Whole-genome sequencing and annotation of Bacillus safensis RIT372 and Pseudomonas oryzihabitans RIT370 from Capsicum annuum (bird\u27s eye chili) and Capsicum chinense (yellow lantern chili), respectively

Here, we report the genome sequences of Bacillus safensis RIT372 and Pseudomonas oryzihabitans RIT370 from Capsicum spp. Annotation revealed gene clusters for the synthesis of bacilysin, lichensin, and bacillibactin and sporulation killing factor (skfA) in Bacillus safensis RIT372 and turnerbactin and carotenoid in Pseudomonas oryzihabitans RIT370

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Health-Related Quality of Life in Older Coastal Residents After Multiple Disasters

OBJECTIVE: Exposure to multiple disasters, both natural and technological, is associated with extreme stress and long-term consequences for older adults that are not well understood. In this article, we address age differences in health-related quality of life in older disaster survivors exposed to the 2005 Hurricanes Katrina and Rita and the 2010 BP Deepwater Horizon oil spill and the role played by social engagement in influencing these differences. METHODS: Participants were noncoastal residents, current coastal residents, and current coastal fishers who were economically affected by the BP oil spill. Social engagement was estimated on the basis of disruptions in charitable work and social support after the 2005 hurricanes relative to a typical year before the storms. Criterion measures were participants\u27 responses to the SF-36 Health Survey which includes composite indexes of physical (PCS) and mental (MCS) health. RESULTS: The results of logistic regressions indicated that age was inversely associated with SF-36 PCS scores. A reduction in perceived social support after Hurricane Katrina was also inversely associated with SF-36 MCS scores. CONCLUSIONS: These results illuminate risk factors that impact well-being among older adults after multiple disasters. Implications of these data for psychological adjustment after multiple disasters are considered. (Disaster Med Public Health Preparedness. 2017;11:90-96)

Spirituality, Humor, and Resilience After Natural and Technological Disasters

PURPOSE: Multiple exposures to disaster are associated with high levels of stress and with long-term consequences for survivors. However, little is known about coping and resilience in multiple disaster contexts. In this study, we focused on spiritual and secular coping resources and the roles they may play in postdisaster resilience. METHODS: Participants were noncoastal and coastal residents exposed to the 2005 Hurricanes Katrina and Rita and the 2010 Deepwater Horizon oil spill. Psychosocial predictors of central interest were (a) spiritual support and (b) use of coping through humor, and both were hypothesized to be associated with resilience. Covariates included group, gender, education, income, social engagement, charitable work done for others, and lifetime trauma. FINDINGS: Logistic regression analyses confirmed that spiritual support (odds ratio [OR] = 1.11, p ≤ .01) and use of coping through humor (OR = 1.17, p ≤ .01) were independently and positively associated with resilience. Disruption in charitable work done for others in a typical year before the hurricanes (OR = 0.49, p ≤ .05) and income of less than $2,000 per month were negatively associated with resilience (OR = 0.47, p ≤ .05). CONCLUSIONS: These data show that spirituality, humor, disruptions in charitable work, and low income were all independently associated with resilience in the years after consecutive disasters. CLINICAL RELEVANCE: Experiencing one or more disasters can create chronic psychosocial stress in an individual, which is associated with long-term health effects such as inflammation and weakened immune function. Recognizing which coping resources bolster resilience rather than harm is important for improving quality of life in disaster victims

Health-Related Quality of Life in Older Coastal Residents After Multiple Disasters

OBJECTIVE: Exposure to multiple disasters, both natural and technological, is associated with extreme stress and long-term consequences for older adults that are not well understood. In this article, we address age differences in health-related quality of life in older disaster survivors exposed to the 2005 Hurricanes Katrina and Rita and the 2010 BP Deepwater Horizon oil spill and the role played by social engagement in influencing these differences. METHODS: Participants were noncoastal residents, current coastal residents, and current coastal fishers who were economically affected by the BP oil spill. Social engagement was estimated on the basis of disruptions in charitable work and social support after the 2005 hurricanes relative to a typical year before the storms. Criterion measures were participants\u27 responses to the SF-36 Health Survey which includes composite indexes of physical (PCS) and mental (MCS) health. RESULTS: The results of logistic regressions indicated that age was inversely associated with SF-36 PCS scores. A reduction in perceived social support after Hurricane Katrina was also inversely associated with SF-36 MCS scores. CONCLUSIONS: These results illuminate risk factors that impact well-being among older adults after multiple disasters. Implications of these data for psychological adjustment after multiple disasters are considered. (Disaster Med Public Health Preparedness. 2017;11:90-96)

Clinical and virologic characteristics of the first 12 patients with coronavirus disease 2019 (COVID-19) in the United States.

Data on the detailed clinical progression of COVID-19 in conjunction with epidemiological and virological characteristics are limited. In this case series, we describe the first 12 US patients confirmed to have COVID-19 from 20 January to 5 February 2020, including 4 patients described previously1,2,3. Respiratory, stool, serum and urine specimens were submitted for SARS-CoV-2 real-time reverse-transcription polymerase chain reaction (rRT-PCR) testing, viral culture and whole genome sequencing. Median age was 53 years (range: 21–68); 8 patients were male. Common symptoms at illness onset were cough (n = 8) and fever (n = 7). Patients had mild to moderately severe illness; seven were hospitalized and demonstrated clinical or laboratory signs of worsening during the second week of illness. No patients required mechanical ventilation and all recovered. All had SARS-CoV-2 RNA detected in respiratory specimens, typically for 2–3 weeks after illness onset. Lowest real-time PCR with reverse transcription cycle threshold values in the upper respiratory tract were often detected in the first week and SARS-CoV-2 was cultured from early respiratory specimens. These data provide insight into the natural history of SARS-CoV-2. Although infectiousness is unclear, highest viral RNA levels were identified in the first week of illness. Clinicians should anticipate that some patients may worsen in the second week of illness