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Cryptosporidium is increasingly being recognized as an important cause of diarrhea worldwide. Although well known for its impact among HIV positive population, improved diagnostic tests have contributed to its emerging recognition one among the most prevalent causes of early childhood moderate to severe diarrhea, persistent diarrhea, and impaired neurocognitive development. The diagnosis of Cryptosporidiosis is generally carried out based on availability of skilled microscopist or advanced equipment for molecularand immunologic-based assays. As an emerging enteric pathogen of medical importance, the need for point-of-care technology is deemed necessary for early identification of the pathogen and application of infection control measures for its potential risk of creating outbreaks. Current point-of-care technologies demonstrate varying sensitivities and specificities and may already address the present diagnostic need.

The spread of the corona virus around the world has spurred travel restrictions and community lockdowns to manage the transmission of infection. In the Philippines, with a large population of overseas Filipino contract workers (OFWs), as well as foreign workers in the local online gaming industry and visitors from nearby countries, the first reported cases were from a Chinese couple visiting the country in mid-January 2020. Three months on, by mid-March, the COVID-19 cases in the Philippines had reached its first 100, before it exploded to the present 178,022 cases (as of August 20, 2020). Here, we report a genomic survey of six (6) whole genomes of the SARS-CoV-2 virus collected from COVID-19 patients seen at the Philippine General Hospital, the major referral hospital for COVID-19 cases in Metro Manila at about the time the Philippines had over a hundred cases. Analysis of commonly observed variants did not reveal a clear pattern of the virus evolving towards a more infectious and severe strain. When combined with other available viral sequences from the Philippines and from GISAID, phylogenomic analysis reveal that the sequenced Philippine isolates can be classified into three primary groups based on collection dates and possible infection sources: (1) January samples collected in the early phases of the pandemic that are closely associated with isolates from Wuhan, China; (2) March samples that are mainly linked to the M/V Diamond Princess Cruise Ship outbreak; and (3) June samples that clustered with European isolates, one of which already harbor the globally prevalent D614G mutation which initially circulated in Europe. The presence of community-acquired viral transmission amidst compulsory and strict quarantine protocols, particularly for repatriated Filipino workers, highlights the need for a refinement of the quarantine, testing, and tracing strategies currently being implemented to adapt to the current pandemic situation.