Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States.

The novel coronavirus SARS-CoV-2 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 United States, 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 effects of federal travel restrictions. This study provides evidence of widespread sustained transmission of SARS-CoV-2 within the United States and highlights the critical need for local surveillance.

Impact of a Public Policy Restricting Staff Mobility Between Nursing Homes in Ontario, Canada During the COVID-19 Pandemic.

OBJECTIVES: To assess changes in the mobility of staff between nursing homes in Ontario, Canada, before and after enactment of public policy restricting staff from working at multiple homes. DESIGN: Pre-post observational study. SETTING AND PARTICIPANTS: 623 nursing homes in Ontario, Canada, between March 2020 and June 2020. METHODS: We used GPS location data from mobile devices to approximate connectivity between all 623 nursing homes in Ontario during the 7 weeks before (March 1-April 21) and after (April 22-June 13) the policy restricting staff movement was implemented. We constructed a network diagram visualizing connectivity between nursing homes in Ontario and calculated the number of homes that had a connection with another nursing home and the average number of connections per home in each period. We calculated the relative difference in these mobility metrics between the 2 time periods and compared within-home changes using McNemar test and the Wilcoxon rank-sum test. RESULTS: In the period preceding restrictions, 266 (42.7%) nursing homes had a connection with at least 1 other home, compared with 79 (12.7%) homes during the period after restrictions, a drop of 70.3% (P < .001). Including all homes, the average number of connections in the before period was 3.90 compared to 0.77 in the after period, a drop of 80.3% (P < .001). In both periods, mobility between nursing homes was higher in homes located in larger communities, those with higher bed counts, and those part of a large chain. CONCLUSIONS AND IMPLICATIONS: Mobility between nursing homes in Ontario fell sharply after an emergency order by the Ontario government limiting long-term care staff to a single home, though some mobility persisted. Reducing this residual mobility should be a focus of efforts to reduce risk within the long-term care sector during the COVID-19 pandemic.

Global trends in air travel: implications for connectivity and resilience to infectious disease threats.

BACKGROUND: Increased connectivity via air travel can facilitate the geographic spread of infectious diseases. The number of travellers alone does not explain risk; passenger origin and destination will also influence risk of disease introduction and spread. We described trends in international air passenger numbers and connectivity between countries with different capacities to detect and respond to infectious disease threats. METHODS: We used the Fragile States Index (FSI) as an annual measure of country-level resilience and capacity to respond to infectious disease events. Countries are categorized as: Sustainable, Stable, Warning or Alert, in order of increasing fragility. We included data for 177 sovereign states for the years 2010 to 2019. Annual inbound and outbound international air passengers for each country were obtained for the same time period. We examined trends in FSI score, trends in worldwide air travel and the association between a state's FSI score and air travel. RESULTS: Among countries included in the FSI rankings, the total number of outbound passengers increased from 0.865 billion to 1.58 billion between 2010 and 2019. Increasing fragility was associated with a decrease in travel volumes, with a 2.5% (95% CI: 2.0-3.1%) reduction in passengers per 1-unit increase in FSI score. Overall, travel between countries of different FSI categories either increased or remained stable. CONCLUSIONS: The world's connectivity via air travel has increased dramatically over the past decade. There has been notable growth in travel from Warning and Stable countries, which comprise more than three-quarters of international air travel passengers. These countries may have suboptimal capacity to detect and respond to infectious disease threats that emerge within their borders.

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

Since 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.

Ebola virus outbreak in North Kivu and Ituri provinces, Democratic Republic of Congo, and the potential for further transmission through commercial air travel.

BACKGROUND: The 2018-2019 Ebola virus disease (EVD) outbreak in North Kivu and Ituri provinces, Democratic Republic of Congo (DRC), continues to spread. The recent discovery of cases in Uganda and in Goma, a major city in the eastern DRC, raises concern for potential EVD transmission in distant locales via commercial air travel. METHODS: We examined air travel patterns from the affected region with itinerary-level data from the International Air Transport Association for the year 2018 between July and October, inclusive. We focused on three scenarios: (i) travel from Beni airport, (ii) travel from Beni, Goma and Bunia airports and (iii) travel from Beni, Goma and Bunia, and Kigali airports. We evaluated country-level Infectious Disease Vulnerability Index (IDVI) scores for traveller destinations. RESULTS: There were 2255 commercial air passengers departing from Beni Airport during the specified time frame, all with domestic destinations, and 55% of which were to Goma. A total of 29 777 passengers travelled from Beni, Bunia and Goma airports during this time frame, with most travel (94.6%) departing from Goma Airport. A total of 72.4% of passengers' final destination from these three airports were within the DRC, primarily to Kinshasa. There were 166 281 outbound passengers from Beni, Bunia, Goma and Kigali airports with the majority (82.1%) of passengers departing from Kigali. The most frequent destinations from these airports were Nairobi, Kinshasa and Entebbe. Eight of the 10 destinations with greatest passenger volumes are to countries with IDVI scores less than 0.4. CONCLUSION: There is little commercial airline connectivity from the current EVD-affected area; however, larger cities in DRC and throughout East Africa should be aware of the low potential for EVD importation through this route. Most countries at greatest risk for EVD importation have limited capacity to manage these cases.

Countries at risk of importation of chikungunya virus cases from Southern Thailand: A modeling study.

Southern Thailand has been experiencing a large chikungunya virus (CHIKV) outbreak since October 2018. Given the magnitude and duration of the outbreak and its location in a popular tourist destination, we sought to determine international case exportation risk and identify countries at greatest risk of receiving travel-associated imported CHIKV cases. We used a probabilistic model to estimate the expected number of exported cases from Southern Thailand between October 2018 and April 2019. The model incorporated data on CHIKV natural history, infection rates in Southern Thailand, average length of stay for tourists, and international outbound air passenger numbers from the outbreak area. For countries highly connected to Southern Thailand by air travel, we ran 1000 simulations to estimate the expected number of imported cases. We also identified destination countries with conditions suitable for autochthonous CHIKV transmission. Over the outbreak period, we estimated that an average of 125 (95% credible interval (CrI): 102-149) cases would be exported from Southern Thailand to international destinations via air travel. China was projected to receive the most cases (43, 95% CrI: 30-56), followed by Singapore (7, 95% CrI: 2-12) and Malaysia (5, 95% CrI: 1-10). Twenty-three countries were projected to receive at least one imported case, and 64% of these countries had one or more regions that could potentially support autochthonous CHIKV transmission. The overall risk of international exportation of CHIKV cases associated with the outbreak is Southern Thailand is high. Our model projections are consistent with recent reports of CHIKV in travelers returning from the region. Countries should be alert to the possibility of CHIKV infection in returning travelers, particularly in regions where autochthonous transmission is possible.

Potential for Seasonal Lassa Fever Case Exportation from Nigeria.

The largest epidemic of Lassa fever in recent history occurred in Nigeria in 2018. We assessed the potential for cases of Lassa fever originating in Nigeria to arrive at international destinations via air travel using a probabilistic model. We estimated no exported cases in 62% of 1,000 model simulations. In 30% of simulations, a single exported case was projected. Greater than 40% of outbound travelers from Nigeria arrived in the United States, the United Kingdom, and Ghana, placing these countries at greatest risk for receiving an exported case. There was a wide range in the capacity of highly connected countries to respond to infectious disease threats, as measured by the Infectious Disease Vulnerability Index. Although we quantified a low probability of case exportation during this outbreak, countries with the greatest connectivity to Nigeria should be alert to the potential risks of Lassa fever importation and be prepared to manage infected individuals.

Association between air travel and importation of chikungunya into the USA.

Background: During infectious disease outbreaks with pandemic potential, the number of air passengers travelling from the outbreak source to international destinations has been used as a proxy for disease importation risk to new locations. However, evaluations of the validity of this approach are limited. We sought to quantify the association between international air travel and disease importation using the 2014-2016 chikungunya outbreak in the Americas as a case study.Methods: We used country-level chikungunya case data to define a time period of epidemic activity for each of the 45 countries and territories in the Americas reporting outbreaks between 2014 and 2016. For each country, we identified airports within or proximate to areas considered suitable for chikungunya transmission and summed the number of commercial air passengers departing from these airports during the epidemic period to each US state. We used negative binomial models to quantify the association between the number of incoming air passengers from countries experiencing chikungunya epidemics and the annual rate of chikungunya importation into the USA at the state level.Results: We found a statistically significant positive association between passenger flows via airline travel from countries experiencing chikungunya epidemics and the number of imported cases in the USA at the state level (P < 0.0001). Additionally, we found that as the number of arriving airline passengers increased by 10%, the estimated number of imported cases increased by 5.2% (95% CI: 3.0-7.6).Conclusion: This validation study demonstrated that air travel was strongly associated with observed importation of chikungunya cases in the USA and can be a useful proxy for identifying areas at increased risk for disease importation. This approach may be useful for understanding exportation risk of other arboviruses.

Emergence of the Asian lineage of Zika virus in Angola: an outbreak investigation.

BACKGROUND: Zika virus infections and suspected microcephaly cases have been reported in Angola since late 2016, but no data are available about the origins, epidemiology, and diversity of the virus. We aimed to investigate the emergence and circulation of Zika virus in Angola. METHODS: Diagnostic samples collected by the Angolan Ministry of Health as part of routine arboviral surveillance were tested by real-time reverse transcription PCR by the Instituto Nacional de Investigação em Saúde (Ministry of Health, Luanda, Angola). To identify further samples positive for Zika virus and appropriate for genomic sequencing, we also tested samples from a 2017 study of people with HIV in Luanda. Portable sequencing was used to generate Angolan Zika virus genome sequences from three people positive for Zika virus infection by real-time reverse transcription PCR, including one neonate with microcephaly. Genetic and mobility data were analysed to investigate the date of introduction and geographical origin of Zika virus in Angola. Brain CT and MRI, and serological assays were done on a child with microcephaly to confirm microcephaly and assess previous Zika virus infection. FINDINGS: Serum samples from 54 people with suspected acute Zika virus infection, 76 infants with suspected microcephaly, 24 mothers of infants with suspected microcephaly, 336 patients with suspected dengue virus or chikungunya virus infection, and 349 samples from the HIV study were tested by real-time reverse transcription PCR. Four cases identified between December, 2016, and June, 2017, tested positive for Zika virus. Analyses of viral genomic and human mobility data suggest that Zika virus was probably introduced to Angola from Brazil between July, 2015, and June, 2016. This introduction probably initiated local circulation of Zika virus in Angola that continued until at least June, 2017. The infant with microcephaly in whom CT and MRI were done had brain abnormalities consistent with congenital Zika syndrome and serological evidence for Zika virus infection. INTERPRETATION: Our analyses show that autochthonous transmission of the Asian lineage of Zika virus has taken place in Africa. Zika virus surveillance and surveillance of associated cases of microcephaly throughout the continent is crucial. FUNDING: Royal Society, Wellcome Trust, Global Challenges Research Fund (UK Research and Innovation), Africa Oxford, John Fell Fund, Oxford Martin School, European Research Council, Departamento de Ciência e Tecnologia/Ministério da Saúde/National Council for Scientific and Technological Development, and Ministério da Educação/Coordenação de Aperfeicoamento de Pessoal de Nível Superior.

Elevation as a proxy for mosquito-borne Zika virus transmission in the Americas.

INTRODUCTION: When Zika virus (ZIKV) first began its spread from Brazil to other parts of the Americas, national-level travel notices were issued, carrying with them significant economic consequences to affected countries. Although regions of some affected countries were likely unsuitable for mosquito-borne transmission of ZIKV, the absence of high quality, timely surveillance data made it difficult to confidently demarcate infection risk at a sub-national level. In the absence of reliable data on ZIKV activity, a pragmatic approach was needed to identify subnational geographic areas where the risk of ZIKV infection via mosquitoes was expected to be negligible. To address this urgent need, we evaluated elevation as a proxy for mosquito-borne ZIKV transmission. METHODS: For sixteen countries with local ZIKV transmission in the Americas, we analyzed (i) modelled occurrence of the primary vector for ZIKV, Aedes aegypti, (ii) human population counts, and (iii) reported historical dengue cases, specifically across 100-meter elevation levels between 1,500m and 2,500m. Specifically, we quantified land area, population size, and the number of observed dengue cases above each elevation level to identify a threshold where the predicted risks of encountering Ae. aegypti become negligible. RESULTS: Above 1,600m, less than 1% of each country's total land area was predicted to have Ae. aegypti occurrence. Above 1,900m, less than 1% of each country's resident population lived in areas where Ae. aegypti was predicted to occur. Across all 16 countries, 1.1% of historical dengue cases were reported above 2,000m. DISCUSSION: These results suggest low potential for mosquito-borne ZIKV transmission above 2,000m in the Americas. Although elevation is a crude predictor of environmental suitability for ZIKV transmission, its constancy made it a pragmatic input for policy decision-making during this public health emergency.

Potential for Zika virus introduction and transmission in resource-limited countries in Africa and the Asia-Pacific region: a modelling study.

BACKGROUND: As the epidemic of Zika virus expands in the Americas, countries across Africa and the Asia-Pacific region are becoming increasingly susceptible to the importation and possible local spread of the virus. To support public health readiness, we aim to identify regions and times where the potential health, economic, and social effects from Zika virus are greatest, focusing on resource-limited countries in Africa and the Asia-Pacific region. METHODS: Our model combined transportation network analysis, ecological modelling of mosquito occurrences, and vector competence for flavivirus transmission, using data from the International Air Transport Association, entomological observations from Zika's primary vector species, and climate conditions using WorldClim. We overlaid monthly flows of airline travellers arriving to Africa and the Asia-Pacific region from areas of the Americas suitable for year-round transmission of Zika virus with monthly maps of climatic suitability for mosquito-borne transmission of Zika virus within Africa and the Asia-Pacific region. FINDINGS: An estimated 2·6 billion people live in areas of Africa and the Asia-Pacific region where the presence of competent mosquito vectors and suitable climatic conditions could support local transmission of Zika virus. Countries with large volumes of travellers arriving from Zika virus-affected areas of the Americas and large populations at risk of mosquito-borne Zika virus infection include India (67 422 travellers arriving per year; 1·2 billion residents in potential Zika transmission areas), China (238 415 travellers; 242 million residents), Indonesia (13 865 travellers; 197 million residents), Philippines (35 635 travellers; 70 million residents), and Thailand (29 241 travellers; 59 million residents). INTERPRETATION: Many countries across Africa and the Asia-Pacific region are vulnerable to Zika virus. Strategic use of available health and human resources is essential to prevent or mitigate the health, economic, and social consequences of Zika virus, especially in resource-limited countries. FUNDING: Canadian Institutes of Health Research and the US Centers for Disease Control and Prevention.

Urbanization, Grassland, and Diet Influence Coyote (Canis latrans) Parasitism Structure.

Land use change can alter the ecological mechanisms that influence infectious disease exposure in animal populations. However, few studies have empirically integrated the environmental, spatial, and dietary patterns of wildlife epidemiology. We investigate how urbanization, habitat type, and dietary behavior are associated with coyote (Canis latrans) parasitism structure along a gradient of rural to urban land cover using multivariate redundancy analyses. Coyote fecal samples were collected in eight urban and six rural sites in Calgary, Alberta, Canada. Parasite and diet components were identified using common flotation procedures and fecal dietary analysis, respectively. Redundancy analysis was used to identify the best land cover, connectivity, and dietary predictors. We tested for significance using multiple permutation tests and ANOVAs. Significant factors affecting enteric parasite prevalence included dietary and land cover factors (R (2) = 0.4130, P < 0.05). Variation in dietary behavior was observed between urban and rural sites (R (2) = 0.4712, P < 0.05), as anthropogenic diet items (i.e., garbage, crabapples) were strongly influenced by urbanization. Our research supports that developed habitat, grassland cover, and dietary choice interact to possibly influence the exposure of coyote hosts to enteric parasites and pioneers future investigation of disease ecology for natural populations in anthropogenic landscapes.

How spatio-temporal habitat connectivity affects amphibian genetic structure.

Heterogeneous landscapes and fluctuating environmental conditions can affect species dispersal, population genetics, and genetic structure, yet understanding how biotic and abiotic factors affect population dynamics in a fluctuating environment is critical for species management. We evaluated how spatio-temporal habitat connectivity influences dispersal and genetic structure in a population of boreal chorus frogs (Pseudacris maculata) using a landscape genetics approach. We developed gravity models to assess the contribution of various factors to the observed genetic distance as a measure of functional connectivity. We selected (a) wetland (within-site) and (b) landscape matrix (between-site) characteristics; and (c) wetland connectivity metrics using a unique methodology. Specifically, we developed three networks that quantify wetland connectivity based on: (i) P. maculata dispersal ability, (ii) temporal variation in wetland quality, and (iii) contribution of wetland stepping-stones to frog dispersal. We examined 18 wetlands in Colorado, and quantified 12 microsatellite loci from 322 individual frogs. We found that genetic connectivity was related to topographic complexity, within- and between-wetland differences in moisture, and wetland functional connectivity as contributed by stepping-stone wetlands. Our results highlight the role that dynamic environmental factors have on dispersal-limited species and illustrate how complex asynchronous interactions contribute to the structure of spatially-explicit metapopulations.