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

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.

Genomic and Epidemiological Analysis of SARS-CoV-2 Viruses in Sri Lanka

Background: In order to understand the molecular epidemiology of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in Sri Lanka, since March 2020, we carried out genomic sequencing overlaid on available epidemiological data until April 2021.Methods: Whole genome sequencing was carried out on diagnostic sputum or nasopharyngeal swabs from 373 patients with COVID-19. Molecular clock phylogenetic analysis was undertaken to further explore dominant lineages.Results: The B.1.411 lineage was most prevalent, which was established in Sri Lanka and caused outbreaks throughout the country until March 2021. The estimated time of the most recent common ancestor (tMRCA) of this lineage was June 1, 2020 (with 95% lower and upper bounds March 30 to July 27) suggesting cryptic transmission may have occurred, prior to a large epidemic starting in October 2020. Returning travellers were identified with infections caused by lineage B.1.258, as well as the more transmissible B.1.1.7 lineage, which has replaced B.1.411 to fuel the ongoing large outbreak in the country.Conclusions: The large outbreak that started in early October, is due to spread of a single virus lineage, B.1.411 until the end of March 2021, when B.1.1.7 emerged and became the dominant lineage.

Tracking the introduction and spread of SARS-CoV-2 in coastal Kenya

Genomic surveillance of SARS-CoV-2 is important for understanding both the evolution and the patterns of local and global transmission. Here, we generated 311 SARS-CoV-2 genomes from samples collected in coastal Kenya between 17th March and 31st July 2020. We estimated multiple independent SARS-CoV-2 introductions into the region were primarily of European origin, although introductions could have come through neighbouring countries. Lineage B.1 accounted for 74% of sequenced cases. Lineages A, B and B.4 were detected in screened individuals at the Kenya-Tanzania border or returning travellers. Though multiple lineages were introduced into coastal Kenya following the initial confirmed case, none showed extensive local expansion other than lineage B.1. International points of entry were important conduits of SARS-CoV-2 importations into coastal Kenya and early public health responses prevented established transmission of some lineages. Undetected introductions through points of entry including imports from elsewhere in the country gave rise to the local epidemic at the Kenyan coast.

Increasingly limited options for the treatment of enteric fever in travellers returning to England, 2014–2019: a cross-sectional analytical study

Introduction. Enteric fever (caused by Salmonella enterica serovars Typhi and Paratyphi) frequently presents as an acute, undifferentiated febrile illness in returning travellers, requiring timely empirical antibiotics. Gap Statement. Determining which empirical antibiotics to prescribe for enteric fever requires up-to-date knowledge of susceptibility patterns. Aim. By characterising factors associated with antimicrobial resistance in cases of S. Typhi and S. Paratyphi imported to England, we aim to guide effective empirical treatment. Methodology. All English isolates of S. Typhi and S. Paratyphi 2014–2019 underwent antimicrobial susceptibility testing; results were compared to a previous survey in London 2005–2012. Risk factors for antimicrobial resistance were analysed with logistic regression models to predict adjusted odds ratios (aOR) for resistance to individual antibiotics and multi-drug resistance. Results. We identified 1088 cases of S. Typhi, 729 S. Paratyphi A, 93 S. Paratyphi B, and one S. Paratyphi C. In total, 93 % were imported. Overall, 90 % of S. Typhi and 97 % of S. Paratyphi A isolates were resistant to ciprofloxacin; 26 % of S. Typhi were multidrug resistant to ciprofloxacin, amoxicillin, co-trimoxazole, and chloramphenicol (MDR+FQ). Of the isolates, 4 % of S. Typhi showed an extended drug resistance (XDR) phenotype of MDR+FQ plus resistance to third-generation cephalosporins, with cases of XDR rising sharply in recent years (none before 2017, one in 2017, six in 2018, 32 in 2019). For S. Typhi isolates, resistance to ciprofloxacin was associated with travel to Pakistan (aOR=32.0, 95 % CI: 15.4–66.4), India (aOR=21.8, 95 % CI: 11.6–41.2), and Bangladesh (aOR=6.2, 95 % CI: 2.8–13.6) compared to travel elsewhere, after adjusting for rising prevalence of resistance over time. MDR+FQ resistance in S. Typhi isolates was associated with travel to Pakistan (aOR=3.5, 95 % CI: 2.4–5.2) and less likely with travel to India (aOR=0.07, 95 % CI 0.04–0.15) compared to travel elsewhere. All XDR cases were imported from Pakistan. No isolate was resistant to azithromycin. Comparison with the 2005–2012 London survey indicates substantial increases in the prevalence of resistance of S. Typhi isolates to ciprofloxacin associated with travel to Pakistan (from 79–98 %) and Africa (from 12–60 %). Conclusion. Third-generation cephalosporins and azithromycin remain appropriate choices for empirical treatment of enteric fever in most returning travellers to the UK from endemic countries, except from Pakistan, where XDR represents a significant risk.

Genomic and epidemiological analysis of SARS-CoV-2 viruses in Sri Lanka

Since identification of the first Sri Lankan individual with the SARS-CoV-2 in early March 2020, small clusters that occurred were largely contained until the current extensive outbreak that started in early October 2020. In order to understand the molecular epidemiology of SARS-CoV-2 in Sri Lanka, we carried out genomic sequencing overlaid on available epidemiological data. The B.1.411 lineage was most prevalent, which was established in Sri Lanka and caused outbreaks throughout the country. The estimated time of the most recent common ancestor of this lineage was 10th August 2020 (95% lower and upper bounds 6th July to 7th September), suggesting cryptic transmission may have occurred, prior to a large epidemic starting in October 2020. Returning travellers were identified with infections caused by lineage B.1.258 , as well as the more transmissible B.1.1.7 lineage. Ongoing genomic surveillance in Sri Lanka is vital as vaccine roll-out increases.

Analysis and Simulation of Epidemic COVID-19 Curves with the Verhulst Model Applied to Statistical Inhomogeneous Age Groups

Pandemic curves, such as COVID-19, often show multiple and unpredictable contamination peaks, often called second, third and fourth waves, which are separated by wide plateaus. Here, by considering the statistical inhomogeneity of age groups, we show a quantitative understanding of the different behaviour rules to flatten a pandemic COVID-19 curve and concomitant multi-peak recurrence. The simulations are based on the Verhulst model with analytical generalized logistic equations for the limited growth. From the log–lin plot, we observe an early exponential growth proportional to . The first peak is often τgrow @ 5 d. The exponential growth is followed by a recovery phase with an exponential decay proportional to . For the characteristic time holds: . Even with isolation, outbreaks due to returning travellers can result in a recurrence of multi-peaks visible on log–lin scales. The exponential growth for the first wave is faster than for the succeeding waves, with characteristic times, τ of about 10 d. Our analysis ascertains that isolation is an efficient method in preventing contamination and enables an improved strategy for scientists, governments and the general public to timely balance between medical burdens, mental health, socio-economic and educational interests.

Experiences of supported isolation in returning travellers during the early COVID-19 response: an interview study

ObjectivesTo understand the experiences of those who underwent supported isolation as part of the response to the COVID-19 pandemic, after returning to the UK from Wuhan, China.DesignWe used semi-structured interviews to capture participants’ experiences and perceptions of supported isolation.SettingTelephone interviews carried out within approximately one month of an individual leaving supported isolation.Participants26 people who underwent supported isolation at either Arrowe Park Hospital (n = 18) or Kents Hill Park Conference Centre (n = 8) after being repatriated from Wuhan in January – February 2020.ResultsParticipants were willing to undergo supported isolation because they understood that it would protect themselves and others. Positive treatment by staff was fundamental to participants’ willingness to comply with isolation procedures. Despite the high level of compliance, participants expressed some uncertainty about what the process would involve.ConclusionsAs hotel quarantine is introduced across the UK for international arrivals, our findings suggest that those in charge should: communicate effectively before, during and after quarantine, emphasising why quarantine is important and how it will protect others; avoid enforcement and focus on supporting and promoting voluntary compliance; facilitate shared social experiences for those in quarantine; and ensure all necessary supplies are provided. Doing so will increase adherence and reduce any negative effects on wellbeing.

Critical illness in the returning traveller

A 70 year old man, who had recently travelled in rural Iraq, presented with fevers, rigors, and developed multiorgan failure. An extensive range of diagnostic tests was undertaken in an attempt to identify the cause. He was treated with multi-organ support and a number of antibiotics. Critical illness in the returning traveller presents a number of challenges on the ICU: obtaining adequate history, the potentially broad differential diagnosis, the requirement for numerous and sometimes specialised investigations and risks of infection transmission to staff and other patients. Travellers are more often elderly, more likely to have comorbidities and immunosuppression whilst global disease patterns are changing. Particular consideration should be given to unusual infections and venous thromboembolic disease from prolonged immobility whilst in transit, alongside more commonly encountered diseases. Antimicrobial resistance may be encountered and appropriate infection control is essential for the protection of patients, staff and others. Specialist support is available in the UK via the Imported Fever Service, especially for High Consequence Infectious Diseases. Consideration of non-infectious causes of fever and critical illness in returning travellers is also warranted. Crucially, a multidisciplinary team approach with thorough information gathering, repeated clinical review and judicious use of investigations are essential for optimal patient care.

Quantifying the impact of quarantine duration on COVID-19 transmission

The large number of individuals placed into quarantine because of possible SARS CoV-2 exposure has high societal and economic costs. There is ongoing debate about the appropriate duration of quarantine, particularly since the fraction of individuals who eventually test positive is perceived as being low. We use empirically determined distributions of incubation period, infectivity, and generation time to quantify how the duration of quarantine affects onward transmission from traced contacts of confirmed SARS-CoV-2 cases and from returning travellers. We also consider the roles of testing followed by release if negative (test-and-release), reinforced hygiene, adherence, and symptoms in calculating quarantine efficacy. We show that there are quarantine strategies based on a test-and-release protocol that, from an epidemiological viewpoint, perform almost as well as a 10 day quarantine, but with fewer person days spent in quarantine. The findings apply to both travellers and contacts, but the specifics depend on the context.

Control of COVID-19 in Australia through quarantine: the role of special health accommodation (SHA) in New South Wales, Australia

Background The first COVID-19 cases were diagnosed in Australia on 25 January 2020. Initial epidiemiology showed that the majority of cases were in returned travellers from overseas. One aspect of Public Health response was to introduce compulsory 14 day quarantine for all travellers returning to New South Wales (NSW) by air or sea in Special Health Accommodation (SHA). We aim to outline the establishment of a specialised health quarantine accommodation service in the context of the COVID-19 pandemic, and describe the first month of COVID-19 screening. Methods The SHA was established with a comprehensive governance structure, remote clinical management through Royal Prince Alfred Virtual Hospital (rpavirtual) and site management with health care workers, NSW Police and accommodation staff. Results From 29 March to 29 April 2020, 373 returning travellers were admitted to the SHA from Sydney Airport. 88 (26.1%) of those swabbed were positive for SARS-CoV 2. The day of diagnosis of COVID-19 varied from Day 1 to Day 13, with 63.6% (n = 56) of these in the first week of quarantine. 50% of the people in the SHA were referred to rpavirtual for ongoing clinical management. Seven people required admission to hospital for ongoing clinical care. Conclusion The Public Health response to COVID-19 in Australia included early and increased case detection through testing, tracing of contacts of confirmed cases, social distancing and prohibition of gatherings. In addition to these measures, the introduction of mandated quarantine for travellers to Australia was integral to the successful containment of COVID-19 in NSW and Australia through the prevention of transmission locally and interstate from returning travellers.