Genomic sequencing of SARS-CoV-2 in Rwanda reveals the importance of incoming travelers on lineage diversity

COVID-19 transmission rates are often linked to locally circulating strains of SARS-CoV-2. Here we describe 203 SARS-CoV-2 whole genome sequences analyzed from strains circulating in Rwanda from May 2020 to February 2021. In particular, we report a shift in variant distribution towards the emerging sub-lineage A.23.1 that is currently dominating. Furthermore, we report the detection of the first Rwandan cases of the B.1.1.7 and B.1.351 variants of concern among incoming travelers tested at Kigali International Airport. To assess the importance of viral introductions from neighboring countries and local transmission, we exploit available individual travel history metadata to inform spatio-temporal phylogeographic inference, enabling us to take into account infections from unsampled locations. We uncover an important role of neighboring countries in seeding introductions into Rwanda, including those from which no genomic sequences were available. Our results highlight the importance of systematic genomic surveillance and regional collaborations for a durable response towards combating COVID-19.info:eu-repo/semantics/publishe

Nanopore sequencing and assembly of a human genome with ultra-long reads

We report the sequencing and assembly of a reference genome for the human GM12878 Utah/Ceph cell line using the MinION (Oxford Nanopore Technologies) nanopore sequencer. 91.2 Gb of sequence data, representing ~30× theoretical coverage, were produced. Reference-based alignment enabled detection of large structural variants and epigenetic modifications. De novo assembly of nanopore reads alone yielded a contiguous assembly (NG50 ~3 Mb). Next, we developed a protocol to generate ultra-long reads (N50 > 100kb, up to 882 kb). Incorporating an additional 5×-coverage of these data more than doubled the assembly contiguity (NG50 ~6.4 Mb). The final assembled genome was 2,867 million bases in size, covering 85.8% of the reference. Assembly accuracy, after incorporating complementary short-read sequencing data, exceeded 99.8%. Ultra-long reads enabled assembly and phasing of the 4 Mb major histocompatibility complex (MHC) locus in its entirety, measurement of telomere repeat length and closure of gaps in the reference human genome assembly GRCh38

Treatment of COVID-19 with remdesivir in the absence of humoral immunity: a case report

Abstract: The response to the coronavirus disease 2019 (COVID-19) pandemic has been hampered by lack of an effective severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antiviral therapy. Here we report the use of remdesivir in a patient with COVID-19 and the prototypic genetic antibody deficiency X-linked agammaglobulinaemia (XLA). Despite evidence of complement activation and a robust T cell response, the patient developed persistent SARS-CoV-2 pneumonitis, without progressing to multi-organ involvement. This unusual clinical course is consistent with a contribution of antibodies to both viral clearance and progression to severe disease. In the absence of these confounders, we take an experimental medicine approach to examine the in vivo utility of remdesivir. Over two independent courses of treatment, we observe a temporally correlated clinical and virological response, leading to clinical resolution and viral clearance, with no evidence of acquired drug resistance. We therefore provide evidence for the antiviral efficacy of remdesivir in vivo, and its potential benefit in selected patients

Treatment of COVID-19 with remdesivir in the absence of humoral immunity: a case report

Abstract: The response to the coronavirus disease 2019 (COVID-19) pandemic has been hampered by lack of an effective severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antiviral therapy. Here we report the use of remdesivir in a patient with COVID-19 and the prototypic genetic antibody deficiency X-linked agammaglobulinaemia (XLA). Despite evidence of complement activation and a robust T cell response, the patient developed persistent SARS-CoV-2 pneumonitis, without progressing to multi-organ involvement. This unusual clinical course is consistent with a contribution of antibodies to both viral clearance and progression to severe disease. In the absence of these confounders, we take an experimental medicine approach to examine the in vivo utility of remdesivir. Over two independent courses of treatment, we observe a temporally correlated clinical and virological response, leading to clinical resolution and viral clearance, with no evidence of acquired drug resistance. We therefore provide evidence for the antiviral efficacy of remdesivir in vivo, and its potential benefit in selected patients

eBat: A Technology-enriched Life Sciences Research Community

We are leveraging Web-based technology to create an online community for Life Science research. Our prototype community for cardiovascular research with live bats, called eBat, consists of local researchers as well as remote collaborators. The eBat project offers scientists and students a remote-controlled microscope for conducting experiments, a message board and a chat system for scheduled as well as spontaneous communication, and an online peer-reviewed manuscript repository. In this paper, we report our observations of the use of the eBat infrastructure by local researchers over a period of six months. Resident researchers quickly adopted the eBat infrastructure. eBat technology has now become an indispensable part of the local research group and is used extensively for coordination, communication, and awareness. eBat complements face-to-face interactions well and has resulted in improved communication amongst lab members. We are currently exploring the extension of eBat technology to include distant researchers in live cardiovascular research experiments. We discuss our initial experiences with adapting the eBat infrastructure for research-at-a-distance and the lessons learned from these initial interactions

Example read from Oxford Nanopore MinION R7 Chemistry

<p>An example 12,017 base-pair read from Oxford Nanopore MinION running R7 chemistry from an isolate of Salmonella enterica serovar Enteritidis, with accompanying BLAST alignment. Read accuracy is approximately 80%. Two-direction reads are produced from a consensus of the template and complement strands passing through an individual nanopore.</p> <p> </p

A P. aeruginosa serotype-defining single read from our first Oxford Nanopore run

<p>Here is, I think, the first publically-available Oxford Nanopore read to be published. This came off our MinION instrument this morning (Wednesday 11th June). The DNA was derived from Pseudomonas aeruginosa strain 910 which originally came from hospital water. DNA was fragmented with Covaris G-Tube as per the Oxford Nanopore standard genomic library preparation protocol. The read maps to part of the P. aeruginosa O6-antigen determining region.</p> <p> </p

Therapeutic Recreation and Limb Differences

Using thematic content analysis, this study examines the role of therapeutic recreation for individuals with limb differences

eBat: A Technology-enriched Life Sciences Research Community

We are leveraging Web-based technology to create an online community for Life Science research. Our prototype community for cardiovascular research with live bats, called eBat, consists of local researchers as well as remote collaborators. The eBat project offers scientists and students a remote-controlled microscope for conducting experiments, a message board and a chat system for scheduled as well as spontaneous communication, and an online peerreviewed manuscript repository. In this paper, we report our observations of the use of the eBat infrastructure by local researchers over a period of six months. Resident researchers quickly adopted the eBat infrastructure. eBat technology has now become an indispensable part of the local research group and is used extensively for co-ordination, communication, and awareness. eBat complements face-to-face interactions well and has resulted in improved communication amongst lab members. We are currently exploring the extension of eBat technology to include distant researchers in live cardiovascular research experiments. We discuss our initial experiences with adapting the eBat infrastructure for research-at-a-distance and the lessons learned from these initial interactions