Investigation of large structural variants (SVs) is a challenging yet important task in understanding trait differences in highly repetitive genomes. Combining different bioinformatic approaches for ...SV detection, we analyzed whole-genome sequencing data from 3000 rice genomes and identified 63 million individual SV calls that grouped into 1.5 million allelic variants. We found enrichment of long SVs in promoters and an excess of shorter variants in 5' UTRs. Across the rice genomes, we identified regions of high SV frequency enriched in stress response genes. We demonstrated how SVs may help in finding causative variants in genome-wide association analysis. These new insights into rice genome biology are valuable for understanding the effects SVs have on gene function, with the prospect of identifying novel agronomically important alleles that can be utilized to improve cultivated rice.
By July 25, Colombia had confirmed 240 795 cases of COVID-19 and 8269 deaths (case fatality rate of 3.4%).
All departments had reported cases, but 292 municipalities were apparently free of COVID-19 ...(26%) and 373 (33.2%) had seen limited transmission.
Specific mortality rates by department ranged from 0 in Vichada to 1278 in Amazonas, which was 7.8 times the national rate (incidence rate ratio (IRR) = 7.8, 95% confidence interval 6.4–9.5).
Using a conservative approach to assess the potential underestimation of cases, it was estimated that, by July 25, Colombia should have detected 1 328 175 cases instead of the actual 240 795 observed, an underestimation of 82%.
Colombia detected its first coronavirus disease 2019 (COVID-19) case on March 2, 2020. From March 22 to April 25, it implemented a national lockdown that, apparently, allowed the country to keep a low incidence and mortality rate up to mid-May. Forced by the economic losses, the government then opened many commercial activities, which was followed by an increase in cases and deaths. This paper presents a critical analysis of the Colombian surveillance data in order to identify strengths and pitfalls of the control measures.
A descriptive analysis of PCR-confirmed cases between March and July 25 was performed. Data were described according to the level of measurement. Incidence and mortality rates of COVID-19 were estimated by age, sex, and geographical area. Sampling rates for suspected cases were estimated by geographical area, and the potential for case underestimation was assessed using sampling differences.
By July 25, Colombia (population 50 372 424) had reported 240 745 cases and 8269 deaths (case fatality rate of 3.4%). A total of 1 370 271 samples had been analyzed (27 405 samples per million people), with a positivity rate of 17%. Sampling rates per million varied by region from 2664 to 158 681 per million, and consequently the incidence and mortality rates also varied. Due to geographical variations in surveillance capacity, Colombia may have overlooked up to 82% of the actual cases.
Colombia has a lower case and mortality incidence compared to other South American countries. This may be an effect of the lockdown, but may also be attributed, to some extent, to geographical differences in surveillance capacity. Indigenous populations with little health infrastructure have been hit the hardest.
Core Ideas
Inter–gene pool introgressions illustrate multiple admixture events and the breeding history of beans.
A catalog of 40 million genomic variants is available for research on bean genetics.
...Genome‐wide variability is a valuable tool for molecular marker development.
Common bean (Phaseolus vulgaris L.) is the most important grain legume for human consumption and is a major nutrition source in the tropics. Because bean production is reduced by both abiotic and biotic constraints, current breeding efforts are focused on the development of improved varieties with tolerance to these stresses. We characterized materials from different breeding programs spanning three continents to understand their sequence diversity and advance the development of molecular breeding tools. For this, 37 varieties belonging to P. vulgaris, Phaseolus acutifolius (A. Gray), and Phaseolus coccineus L. were sequenced by whole‐genome sequencing, identifying more than 40 million genomic variants. Evaluation of nuclear DNA content and analysis of copy number variation revealed important differences in genomic content not only between P. vulgaris and the two other domesticated Phaseolus species, but also within P. vulgaris, affecting hundreds of protein‐coding genomic regions. A large number of inter–gene pool introgressions were identified. Furthermore, interspecific introgressions for disease resistance in breeding lines were mapped. Evaluation of newly developed single nucleotide polymorphism markers within previously discovered quantitative trait loci for common bacterial blight and angular leaf spot provides improved specificity to tag sources of resistance to these diseases. We expect that this dataset will provide a deeper molecular understanding of breeding germplasm and deliver molecular tools for germplasm development, aiming to increase the efficiency of bean breeding programs.
Across the world, the COVID-19 pandemic has disproportionately affected economically disadvantaged groups. This differential impact has numerous possible explanations, each with significantly ...different policy implications. We examine, for the first time in a low- or middle-income country, which mechanisms best explain the disproportionate impact of the virus on the poor. Combining an epidemiological model with rich data from Bogotá, Colombia, we show that total infections and inequalities in infections are largely driven by inequalities in the ability to work remotely and in within-home secondary attack rates. Inequalities in isolation behavior are less important but non-negligible, while access to testing and contract-tracing plays practically no role because it is too slow to contain the virus. Interventions that mitigate transmission are often more effective when targeted on socioeconomically disadvantaged groups.
Latin America has been severely affected by the COVID-19 pandemic but estimations of rates of infections are very limited and lack the level of detail required to guide policy decisions. We ...implemented a COVID-19 sentinel surveillance study with 59,770 RT-PCR tests on mostly asymptomatic individuals and combine this data with administrative records on all detected cases to capture the spread and dynamics of the COVID-19 pandemic in Bogota from June 2020 to early March 2021. We describe various features of the pandemic that appear to be specific to a middle income countries. We find that, by March 2021, slightly more than half of the population in Bogota has been infected, despite only a small fraction of this population being detected. The initial buildup of immunity contributed to the containment of the pandemic in the first and second waves. We also show that the share of the population infected by March 2021 varies widely by occupation, socio-economic stratum, and location. This, in turn, has affected the dynamics of the spread with different groups being infected in the two waves.
Introduction: More than 90% of children infected with COVID-19 worldwide developed mild to moderate disease. In Colombia, during 2020, COVID-19 infections in children stayed below 9.2% of the total ...cases, with no trends for age group or sex.Objective: To estimate the incidence of acute respiratory symptoms and COVID-19 in children from public schools in Bogotá, Colombia during the second semester of 2020.Material and methods: A telephone survey was conducted in over 5,000 scholar children. Antecedents and use of health services were informed. Descriptive statistics were used.Results: A total of 151.470 persons per day accounting for an IR of 157,8 per 100,000 people; almost three times the rate reported by the official surveillance system in the city.Conclusion: A lack of diagnosis and consultation in children was found compared to the general population. Further research is needed to elucidate the true burden of the disease in children.
Three highly effective vaccines are available to prevent human papillomavirus (HPV) infection, and they have been introduced in many countries around the world. This article describes advances and ...challenges in introducing HPV vaccines in the Expanded Program of Immunization (EPI) of countries in Latin America and the Caribbean (LAC).
We reviewed national and regional sources of information to identify LAC countries with and without universal HPV vaccination, along with the year of introduction, type of HPV vaccine, vaccination scheme, age groups targeted, and coverage level reached. Incidence rates of cervical cancer were compared across countries with and without an HPV vaccination program, in order to identify inequities in access to HPV vaccines.
So far, 10 LAC countries have supplied data on their vaccination policies and vaccination coverage rates to the Pan America Health Organization. The majority of those 10 started their vaccination programs using quadrivalent vaccine. Only Chile, Ecuador, and Mexico started their programs using a two-dose scheme. However, by the end of 2016, most of the other countries had switched from a three-dose to a two-dose scheme. Different age groups are targeted in the various programs. Some countries vaccinate one-year birth cohorts, while others vaccinate multiple-year birth cohorts. By the end of 2014, coverage with at least two doses ranged from a low of 2% to a high of 86%. With the exception of Venezuela, the LAC countries with the largest populations introduced universal HPV vaccination between 2010 and 2014. Despite the progress that has occurred in some LAC countries, there are still 10 LAC nations with cervical cancer rates above the LAC average (21.2 cases per 100 000) that have not introduced an HPV vaccine in their EPI.
With several key adjustments, HPV vaccination programs across Latin America and the Caribbean could be substantially strengthened. Ongoing monitoring of HPV infection outcomes is needed in order to assess the impact of different vaccination policies.
In 2015, the Zika virus was introduced in Colombia. The emergence of this arbovirus is a public health challenge for the country, considering the association between the infection and congenital ...disorders such as microcephaly. Thus, we estimated the burden of disease due to microcephaly associated with Zika in Colombia and its administrative subdivisions for the period 2015-2016. We conducted an exploratory ecological study, using as unit of measurement disability-adjusted life years (DALYs). The cases of microcephaly were obtained from the Zika national and departmental databases built by the National Public Health Surveillance System (SIVIGILA). Deaths attributed to microcephaly were estimated from previous studies. Finally, we calculated mortality rates and incidences, then we performed a sensitivity analysis under three scenarios (conservative, medium, and extreme) to estimate the DALYs. In the 2015-2016 period, 10,609.4 DALYs were caused by microcephaly associated with Zika in Colombia. 71% of the total DALYs were years of life lost and 29% were years lived with disability. Five out of 32 departments (Meta, Córdoba, Tolima, Valle del Cauca, and Norte de Santander) contributed 71% of total DALYs. The burden of microcephaly associated with Zika outweighed the burden of other congenital anomalies such as neural tube defects and Down syndrome in children aged between 0 and 4 years in Colombia. Public health efforts must be made to prevent and monitor these cases.
The apomictic reproductive mode of Brachiaria (syn. Urochloa) forage species allows breeders to faithfully propagate heterozygous genotypes through seed over multiple generations. In Brachiaria, ...reproductive mode segregates as single dominant locus, the apospory-specific genomic region (ASGR). The AGSR has been mapped to an area of reduced recombination on Brachiaria decumbens chromosome 5. A primer pair designed within ASGR-BABY BOOM-like (BBML), the candidate gene for the parthenogenesis component of apomixis in Pennisetum squamulatum, was diagnostic for reproductive mode in the closely related species B. ruziziensis, B. brizantha, and B. decumbens. In this study, we used a mapping population of the distantly related commercial species B. humidicola to map the ASGR and test for conservation of ASGR-BBML sequences across Brachiaria species.
Dense genetic maps were constructed for the maternal and paternal genomes of a hexaploid (2n = 6x = 36) B. humidicola F
mapping population (n = 102) using genotyping-by-sequencing, simple sequence repeat, amplified fragment length polymorphism, and transcriptome derived single nucleotide polymorphism markers. Comparative genomics with Setaria italica provided confirmation for x = 6 as the base chromosome number of B. humidicola. High resolution molecular karyotyping indicated that the six homologous chromosomes of the sexual female parent paired at random, whereas preferential pairing of subgenomes was observed in the apomictic male parent. Furthermore, evidence for compensated aneuploidy was found in the apomictic parent, with only five homologous linkage groups identified for chromosome 5 and seven homologous linkage groups of chromosome 6. The ASGR mapped to B. humidicola chromosome 1, a region syntenic with chromosomes 1 and 7 of S. italica. The ASGR-BBML specific PCR product cosegregated with the ASGR in the F
mapping population, despite its location on a different carrier chromosome than B. decumbens.
The first dense molecular maps of B. humidicola provide strong support for cytogenetic evidence indicating a base chromosome number of six in this species. Furthermore, these results show conservation of the ASGR across the Paniceae in different chromosomal backgrounds and support postulation of the ASGR-BBML as candidate genes for the parthenogenesis component of apomixis.
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