Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2,3,4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease

Evaluation of advanced cassava genotypes in Uganda

In a bid to increase the number of genotypes reaching farmers, on-farm trials were conducted in 2001/2002 with the aim of increasing the number of genotypes available to farmers to be evaluated for performance, adaptation and acceptability. Twenty improved genotypes were planted in Lira, Nakasongola, Gulu, Kumi and Katakwi districts using augmented design. The results indicated that cassava mosaic disease (CMD) varied from location to location but was more influenced by the genotype than the environment. The highest CMD severity (>4) was recorded among the farmers' local varieties across all environments, followed by Alice local (3.8±O.4) in Nakasongola and Lira (2.8±O.2) districts and 160142 (3.0±0.0) in Kumi and Lira (2.8±O.2) districts. Six clones (MM96/0245, MM96/056 I , 192/2324, MM96/3585, MM96/4589 and MM96/0264) showed resistance (score I for CMD) while the rest had severity scores below the average (2.5). At harvest, the highest yield (60.8±3.7 t ha-') was obtained from Alice local followed by clone MM 96/0561 (59.5±6.6 t ha-') in Nakasongola district and clone MM 96/4614 (52.5±13.2 t ha-') in Lira district. The lowest yield was from clone MM 96/3585 (l0.3±4.2 t ha-') followed by Oko Iyawo (I) 99 (l4.2±4.2 t ha-') in Kumi district. All the varieties tested were either sweet or slightly bitter with the scores of I or 2, respectively. Genotype MH97/296I was the most preferred in Kumi and Lira districts, while it was third in Nakasongoladistrict. All these genotypes also had a sweet taste for cooking. The most preferred genotypes in N akasongola were TME 5 and MM96/53 12 and had a sweet taste for cooking. The genotype by environment analysis indicated that genotypes TME 5, MM961 1419, 19210427, and MH97/044 (2) UG were the most stable and adapted across all environments while MM96/4614 and Alice local were more specific for Lira and Nakasongola, respectively. These findings provide a basis for recommendations with regard to cultivation and preference of cassava genotypes in different environments

Evaluation of advanced cassava genotypes in Uganda

In a bid to increase the number of genotypes reaching farmers, on-farm trials were conducted in 2001/2002 with the aim of increasing the number of genotypes available to farmers to be evaluated for performance, adaptation and acceptability. Twenty improved genotypes were planted in Lira, Nakasongola, Gulu, Kumi and Katakwi districts using augmented design. The results indicated that cassava mosaic disease (CMD) varied from location to location but was more influenced by the genotype than the environment. The highest CMD severity (>4) was recorded among the farmers' local varieties across all environments, followed by Alice local (3.8±O.4) in Nakasongola and Lira (2.8±O.2) districts and 160142 (3.0±0.0) in Kumi and Lira (2.8±O.2) districts. Six clones (MM96/0245, MM96/056 I , 192/2324, MM96/3585, MM96/4589 and MM96/0264) showed resistance (score I for CMD) while the rest had severity scores below the average (2.5). At harvest, the highest yield (60.8±3.7 t ha-') was obtained from Alice local followed by clone MM 96/0561 (59.5±6.6 t ha-') in Nakasongola district and clone MM 96/4614 (52.5±13.2 t ha-') in Lira district. The lowest yield was from clone MM 96/3585 (l0.3±4.2 t ha-') followed by Oko Iyawo (I) 99 (l4.2±4.2 t ha-') in Kumi district. All the varieties tested were either sweet or slightly bitter with the scores of I or 2, respectively. Genotype MH97/296I was the most preferred in Kumi and Lira districts, while it was third in Nakasongoladistrict. All these genotypes also had a sweet taste for cooking. The most preferred genotypes in N akasongola were TME 5 and MM96/53 12 and had a sweet taste for cooking. The genotype by environment analysis indicated that genotypes TME 5, MM961 1419, 19210427, and MH97/044 (2) UG were the most stable and adapted across all environments while MM96/4614 and Alice local were more specific for Lira and Nakasongola, respectively. These findings provide a basis for recommendations with regard to cultivation and preference of cassava genotypes in different environments

Ocorrência de Campylobacter spp. em carne e miúdos de frango expostos ao consumo em Belém, Pará Occurence of Campylobacter spp. in chicken meat and giblets exposed to consumption in Northern Brazil

<abstract language="eng">In order to study Campylobacter in chicken meat exposed to consumption in the city of Belém, state of Pará, Brazil, 16 samples (four of liver, four of gizzard, two of heart, two of skin, one of neck, two of carcass and a mixture of neck skin and fragments of the abdominal cavity), collected in clandestine butcher shops, fair-free and supermarkets were submitted to isolation and identification according to the recommended methods. In high percentage, the foods exposed to consumption were contaminated by this agent, meaning a potential risk to the human health

Successful innovations and lessons learnt in cassava improvement and deployment by IITA in Eastern African Region

The International Institute of Tropical of Agriculture (IITA) established its East and Southern Africa Regional Research Centre (ESARC) in Uganda at the former Namulonge Agricultural and Animal Research Institute (NAARI), presently Namulonge Animal and Crops Research Institute (NaCRRI), to address issues of cassava, banana, and plantain development; coordinate all related activities, and work closely with the national agricultural research institutes (NARS). IITA-ESARC began extensive cassava germplasm development to counter the pandemic of African cassava mosaic disease (ACMD) in the region in 1995 through the Eastern Africa Root Crops Research Network (EARRNET). More than 100,000 seeds were evaluated through the conventional plant breeding scheme. Selected genotypes were kept in in-situ conservation from where the regional cassava national programs selected clones for further evaluation in their own countries. Burundi, Democratic Republic of Congo (DRC), Kenya, Rwanda, Tanzania, and Uganda benefited immensely. Through EARRNET, the region gained significantly from the large germplasm base to mitigate the scourge of ACMD and the production of cassava was restored. A new joint effort that was established between Catholic Relief Services and IITA in collaboration with the NARS and other stakeholders promoted the adoption of improved germplasm through participatory variety selection. The breeding approach used enabled to reduce selection period for NARS to release new varieties to farmers as they received elite materials for evaluation. However, the spread of cassava brown streak disease (CBSD) in mid altitude threatened the achievements already made as the new disease attacked most of the ACMD-resistant and high yielding varieties. Its spread in the region calls for more effective collaborative action than before from IITA and its partners to develop new resistant materials to mitigate the effects of both ACMD and CBSD. The present paper attempts to summarize the breeding work efforts made and demonstrate how the germplasm development at this regional center has been useful to the region through effective partnership

Cassava improvement in sub-Saharan Africa: contributions of IITA and its partners

Cassava is well recognized for its capacity to address food needs of vulnerable communities in unstable environments in SSA. IITA and colleagues in African NARS, in collaboration with CIAT and ARIs have played leading roles in the development of improved cassava varieties which are disease and pest resistant, early maturing, and high yielding. Through a combination of conventional and new approaches, over 400 cassava genotypes have been developed. The characteristics of the new generation of cassava germplasm broke what had been an apparent yield barrier in cassava improvement increasing yields in many locations by at least 50–100% without the use of fertilizer. The improved germplasm is shared with NARS within the region as specific genotypes or improved seed populations for evaluation and selection under local conditions. Improvement programs in Africa that received these materials have tested them under local conditions, selected varieties that outperform local varieties, and released them to farmers in virtually every major cassava producing country. Today, about 30% of the area cropped with cassava in Africa is planted with improved varieties. Without the introduction of more productive cultivars with multiple diseases and pest resistance, the effective biological control of the cassava mealybug and, to a certain extent, of the green mite, cassava production in SSA would be 50% or less of what it is today. That translates to over 13 million tons of dry cassavayear, enough to meet the calorie requirements of 65 million people. The significant gains in the crop’s output in farmers’ fields are not only contributing to the African diet but also propelling commercialization of the crop. This paper highlights contributions to cassava improvement in SSA since 1970 by IITA and its partners, and suggests areas needing strengthening in the drive to produce better crop varieties for different regions and enduses in Africa