Dataset Information

High-Density Amplicon Sequencing Identifies Community Spread and Ongoing Evolution of SARS-CoV-2 in the Southern United States.

ABSTRACT: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is constantly evolving. Prior studies focused on high-case-density locations, such as the northern and western metropolitan areas of the United States. This study demonstrates continued SARS-CoV-2 evolution in a suburban southern region of the United States by high-density amplicon sequencing of symptomatic cases. 57% of strains carry the spike D614G variant, which is associated with higher genome copy numbers, and its prevalence expands with time. Four strains carry a deletion in a predicted stem loop of the 3' UTR. The data are consistent with community spread within local populations and the larger continental United States. The data instill confidence in current testing sensitivity and validate "testing by sequencing" as an option to uncover cases, particularly nonstandard coronavirus disease 2019 (COVID-19) clinical presentations. This study contributes to the understanding of COVID-19 through an extensive set of genomes from a non-urban setting and informs vaccine design by defining D614G as a dominant and emergent SARS-CoV-2 isolate in the United States.

SUBMITTER: McNamara RP

PROVIDER: S-EPMC7574689 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

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Publications

High-Density Amplicon Sequencing Identifies Community Spread and Ongoing Evolution of SARS-CoV-2 in the Southern United States.

McNamara Ryan P RP Caro-Vegas Carolina C Landis Justin T JT Moorad Razia R Pluta Linda J LJ Eason Anthony B AB Thompson Cecilia C Bailey Aubrey A Villamor Femi Cleola S FCS Lange Philip T PT Wong Jason P JP Seltzer Tischan T Seltzer Jedediah J Zhou Yijun Y Vahrson Wolfgang W Juarez Angelica A Meyo James O JO Calabre Tiphaine T Broussard Grant G Rivera-Soto Ricardo R Chappell Danielle L DL Baric Ralph S RS Damania Blossom B Miller Melissa B MB Dittmer Dirk P DP

Cell reports 20201020 5

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is constantly evolving. Prior studies focused on high-case-density locations, such as the northern and western metropolitan areas of the United States. This study demonstrates continued SARS-CoV-2 evolution in a suburban southern region of the United States by high-density amplicon sequencing of symptomatic cases. 57% of strains carry the spike D614G variant, which is associated with higher genome copy numbers, and its prevalence expan ...[more]

PMID: 33113345

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Project description:BackgroundProviding HIV/STD testing and prevention education, medical and nonmedical case management, housing assistance, transportation services, and patient navigation are just a few examples of how community-based HIV/AIDS service organizations will help the United States realize the goals of the updated National HIV/AIDS Strategy.ObjectiveIn this study, the aim was to assess electronic data security confidence level, electronic communication behaviors, and interest in using eHealth communication tools with clients of staff at community-based HIV/AIDS service organizations.MethodsStaff were recruited from 7 community-based HIV/AIDS service organizations in the southern United States (3 in South Carolina and 4 in Texas). The principal investigator used state department of health websites to identify community-based HIV/AIDS service organizations. Staff were included if they provided HIV/STD prevention education to clients. A recruitment letter was sent to community-based HIV/AIDS service organization leaders who then used snowball sampling to recruit eligible staff. Chi-square tests were used.ResultsAmong staff (n=59) who participated in the study, 66% (39/59) were very or completely confident that safeguards are in place to keep electronically shared information from being seen by other people; 68% (40/59) used email, 58% (34/59) used text messages, 25% (15/59) used social media, 15% (9/59) used a mobile app, 8% (5/59) used web-enabled videoconferencing, and 3% (2/59) used other tools (eg, electronic medical record, healthnavigator.com website) to communicate electronically with their clients. More than half were very interested in using eHealth communication tools in the future for sharing appointment reminders (67%, 38/59) and general health tips (61%, 34/59) with their clients. Half were very interested in using eHealth communication tools in the future to share HIV medication reminders with their clients (50%, 29/59). Forty percent (23/59) were very interested in using eHealth communication tools to share vaccination reminders with their clients.ConclusionsCommunity-based HIV/AIDS service organization staff had some level of confidence that safeguards were in place to keep electronically shared information from being seen by other people. This is critically important given the sensitivity of the information shared between community-based HIV/AIDS service organization staff and their clients, and because many staff were very interested in using eHealth communication tools with their clients in the future. It is very likely that eHealth communication tools can be used in community settings to improve health outcomes across the HIV care continuum; in the interim, more research is needed to better understand factors that may facilitate or impede community-based HIV/AIDS service organization staff use and client acceptability.

Project description:Abstract' backgroundFor >100 years cattle production in the southern United States has been threatened by cattle fever. It is caused by an invasive parasite-vector complex that includes the protozoan hemoparasites Babesia bovis and B. bigemina, which are transmitted among domestic cattle via Rhipicephalus tick vectors of the subgenus Boophilus. In 1906 an eradication effort was started and by 1943 Boophilus ticks had been confined to a narrow tick eradication quarantine area (TEQA) along the Texas-Mexico border. However, a dramatic increase in tick infestations in areas outside the TEQA over the last decade suggests these tick vectors may be poised to re-invade the southern United States. We investigated historical and potential future distributions of climatic habitats of cattle fever ticks to assess the potential for a range expansion.MethodsWe built robust spatial predictions of habitat suitability for the vector species Rhipicephalus (Boophilus) microplus and R. (B.) annulatus across the southern United States for three time periods: 1906, present day (2012), and 2050. We used analysis of molecular variance (AMOVA) to identify persistent tick occurrences and analysis of bias in the climate proximate to these occurrences to identify key environmental parameters associated with the ecology of both species. We then used ecological niche modeling algorithms GARP and Maxent to construct models that related known occurrences of ticks in the TEQA during 2001-2011 with geospatial data layers that summarized important climate parameters at all three time periods.ResultsWe identified persistent tick infestations and specific climate parameters that appear to be drivers of ecological niches of the two tick species. Spatial models projected onto climate data representative of climate in 1906 reproduced historical pre-eradication tick distributions. Present-day predictions, although constrained to areas near the TEQA, extrapolated well onto climate projections for 2050.ConclusionsOur models indicate the potential for range expansion of climate suitable for survival of R. microplus and R. annulatus in the southern United States by mid-century, which increases the risk of reintroduction of these ticks and cattle tick fever into major cattle producing areas.

Dataset Information

High-Density Amplicon Sequencing Identifies Community Spread and Ongoing Evolution of SARS-CoV-2 in the Southern United States.

Publications

High-Density Amplicon Sequencing Identifies Community Spread and Ongoing Evolution of SARS-CoV-2 in the Southern United States.

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