The Omicron SARS-CoV-2 variant led to a dramatic global epidemic wave following detection in South Africa in November, 2021. The Omicron lineage BA.1 was dominant and responsible for most SARS-CoV-2 outbreaks in countries around the world during December 2021-January 2022, whilst 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 lineage BA.2 underwent sustained transmission in the country, with an estimated emergence around November 18th, 2021 [95% highest posterior density: November 6-28th], whilst despite multiple introductions BA.1 transmission remained limited. These results suggest the Philippines was one of the earliest areas affected by BA.2, and reiterate the importance of whole-genome sequencing for monitoring outbreaks.

Background Despite the effort to eradicate rabies in the Philippines, human rabies cases have not decreased in the past decade. Rabid dogs pose the most significant hazard in the countries with the highest burden of rabies, and 70% rabies vaccine coverage is recommended for dogs in high-risk areas. Ascertaining the owned dog population and community knowledge on rabies can help improve vaccine coverage and information campaigns. Methodology/Principal findings We conducted a cross-sectional survey in six randomly selected communities (five urban, one rural) in Central Luzon, Philippines. We first conducted the complete mapping of 9,173 households and then randomly selected 727 households. More than half (54.1%) of the households owned dogs (1.21 dogs/household). In the 727 households, we identified 878 owned dogs and 3256 humans. According to these results, the dog-to-human ratio was approximately 1:3.7. Only 8.8% of households reported a history of dog bite in 2019. Among dog-owning households, 31% reported that they allow their dogs to roam freely. Of the recorded dogs, 35.9% have never been vaccinated, and only 3.5% were spayed or castrated. Factors associated with lower rabies knowledge include (1) no education aOR: 0.30 (0.16–0.59), and (2) only primary school education aOR: 0.33 (0.22–0.49). In contrast, factors associated with higher knowledge include (1) owning a dog and not allowing them to roam freely aOR: 2.01 (1.41–2.87) and (2) owning a dog and allowing them to roam freely aOR: 1.84 (1.17–2.92), when compared to those with no dogs. Conclusions/Significance We identified a larger dog population in the community than the usual estimates (1:10), suggesting that annual vaccine needs in the Philippines must be reassessed. Our survey shows a relatively good understanding of rabies; however, awareness of the concept of rabies as a disease, and how animals and humans can acquire it, is lacking.

The Omicron SARS-CoV-2 variant led to a dramatic global epidemic wave following detection in South Africa in November, 2021. The Omicron lineage BA.1 was dominant and responsible for most domestic outbreaks during December 2021-January 2022, whilst 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 lineage BA.2 underwent sustained transmission in the country, with an estimated emergence around November 18th, 2021 [95% highest posterior density: November 6-28th], whilst despite multiple introductions BA.1 transmission remained limited. These results suggest the Philippines was one of the earliest areas affected by BA.2, and reiterate the importance of whole-genome sequencing for monitoring outbreaks.

We used KoBo Collect and KoBo Toolbox as an electronic data capture platform for a dog population and rabies knowledge and practices community survey in the Philippines. It has allowed for easy design and deployment of an electronic form with minimal technical knowledge from the investigators. Using this platform allowed for shorter training for data collectors, minimal errors during data collection, and faster turn-around time for data cleaning and analysis.

Background: With the World Health Organization’s declaration of the 2022 multi-country monkeypox outbreak as a Public Health Emergency of International Concern (PHEIC), we report the first confirmed case of monkeypox infection in a Filipino with clinical presentation different from the classic monkeypox cases previously reported in endemic countries of Central and West Africa before the 2022 outbreak. We describe monkeypox infection's gross and dermatopathological appearances on Southeast Asian brown skin. We also discuss the detailed process of monkeypox quantitative real-time polymerase chain reaction (qPCR) testing for diagnostic confirmation and the pioneering application of shotgun metagenomic sequencing to characterize the infecting virus. Case Presentation: This was a case of a 31-year-old male Filipino with a travel history to several European countries. He developed five non-tender, well-defined, umbilicated pustules with erythematous borders on the upper lip, the left gluteal area, bilateral knees, and the left ankle. Skin punch biopsy findings were suggestive of a viral infection. Monkeypox infection from Clade II (previously known as the West African clade) was confirmed by detecting and amplifying the G2R_G, G2R_WA, and C3L gene targets using qPCR. Shotgun metagenomic sequencing subsequently identified a monkeypox genome sequence belonging to B.1.3 lineage of Clade IIb, associated with the current multi-country outbreak. The serologic varicella IgM test was positive but varicella PCR of the skin lesion and metagenomic sequencing did not indicate the presence of the varicella virus. The patient was discharged and continued isolation at home until all scabs had completely fallen off. Conclusions: The presence of pustules among patients with risk factors such as possible close physical contact with infected individuals in areas with reported cases of monkeypox should raise suspicion for such an infection. Dermatopathological findings of the patient’s skin lesions were consistent with a viral infection but were non-specific for monkeypox infection. The establishment and optimization of the qPCR protocol were necessary to confirm monkeypox infection from Clade II. Metagenomic sequencing successfully characterized the etiologic agent of the first laboratory-confirmed monkeypox case in the Philippines belonging to Clade IIb which is mainly responsible for the 2022 monkeypox global outbreak.