Operation Asha: Maternal Health Care Survey and Grant Proposal Executive Summary

Our research focused on what makes Operation ASHA’s TB treatment program elite and what new services it could provide with its last-mile delivery model. Our research consisted of field visits with Operation ASHA field supervisors and surveys of more than 50 community members in the health districts where it operates. Our conclusion is that Operation ASHA has the ability to provide needed deliverables

Operation Asha: Best Practices for Reducing Missing Cases

We hope that this new set of screening criteria will expand the number of potential TB suspects who are testing, increasing the number of TB cases found and treated. This will reduce the number of missed TB cases, as well as the prevalence and incidence of this disease

Operation Asha: USAID Video Request for Proposal

Operation ASHA was awarded a grant from USAID to produce a series of animated videos aimed at raising TB awareness in Mondulkiri, an extremely rural province that has a large indigenous population. Operation ASHA is seeking bids from film studios in Cambodia to produce these videos. As part of the official contract bidding process we wrote the procurement packet which, among other items, included a draft of the video script, an overview key information for the videos, several best practices for targeting indigenous communities, and the evaluation criteria for bids. This packet has been sent to Operation ASHA headquarters in India for technical changes and will be used in the coming months for the official bidding process

Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens

The analysis of human pathogens requires a diverse collection of bioinformatics tools. These tools include standard genomic and phylogenetic software and custom software developed to handle the relatively numerous and short genomes of viruses and bacteria. Researchers increasingly depend on the outputs of these tools to infer transmission dynamics of human diseases and make actionable recommendations to public health officials (Black et al., 2020; Gardy et al., 2015). In order to enable real-time analyses of pathogen evolution, bioinformatics tools must scale rapidly with the number of samples and be flexible enough to adapt to a variety of questions and organisms. To meet these needs, we developed Augur, a bioinformatics toolkit designed for phylogenetic analyses of human pathogens

Genomic analysis of nCoV spread. Situation report 2020-01-23.

Using 24 public shared novel coronavirus (nCoV) genomes, we examined genetic diversity to infer date of common ancestor and rate of spread. We find: 24 sampled genomes are nearly identical, differing by 0-3 mutations This lack of genetic diversity has a parsimonious explanation that the outbreak descends either from a single introduction into the human population or a small number of animal to human transmissions of very similar viruses. This event most likely occurred in November or early December 2019. There has been ongoing human-to-human spread since this point resulting in observed cases. Using estimates of total case count from Imperial College London of several thousand cases, we infer a reproductive number between 1.5 and 3.5 indicating rapid growth in the Nov-Jan period

Cryptic transmission of SARS-CoV-2 in Washington state.

After its emergence in Wuhan, China, in late November or early December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus rapidly spread globally. Genome sequencing of SARS-CoV-2 allows the reconstruction of its transmission history, although this is contingent on sampling. We analyzed 453 SARS-CoV-2 genomes collected between 20 February and 15 March 2020 from infected patients in Washington state in the United States. We find that most SARS-CoV-2 infections sampled during this time derive from a single introduction in late January or early February 2020, which subsequently spread locally before active community surveillance was implemented

Cryptic transmission of SARS-CoV-2 in Washington state

After its emergence in Wuhan, China, in late November or early December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus rapidly spread globally. Genome sequencing of SARS-CoV-2 allows the reconstruction of its transmission history, although this is contingent on sampling. We analyzed 453 SARS-CoV-2 genomes collected between 20 February and 15 March 2020 from infected patients in Washington state in the United States. We find that most SARS-CoV-2 infections sampled during this time derive from a single introduction in late January or early February 2020, which subsequently spread locally before active community surveillance was implemented