Analysis of SARS-CoV-2 Recombinant Lineages XBC and XBC.1 in the Philippines and Evidence for Delta-Omicron Co-infection as a Potential Origin (preprint)

We report the sequencing and analysis of 60 XBC and 114 XBC.1 SARS-CoV-2 lineages detected in the Philippines from August to September 2022, which are regarded as recombinant lineages of the BA.2 Omicron and B.1.617.2 Delta (21I Clade) variants. The sequences described here place the Philippines as the country with the earliest and highest number of XBC and XBC.1 cases within the included period. Majority of the detected cases were sampled from the adjacent Davao and Soccskargen regions in southern Philippines, but have also been observed at lower proportions in other regions of the country. Time-scaled phylogenetic analysis with global samples from GISAID reaffirms the supposed root of XBC-like cases from the Philippines. Furthermore, the apparent clustering of some foreign cases separate from those collected in the country suggests several occurrences of cross-border transmissions resulting in the spread of XBC-like lineages within and among those countries. The consensus mutation profile shows regions harboring mutations specific to either the Omicron BA.2 or Delta B.1.617.2 lineages, supporting the recombinant nature of XBC. Finally, alternative allele fraction pattern and intrahost mutation analysis revealed that a relatively early case of XBC collected in March 2022 is likely to be an active co-infection event. This suggests that co-infection of Omicron and Delta was already occurring in the Philippines early in 2022, facilitating the generation of recombinants that may have further evolved and gained additional mutations enabling its spread across certain local populations at a later time.

Incorporating Value of Health System Impact in Economic Evaluations of Therapies of Chronic Diseases

Objectives: Economic assessments of healthcare interventions for health technology assessments (HTAs) limit societal impact to productivity losses. Other societal impact has been highlighted by the Covid-19 pandemic that was associated with a severe impairment of the ability of the healthcare system to provide adequate and timely care to patients in many indications due to unprecedented increases in hospitalizations. The impact of healthcare interventions on health care system capacity and security has been identified as a priority value item for consideration by HTA recently. In imperfect markets with permanent excess demand, the accounting costs of resources underestimate their opportunity costs. Hence, reliance on accounting costs in economic evaluations of interventions that can avoid future demand for care leads to undervaluation of these interventions. Attempts have been made to evaluate the value of vaccines by accounting for their impact on health system capacity, through valuing bed-days used by patients with vaccine-preventable disease by their opportunity cost. Method(s): We apply theoretical methods for calculating opportunity costs of services proposed by Sandmann et al. to interventions in a chronic disease. An example is shown for chronic kidney disease that has high and increasing prevalence, and an associated surge in the demand for renal care services, coupled with supply shortages of dialysis equipment and adequate workforce, creating a situation of permanent overdemand on the market of renal care services. The quantitative magnitude of the undervaluation of delaying dialysis and renal transplant is demonstrated by accounting for opportunity costs of resource use as opposed to valuing used resources on accounting price. Its potential impact on results of economic evaluations of CKD therapies and HTA decisions is shown in a simple model on eGFR slope, and methods are assessed and compared. We generalize our findings to other chronic therapies. Copyright © 2022

Deans as Agents of Change for Inclusive Teacher Education

Few resources are available to support deans who lead reform while they navigate competing complex issues. Understanding how deans succeed in leading a reform agenda carries much significance in today’s context where issues of equity and Covid-19 are challenging educators to reexamine the content and delivery of programs, while also grappling with a myriad of other challenges (e.g., declining enrollment and fiscal demands). Little research examines the actions that deans take to lead change in their colleges or schools. This exploratory study employing grounded theory methods was designed to unpack what deans actually do when engaging their college or school in a reform effort. The results suggest that there are strategic actions deans take to facilitate change on their campuses, and these actions are reflected in an emerging theory of action. © 2022 Taylor & Francis Group, LLC.

Lineage BA.2 dominated the Omicron SARS-CoV-2 epidemic wave in the Philippines.

The Omicron severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant led to a dramatic global epidemic wave following detection in South Africa in November 2021. The BA.1 Omicron lineage was dominant and responsible for most SARS-CoV-2 outbreaks in countries around the world during December 2021-January 2022, while other Omicron lineages, including BA.2, accounted for the minority of global isolates. Here, we describe the Omicron wave in the Philippines by analysing genomic data. Our results identify the presence of both BA.1 and BA.2 lineages in the Philippines in December 2021, before cases surged in January 2022. We infer that only the BA.2 lineage underwent sustained transmission in the country, with an estimated emergence around 18 November 2021 (95 per cent highest posterior density: 6-28 November), while despite multiple introductions, BA.1 transmission remained limited. These results suggest that the Philippines was one of the earliest areas affected by BA.2 and reiterate the importance of whole genome sequencing for monitoring outbreaks.

Pilot Recommender System Enabling Students to Indirectly Help Each Other and Foster Belonging Through Reflections

Without a sense of belonging, students may become disheartened and give up when faced with new challenges. Moreover, with the sudden growth of remote learning due to COVID-19, it may be even more difficult for students to feel connected to the course and peers in isolation. Therefore, we propose a recommendation system to build connections between students while recommending solutions to challenges. This pilot system utilizes students' reflections from previous semesters, asking about learning challenges and potential solutions. It then generates sentence embeddings and calculates cosine similarities between the challenges of current and prior students. The possible solutions given by previous students are then recommended to present students with similar challenges. Self-reflection encourages students to think deeply about their learning experiences and benefit both learners and instructors. This system has the potential to allow reflections also to help future learners. By demonstrating that previous students encountered and overcame similar challenges, we could help improve students' sense of belonging. We then perform user studies to evaluate this system's potential and find that participants rated 70% of the recommended solutions as useful. Our findings suggest an increase in students' sense of membership and acceptance, and a decrease in the desire to withdraw. © 2022 ACM.

Detection and Genome Sequencing of SARS-CoV-2 Variants Belonging to the B.1.1.7 Lineage in the Philippines.

We report the sequencing and detection of 36 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) samples containing lineage-defining mutations specific to viruses belonging to the B.1.1.7 lineage in the Philippines.

Genome sequencing and detection of Philippine SARS-CoV-2 infections with viruses classified under the B.1.1.7 lineage (preprint)

We report the sequencing and detection of 39 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infections in the Philippines identified to be caused by viruses under the B.1.1.7 lineage (UK variant). Genome sequences obtained from these samples carry the lineage-defining mutations associated with the said variant of concern.

Genome sequencing and analysis of an emergent SARS-CoV-2 variant characterized by multiple spike protein mutations detected from the Central Visayas Region of the Philippines (preprint)

The emergence of SARS-CoV-2 variants of concern such as the B.1.1.7, B.1.35 and the P.1 have prompted calls for governments worldwide to increase their genomic biosurveillance efforts. Globally, quarantine and outbreak management measures have been implemented to stem the introduction of these variants and to monitor any emerging variants of potential clinical significance domestically. Here, we describe the emergence of a new SARS-CoV-2 lineage, mainly from the Central Visayas region of the Philippines. This emergent variant is characterized by 13 lineage-defining mutations, including the co-occurrence of the E484K, N501Y, and P681H mutations at the spike protein region, as well as three additional radical amino acid replacements towards the C-terminal end of the said protein. A three-amino acid deletion at positions 141 to 143 (LGV141_143del) in the spike protein was likewise seen in a region preceding the 144Y deletion found in the B.1.1.7 variant. A single amino acid replacement, K2Q, at the N-terminus of ORF8 was also shared by all 33 samples sequenced. The mutation profile of this new virus variant warrants closer investigation due to its potential public health implications. The current distribution of this emergent variant in the Philippines and its transmission are being monitored and addressed by relevant public health agencies to stem its spread in nearby islands and regions in the country.

ANALYSIS OF SARS-COV-2 GENOME SEQUENCES FROM THE PHILIPPINES: GENETIC SURVEILLANCE AND TRANSMISSION DYNAMICS (preprint)

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.