Measures ◽  
Trained Personnel ◽  
Close Contacts

Abstract This study estimates the incubation period of COVID-19 among locally transmitted cases, and its association with age to better inform public health measures in containing COVID-19. Epidemiological data of all PCR-confirmed COVID-19 cases from all restructured hospitals in Singapore were collected between 23 January 2020 and 2 April 2020. Activity mapping and detailed epidemiological investigation were conducted by trained personnel. Positive cases without clear exposure to another positive case were excluded from the analysis. One hundred and sixty-four cases (15.6% of patients) met the inclusion criteria during the defined period. The crude median incubation period was 5 days (range 1–12 days) and median age was 42 years (range 5–79 years). The median incubation period among those 70 years and older was significantly longer than those younger than 70 years (8 vis-à-vis 5 days, P = 0.040). Incubation period was negatively correlated with day of illness in both groups. These findings support current policies of 14-day quarantine periods for close contacts of confirmed cases and 28 days for monitoring infections in known clusters. An elderly person who may have a longer incubation period than a younger counterpart may benefit from earlier and proactive testing, especially after exposure to a positive case.

scholarly journals Notifiable diseases after implementation of COVID-19 public health prevention measures in Central Queensland, Australia

2021 ◽  
Vol 45 ◽  
Author(s):  
Odewumi Adegbija ◽  
Jacina Walker ◽  
Nicholas Smoll ◽  
Arifuzzaman Khan ◽  
Julieanne Graham ◽  
...  
Keyword(s):  
Public Health ◽  
Disease Surveillance ◽  
Communicable Disease ◽  
Communicable Diseases ◽  
Prevention Measures ◽  
Vector Borne Diseases ◽  
Vaccine Preventable Diseases ◽  
Notifiable Diseases ◽  
Health Measures ◽  
Travel Restrictions

The implementation of public health measures to control the current COVID-19 pandemic (such as wider lockdowns, overseas travel restrictions and physical distancing) is likely to have affected the spread of other notifiable diseases. This is a descriptive report of communicable disease surveillance in Central Queensland (CQ) for six months (1 April to 30 September 2020) after the introduction of physical distancing and wider lockdown measures in Queensland. The counts of notifiable communicable diseases in CQ in the six months were observed and compared with the average for the same months during the years 2015 to 2019. During the study’s six months, there were notable decreases in notifications of most vaccine-preventable diseases such as influenza, pertussis and rotavirus. Conversely, notifications increased for disease groups such as blood-borne viruses, sexually transmitted infections and vector-borne diseases. There were no reported notifications for dengue fever and malaria which are mostly overseas acquired. The notifications of some communicable diseases in CQ were variably affected and the changes correlated with the implementation of the COVID-19 public health measures.

scholarly journals High COVID-19 incidence among Norwegian travellers returned from Lombardy: implications for travel restrictions

2020 ◽  
Author(s):  
Ola Brynildsrud ◽  
Vegard Eldholm
Keyword(s):  
Incidence Rates ◽  
Common Source ◽  
Epidemic Spread ◽  
Tourist Destinations ◽  
Patient Level ◽  
Level Data ◽  
Travel Restrictions ◽  
Returning Travellers ◽  
Imported Infections ◽  
Temporal Overlap

On February 27th, three cases of COVID-19 were reported among Norwegians that had recently returned from Lombardy, Italy. Travellers from the region rapidly became the most common source of imported infections in the earliest stage of the Norwegian COVID-19 epidemic. The situation was exacerbated by the unfortunate temporal overlap between the Norwegian winter holidays and intense epidemic spread of COVID-19 in Northern Italy, resulting in a large number of infected travellers. Here we combined flight data on travels between Norway and Lombardy with patient-level data to determine the fraction of travellers returning to Norway that had been infected with SARS-CoV-2.Travellers returning to Norway from Lombardy contracted COVID-19 at incidence rates up to 0.02 per person-day in the period spanning February 21st and March 1st, with a clear uptick in transmission in the middle of the period.This shows an example of the infection risk in tourist destinations being several fold higher than elsewhere in the region. In Norway, this is also supported by high rates of infections among tourists returning from Austria in February and March, despite a low number of reported cases in the country at the time.The massive COVID-19 prevalence among travellers suggest that mandatory quarantine of returning travellers or suspension of non-essential international flights is essential if the aim is to control or suppress the COVID-19 pandemic.

scholarly journals Coast-to-coast spread of SARS-CoV-2 in the United States revealed by genomic epidemiology

2020 ◽  
Author(s):  
Joseph R. Fauver ◽  
Mary E. Petrone ◽  
Emma B. Hodcroft ◽  
Kayoko Shioda ◽  
Hanna Y. Ehrlich ◽  
...  
Keyword(s):  
United States ◽  
Pacific Northwest ◽  
The United States ◽  
International Travel ◽  
Viral Genomes ◽  
Genomic Epidemiology ◽  
The Pacific ◽  
Travel Restrictions ◽  
Novel Coronavirus ◽  
The U.S

SummarySince its emergence and detection in Wuhan, China in late 2019, the novel coronavirus SARS-CoV-2 has spread to nearly every country around the world, resulting in hundreds of thousands of infections to date. The virus was first detected in the Pacific Northwest region of the United States in January, 2020, with subsequent COVID-19 outbreaks detected in all 50 states by early March. To uncover the sources of SARS-CoV-2 introductions and patterns of spread within the U.S., we sequenced nine viral genomes from early reported COVID-19 patients in Connecticut. Our phylogenetic analysis places the majority of these genomes with viruses sequenced from Washington state. By coupling our genomic data with domestic and international travel patterns, we show that early SARS-CoV-2 transmission in Connecticut was likely driven by domestic introductions. Moreover, the risk of domestic importation to Connecticut exceeded that of international importation by mid-March regardless of our estimated impacts of federal travel restrictions. This study provides evidence for widespread, sustained transmission of SARS-CoV-2 within the U.S. and highlights the critical need for local surveillance.

scholarly journals Chagas disease in Italy: breaking an epidemiological silence

2011 ◽  
Vol 16 (37) ◽  
Author(s):  
A Angheben ◽  
M Anselmi ◽  
F Gobbi ◽  
S Marocco ◽  
G Monteiro ◽  
...  
Keyword(s):  
Chagas Disease ◽  
Latin American ◽  
Wide Spectrum ◽  
Epidemiological Data ◽  
Tropical Diseases ◽  
Positive Serology ◽  
Population Movements ◽  
Health Measures ◽  
University Of Florence ◽  
Acute Chagas Disease

Chagas disease, a neglected tropical disease that due to population movements is no longer limited to Latin America, threatens a wide spectrum of people (travellers, migrants, blood or organ recipients, newborns, adoptees) also in non-endemic countries where it is generally underdiagnosed. In Italy, the available epidemiological data about Chagas disease have been very limited up to now, although the country is second in Europe only to Spain in the number of residents from Latin American. Among 867 at-risk subjects screened between 1998 and 2010, the Centre for Tropical Diseases in Negrar (Verona) and the Infectious and Tropical Diseases Unit, University of Florence found 4.2% patients with positive serology for Chagas disease (83.4% of them migrants, 13.8% adoptees). No cases of Chagas disease were identified in blood donors or HIV-positive patients of Latin American origin. Among 214 Latin American pregnant women, three were infected (resulting in abortion in one case). In 2005 a case of acute Chagas disease was recorded in an Italian traveller. Based on our observations, we believe that a wider assessment of the epidemiological situation is urgently required in our country and public health measures preventing transmission and improving access to diagnosis and treatment should be implemented.

scholarly journals Recovery Ratios Reliably Anticipate COVID-19 Pandemic Progression

2020 ◽  
Author(s):  
Dan V. Nicolau ◽  
Alexander Hasson ◽  
Mona Bafadhel
Keyword(s):  
Public Health ◽  
Predictive Models ◽  
Recovery Phase ◽  
Healthcare Systems ◽  
Epidemiological Models ◽  
Health Measures ◽  
The World ◽  
Insight Into ◽  
Pandemic Wave ◽  
Gaining Insight

AbstractThe COVID-19 pandemic is placing unprecedented demands on healthcare systems worldwide and exacting a massive humanitarian toll. This makes the development of accurate predictive models imperative, not just for understanding the course of the pandemic but more importantly for gaining insight into the efficacy of public health measures and planning accordingly. Epidemiological models are forced to make assumptions about many unknowns and therefore can be unreliable. Here, taking an empirical approach, we report a 20-30 day lag between the peak of confirmed to recovered cases and the peak of daily deaths in each country, independent of the epoch of that country in its pandemic cycle. This analysis is expected to be largely independent of the proportion of the population being tested and therefore should aid in planning around the timing and easing of public health measures. Our data also suggests broad predictions for the number of fatalities, generally somewhat lower than most other models. Finally, our model suggests that the world as a whole is shortly to enter a recovery phase, at least as far as the first pandemic wave is concerned.

scholarly journals What Can We Learn from the Time Evolution of COVID-19 Epidemic in Slovenia?

2020 ◽  
Author(s):  
Ioan Bâldea
Keyword(s):  
Social Science ◽  
Time Dependence ◽  
European Country ◽  
Recent Work ◽  
Epidemiological Data ◽  
Theoretical Assumption ◽  
Time Dynamics ◽  
Travel Restrictions ◽  
Containment Measures ◽  
Self Protection

AbstractA recent work (DOI 10.1101/2020.05.06.20093310) indicated that temporarily splitting larger populations into smaller groups can efficiently mitigate the spread of SARS-CoV-2 virus. The fact that, soon afterwards, on May 15, 2020, the two million people Slovenia was the first European country proclaiming the end of COVID-19 epidemic within national borders may be relevant from this perspective. Motivated by this evolution, in this paper we investigate the time dynamics of coronavirus cases in Slovenia with emphasis on how efficient various containment measures act to diminish the number of COVID-19 infections. Noteworthily, the present analysis does not rely on any speculative theoretical assumption; it is solely based on raw epidemiological data. Out of the results presented here, the most important one is perhaps the finding that, while imposing drastic curfews and travel restrictions reduce the infection rate k by a factor of four with respect to the unrestricted state, they only improve the κ-value by ~ 15% as compared to the much bearable state of social and economical life wherein (justifiable) wearing face masks and social distancing rules are enforced/followed. Significantly for behavioral and social science, our analysis of the time dependence κ = κ(t) may reveal an interesting self-protection instinct of the population, which became manifest even before the official lockdown enforcement.

scholarly journals The effect of COVID-19 public health measures on nationally notifiable diseases in Australia: preliminary analysis

2020 ◽  
Vol 44 ◽  
Author(s):  
Amy Bright ◽  
Anna-Jane Glynn-Robinson ◽  
Stacey Kane ◽  
Rose Wright ◽  
Nathan Saul
Keyword(s):  
Public Health ◽  
Preliminary Analysis ◽  
Disease Spread ◽  
Health Seeking ◽  
Income Loss ◽  
Notifiable Diseases ◽  
Health Measures ◽  
Healthcare It ◽  
Travel Restrictions ◽  
Financial Impacts

Since the introduction of COVID-19-related public health measures, notifications for most nationally notifiable diseases have declined when compared to previous years. Physical distancing, travel restrictions, and emphasis on hygiene are likely to have affected the number of expected notifications, with the greatest reductions observed among disease spread via person-to-person contact such as influenza, and among overseas-acquired infections such as dengue virus and measles. However, quantifying the magnitude of the effect of COVID-19 public health measures on communicable diseases in Australia will be difficult, due to confounding factors such as: changes in testing priorities in laboratories; diversion of resources to the COVID-19 response; changes in health-seeking behaviours; greater utilisation of telehealth practices; and financial impacts such as income loss and ability to afford healthcare. It is considered likely that these other factors will have also impacted notification numbers.

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