SARS-CoV-2 transmission potential and rural-urban disease burden disparities across Alabama, Louisiana, and Mississippi, March 2020 — May 2021

Purpose: To quantify and compare SARS-CoV-2 transmission potential across Alabama, Louisiana, and Mississippi and selected counties with populations in the 50th, 75th, and 100th percentile. Methods: To determine the time-varying reproduction number Rt of SARS-CoV-2, we applied the R package EpiEstim to the time series of daily incidence of confirmed cases. Median Rt percentage change when policies changed was determined. Linear regression was performed between log10-transformed cumulative incidence and log10-transformed population size at four time points. Results: Stay-at-home orders, face mask mandates, and vaccinations were associated with the most significant reductions in SARS-CoV-2 transmission in the three southern states. Rt across the three states decreased significantly by 20% following stay-at-home orders. We observed varying degrees of reductions in Rt across states following other policies. Rural Alabama counties experienced higher per capita cumulative cases relative to urban ones as of June 17 and October 17, 2020. Meanwhile, Louisiana and Mississippi saw the disproportionate impact of SARS-CoV-2 in rural counties compared to urban ones throughout the study period. Conclusion: State and county policies had an impact on local pandemic trajectories. The rural-urban disparities in case burden call for evidence-based approaches in tailoring health promotion interventions and vaccination campaigns to rural residents.

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Transmission potential of COVID-19 in South Korea

10.1101/2020.02.27.20028829 ◽

2020 ◽

Cited By ~ 23

Author(s):

Eunha Shim ◽

Amna Tariq ◽

Wongyeong Choi ◽

Yiseul Lee ◽

Gerardo Chowell

Keyword(s):

South Korea ◽

Reproduction Number ◽

Social Distancing ◽

Transmission Potential ◽

Incidence Data ◽

Novel Coronavirus

AbstractSince the first identified individual of 2019 novel coronavirus (COVID-19) infection on Jan 20, 2020 in South Korea, the number of confirmed cases rapidly increased. As of Feb 26, 2020, 1,261 cases of COVID-19 including 12 deaths were confirmed in South Korea. Using the incidence data of COVID-19, we estimate the reproduction number at 1.5 (95% CI: 1.4-1.6), which indicates sustained transmission and support the implementation of social distancing measures to rapidly control the outbreak.

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Early epidemiological assessment of the transmission potential and virulence of coronavirus disease 2019 (COVID-19) in Wuhan City: China, January-February, 2020

10.1101/2020.02.12.20022434 ◽

2020 ◽

Cited By ~ 40

Author(s):

Kenji Mizumoto ◽

Katsushi Kagaya ◽

Gerardo Chowell

Keyword(s):

Basic Reproduction Number ◽

Reproduction Number ◽

Public Health Intervention ◽

Ecological Modelling ◽

The Novel ◽

Wuhan City ◽

Transmission Potential ◽

The World ◽

Novel Coronavirus ◽

Epidemiological Parameters

AbstractBackgroundSince the first cluster of cases was identified in Wuhan City, China, in December, 2019, coronavirus disease 2019 (COVID-19) rapidly spread around the world. Despite the scarcity of publicly available data, scientists around the world have made strides in estimating the magnitude of the epidemic, the basic reproduction number, and transmission patterns. Accumulating evidence suggests that a substantial fraction of the infected individuals with the novel coronavirus show little if any symptoms, which highlights the need to reassess the transmission potential of this emerging disease. In this study, we derive estimates of the transmissibility and virulence of COVID-19 in Wuhan City, China, by reconstructing the underlying transmission dynamics using multiple data sources.MethodsWe employ statistical methods and publicly available epidemiological datasets to jointly derive estimates of transmissibility and severity associated with the novel coronavirus. For this purpose, the daily series of laboratory–confirmed COVID-19 cases and deaths in Wuhan City together with epidemiological data of Japanese repatriated from Wuhan City on board government–chartered flights were integrated into our analysis.ResultsOur posterior estimates of basic reproduction number (R) in Wuhan City, China in 2019–2020 reached values at 3.49 (95%CrI: 3.39–3.62) with a mean serial interval of 6.0 days, and the enhanced public health intervention after January 23rd in 2020 was associated with a significantly reduced R at 0.84 (95%CrI: 0.81–0.88), with the total number of infections (i.e. cumulative infections) estimated at 1906634 (95%CrI: 1373500–2651124) in Wuhan City, elevating the overall proportion of infected individuals to 19.1% (95%CrI: 13.5–26.6%). We also estimated the most recent crude infection fatality ratio (IFR) and time–delay adjusted IFR at 0.04% (95% CrI: 0.03%–0.06%) and 0.12% (95%CrI: 0.08–0.17%), respectively, estimates that are several orders of magnitude smaller than the crude CFR estimated at 4.06%ConclusionsWe have estimated key epidemiological parameters of the transmissibility and virulence of COVID-19 in Wuhan, China during January-February, 2020 using an ecological modelling approach. The power of this approach lies in the ability to infer epidemiological parameters with quantified uncertainty from partial observations collected by surveillance systems.

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The Role of Migration in Maintaining the Transmission of Avian Influenza in Waterfowl: A Multisite Multispecies Transmission Model along East Asian-Australian Flyway

Canadian Journal of Infectious Diseases and Medical Microbiology ◽

10.1155/2018/3420535 ◽

2018 ◽

Vol 2018 ◽

pp. 1-7 ◽

Cited By ~ 1

Author(s):

Akira Endo ◽

Hiroshi Nishiura

Keyword(s):

Avian Influenza ◽

Reproduction Number ◽

Transmission Rate ◽

Temporal Variations ◽

Transmission Model ◽

Global Dynamics ◽

Long Distance ◽

Transmission Potential ◽

Influenza Transmission

Background. Migratory waterfowl annually migrate over the continents along the routes known as flyways, serving as carriers of avian influenza virus across distant locations. Prevalence of influenza varies with species, and there are also geographical and temporal variations. However, the role of long-distance migration in multispecies transmission dynamics has yet to be understood. We constructed a mathematical model to capture the global dynamics of avian influenza, identifying species and locations that contribute to sustaining transmission.Methods. We devised a multisite, multispecies SIS (susceptible-infectious-susceptible) model, and estimated transmission rates within and between species in each geographical location from prevalence data. Parameters were directly sampled from posterior distribution under Bayesian inference framework. We then analyzed contribution of each species in each location to the global patterns of influenza transmission.Results. Transmission and migration parameters were estimated by Bayesian posterior sampling. The basic reproduction number was estimated at 1.1, slightly above the endemic threshold. Mallard was found to be the most important host with the highest transmission potential, and high- and middle-latitude regions appeared to act as hotspots of influenza transmission. The local reproduction number suggested that the prevalence of avian influenza in the Oceania region is dependent on the inflow of infected birds from other regions.Conclusion. Mallard exhibited the highest transmission rate among the species explored. Migration was suggested to be a key factor of the global prevalence of avian influenza, as transmission is locally sustainable only in the northern hemisphere, and the virus could be extinct in the Oceania region without migration.

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Variation in relapse frequency and the transmission potential of Plasmodium vivax malaria

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2016.0048 ◽

2016 ◽

Vol 283 (1827) ◽

pp. 20160048 ◽

Cited By ~ 32

Author(s):

Michael T. White ◽

George Shirreff ◽

Stephan Karl ◽

Azra C. Ghani ◽

Ivo Mueller

Keyword(s):

Plasmodium Vivax ◽

Reproduction Number ◽

Phenotypic Diversity ◽

Substantial Variation ◽

Seasonal Transmission ◽

Transmission Potential ◽

Plasmodium Vivax Malaria ◽

Tropical Areas ◽

First Relapse ◽

Selection Of

There is substantial variation in the relapse frequency of Plasmodium vivax malaria, with fast-relapsing strains in tropical areas, and slow-relapsing strains in temperate areas with seasonal transmission. We hypothesize that much of the phenotypic diversity in P. vivax relapses arises from selection of relapse frequency to optimize transmission potential in a given environment, in a process similar to the virulence trade-off hypothesis. We develop mathematical models of P. vivax transmission and calculate the basic reproduction number R 0 to investigate how transmission potential varies with relapse frequency and seasonality. In tropical zones with year-round transmission, transmission potential is optimized at intermediate relapse frequencies of two to three months: slower-relapsing strains increase the opportunity for onward transmission to mosquitoes, but also increase the risk of being outcompeted by faster-relapsing strains. Seasonality is an important driver of relapse frequency for temperate strains, with the time to first relapse predicted to be six to nine months, coinciding with the duration between seasonal transmission peaks. We predict that there is a threshold degree of seasonality, below which fast-relapsing tropical strains are selected for, and above which slow-relapsing temperate strains dominate, providing an explanation for the observed global distribution of relapse phenotypes.

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Estimation of the Time-dependent Reproduction Number of Influenza A(H1N1)pdm2009 in South Korea

10.21203/rs.3.rs-20387/v1 ◽

2020 ◽

Author(s):

Yunjeong Lee ◽

Dong Han Lee ◽

Hee-Dae Kwon ◽

Changsoo Kim ◽

Jeehyun Lee

Keyword(s):

South Korea ◽

Influenza A ◽

Reproduction Number ◽

Time Estimation ◽

Time Dependent ◽

Estimation Of Parameters ◽

Transmission Potential ◽

Reproduction Numbers ◽

Influenza A H1n1 ◽

Feasible Range

Abstract Background: The reproduction number is one of the most crucial parameters in determining disease dynamics, providing a summary measure of the transmission potential. However, estimating this value is particularly challenging owing to the characteristics of epidemic data, including non-reproducibility and incompleteness.Methods: In this study, we propose mathematical models with different population structures; each of these models can produce data on the number of cases of the influenza A(H1N1)pdm09 epidemic in South Korea. These structured models incorporating the heterogeneity of age and region are used to estimate the time-dependent effective reproduction numbers. Subsequently, the age- and region-specific reproduction numbers are also computed to analyze the differences illustrated in the incidence data.Results: The basic SIR fails to provide a reasonable estimation of the reproduction numbers. The estimated values demonstrate a large variation and remains outside of the feasible range for the influenza, regardless of the time period for data. Real-time estimation using age- and region-structured models demonstrated that the effective reproduction number rose sharply during mid-October when the ㅜumber of patients increased dramatically. The reproduction number fell below unity at the end of October and stayed lower than unity indicating that the epidemic starts decreasing, which is consistent with the incidence data.Conclusions: Numerical results reveal that the introduction of heterogeneity into the population to represent the general characteristics of dynamics is essential for the robust estimation of parameters.

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Transmission potential of COVID-19 in Iran

10.1101/2020.03.08.20030643 ◽

2020 ◽

Cited By ~ 7

Author(s):

Kamalich Muniz-Rodriguez ◽

Isaac Chun-Hai Fung ◽

Shayesteh R. Ferdosi ◽

Sylvia K. Ofori ◽

Yiseul Lee ◽

...

Keyword(s):

Growth Model ◽

Doubling Time ◽

Reproduction Number ◽

Transmission Potential

AbstractWe estimated the reproduction number of 2020 Iranian COVID-19 epidemic using two different methods: R0 was estimated at 4.4 (95% CI, 3.9, 4.9) (generalized growth model) and 3.50 (1.28, 8.14) (epidemic doubling time) (February 19 - March 1) while the effective R was estimated at 1.55 (1.06, 2.57) (March 6-19).

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Disease Burden of Patients Living With Hypoparathyroidism: Results From the Voices of Hypopara Survey

Journal of the Endocrine Society ◽

10.1210/jendso/bvab048.529 ◽

2021 ◽

Vol 5 (Supplement_1) ◽

pp. A260-A261

Author(s):

Deborah Murphy ◽

Bob Sanders ◽

Loretta Gulley ◽

Ami Knoefler ◽

Alden Smith ◽

...

Keyword(s):

Vitamin D ◽

Serum Calcium ◽

Disease Burden ◽

Vitamin D Supplementation ◽

Urgent Care ◽

Monitoring Device ◽

Active Vitamin ◽

The Past ◽

Active Vitamin D ◽

At Home

Abstract Background: Hypoparathyroidism (HP) is a rare disease that is characterized by insufficient levels of parathyroid hormone, resulting in hypocalcemia, hyperphosphatemia and hypercalciuria. Standard of care (SoC) consists of calcium and active vitamin D supplementation. Some patients may suffer from “calcium crashes”, sudden hypocalcemia symptoms that can be severe enough to require a visit to the emergency room (ER) or urgent care. Conversely, chronic use of SoC supplements can also increase risk of hypercalciuria and renal failure. The HypoPARAthyroidism Association (HPA), a nonprofit organization dedicated to improving the lives of hypoparathyroid patients, developed the “Voices of Hypopara” survey to capture the journey of patients with HP in the US. Methods: The online survey was distributed to all HPA members (approximately 1,000) in May 2020. Questions focused on evaluating patients’ experiences including diagnosis, treatment, quality of care, and impact on daily living. Results: The survey was completed by 146 HPA members (89% female; mean age 51). Most participants reported they are currently taking SoC (calcium 91%; active vitamin D 77%). However, over half felt that this did not optimally address their disease and 29% were extremely concerned about hypocalcemia despite supplementation. Many (69%) felt that taking SoC was moderately to extremely burdensome. More than two-thirds (69%) of respondents reported a “calcium crash” in the past year; of these, 43% reported calcium crashes monthly or weekly. Almost half (42%) of all participants required a visit to an ER/urgent care in the last year as a result of HP symptoms; of these, 56% believed that the staff was inexperienced with management of a calcium crash. More than 60% of participants checked serum calcium levels at least every couple of months at a physician’s office or lab in the past year, with 36% checking monthly or more frequently; the majority of respondents (70%) said the reason was due to symptoms of hypocalcemia. Participants viewed an at-home device for measuring serum calcium, phosphate, and magnesium levels as one key approach to manage their HP symptoms (47% ranked as “most preferred”), followed by more effective medications as the second most preferred option (23%). Almost all (99%) responded that they would use an at-home monitoring device and would test frequently. Conclusions: Results from this survey underscore the high disease burden of patients with HP, highlighting sudden hypocalcemic episodes as a key morbidity despite treatment with calcium and active vitamin D supplementation, and sub-optimal management by clinicians as an impediment to optimal treatment. These findings reinforce the need for more frequent, easily accessible, and real-time serum calcium level monitoring device, more efficacious therapies, and greater disease understanding among health care workers to best manage patients with HP.

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Rising evidence of COVID-19 transmission potential to and between animals: do we need to be concerned?

10.1101/2020.05.21.20109041 ◽

2020 ◽

Cited By ~ 1

Author(s):

Andrei R. Akhmetzhanov ◽

Natalie M. Linton ◽

Hiroshi Nishiura

Keyword(s):

Severe Acute Respiratory Syndrome ◽

Confidence Interval ◽

Reproduction Number ◽

Close Contact ◽

Case Reports ◽

Domestic Dogs ◽

Transmission Potential ◽

Pet Owners ◽

Using Data ◽

The Basic Reproduction Number

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2)—the virus that causes coronavirus disease (COVID-19)—has been detected in domestic dogs and cats, raising concerns of transmission from, to, or between these animals. There is currently no indication that feline- or canine-to-human transmission can occur, though there is rising evidence of the reverse. To explore the extent of animal-related transmission, we aggregated 17 case reports on confirmed SARS-CoV-2 infections in animals as of 15 May 2020. All but two animals fully recovered and had only mild respiratory or digestive symptoms. Using data from probable cat-to-cat transmission in Wuhan, China, we estimated the basic reproduction number R0 under this scenario at 1.09 (95% confidence interval: 1.05, 1.13). This value is much lower than the R0 reported for humans and close to one, indicating that the sustained transmission between cats is unlikely to occur. Our results support the view that the pet owners and other persons with COVID-19 in close contact with animals should be cautious of the way they interact with them.

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Transmission potential of the novel coronavirus (COVID-19) onboard the Diamond Princess Cruises Ship, 2020

10.1101/2020.02.24.20027649 ◽

2020 ◽

Cited By ~ 8

Author(s):

Kenji Mizumoto ◽

Gerardo Chowell

Keyword(s):

Mathematical Modeling ◽

Time Series ◽

Reproduction Number ◽

Transmission Dynamics ◽

The Novel ◽

Epidemic Threshold ◽

Transmission Potential ◽

Incidence Data ◽

The Mean ◽

Novel Coronavirus

AbstractAn outbreak of COVID-19 developed aboard the Princess Cruises Ship during January-February 2020. Using mathematical modeling and time-series incidence data describing the trajectory of the outbreak among passengers and crew members, we characterize how the transmission potential varied over the course of the outbreak. Our estimate of the mean reproduction number in the confined setting reached values as high as ∼11, which is higher than mean estimates reported from community-level transmission dynamics in China and Singapore (approximate range: 1.1-7). Our findings suggest that Rt decreased substantially compared to values during the early phase after the Japanese government implemented an enhanced quarantine control. Most recent estimates of Rt reached values largely below the epidemic threshold, indicating that a secondary outbreak of the novel coronavirus was unlikely to occur aboard the Diamond Princess Ship.

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The long-term dynamics of tuberculosis and other diseases with long serial intervals: implications of and for changing reproduction numbers

Epidemiology and Infection ◽

10.1017/s0950268898001113 ◽

1998 ◽

Vol 121 (2) ◽

pp. 309-324 ◽

Cited By ~ 36

Author(s):

E. VYNNYCKY ◽

P. E. M. FINE

Keyword(s):

Infectious Disease ◽

Basic Reproduction Number ◽

Reproduction Number ◽

England And Wales ◽

Transmission Potential ◽

Reproduction Numbers ◽

Serial Interval ◽

Net Reproduction ◽

Epidemiological Parameters ◽

The Basic Reproduction Number

The net and basic reproduction numbers are among the most widely-applied concepts in infectious disease epidemiology. A net reproduction number (the average number of secondary infectious cases resulting from each case in a given population) of above 1 is conventionally associated with an increase in incidence; the basic reproduction number (defined analogously for a ‘totally susceptible’ population) provides a standard measure of the ‘transmission potential’ of an infection. Using a model of the epidemiology of tuberculosis in England and Wales since 1900, we demonstrate that these measures are difficult to apply if disease can follow reinfection, and that they lose their conventional interpretations if important epidemiological parameters, such as the rate of contact between individuals, change over the time interval between successive cases in a chain of transmission (the serial interval).The net reproduction number for tuberculosis in England and Wales appears to have been approximately 1 from 1900 until 1950, despite concurrent declines in morbidity and mortality rates, and it declined rapidly in the second half of this century. The basic reproduction number declined from about 3 in 1900, reached 2 by 1950, and first fell below 1 in about 1960. Reductions in effective contact between individuals over this period, measured in terms of the average number of individuals to whom each case could transmit the infection, meant that the conventional basic reproduction number measure (which does not consider subsequent changes in epidemiological parameters) for a given year failed to reflect the ‘actual transmission potential’ of the infection. This latter property is better described by a variant of the conventional measure which takes secular trends in contact into account. These results are relevant for the interpretation of trends in any infectious disease for which epidemiological parameters change over time periods comparable to the infectious period, incubation period or serial interval.

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