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.

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.

BACKGROUND Following the detection of the first laboratory-confirmed Monkeypox (MPXV) infection in the Philippines, guidelines on Monkeypox diagnosis, treatment, and prevention have been strengthened to further help healthcare providers in differentiating it properly from other diseases with similar clinical presentation, one of which is Varicella zoster (VZV) infection. Interestingly, co-infection with Monkeypox and Varicella has been previously reported in Monkeypox endemic countries. We then report the first travel-related case of MPXV-VZV co-infection in the Philippines, a country that is endemic for Varicella but non-endemic for Monkeypox. CASE PRESENTATION A 29-year-old Filipino, female, with a travel history to Switzerland and with no prior history of VZV infection consulted due to rashes. She presented with multiple papular, pustular, and vesicular skin lesions, some with umbilication and with irregular borders, on the face, neck, trunk, inguinal area, upper extremities, and right leg. She also had bilateral submandibular and post-auricular lymphadenopathies. Tzanck smear exhibited viral cytopathic effects. She was confirmed to have Monkeypox infection from Clade II and Varicella infection via quantitative real-time polymerase chain reaction (qPCR) tests. Shotgun metagenomic sequencing (mNGS) successfully recovered sequences from the Varicella zoster virus which corroborated with the high viral load detected using qPCR. In contrast, shotgun mNGS showed too few reads mapped to the Monkeypox virus reference sequence. Systemic and topical acyclovir was given to the patient. She was discharged and continued home isolation for 30 days from the rash onset. CONCLUSION Strategies have been formed by the country’s healthcare facilities to properly identify monkeypox infection. However, Monkeypox co-infection with other viral diseases presented a challenge in the proper diagnosis of our patient. This prompted a high index of suspicion and the usage of suitable diagnostic tests. The qPCR tests confirmed the presence of both Monkeypox and Varicella zoster virus infections in the patient. Shotgun metagenomic sequencing (mNGS) successfully recovered sequences from the Varicella zoster virus, while there were too few reads mapped to the Monkeypox virus reference sequence. With proper clinical evaluation and utilization of appropriate diagnostic tests, we were able to diagnose the first Filipino patient with Monkeypox and Varicella zoster virus co-infection.

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.

The Philippines has had a rapidly growing HIV epidemic with a shift in the prevalent subtype from B to CRF01_AE. However, the phylodynamic history of CRF01_AE in the Philippines has yet to be reconstructed. We conducted a descriptive retrospective study reconstructing the history of HIV-1 CRF01_AE transmissions in the Philippines through molecular epidemiology. Partial polymerase sequences (n = 1429) collected between 2008 and 2018 from 13 Philippine regions were collated from the RITM drug resistance genotyping database. Subsampling was performed on these Philippine and Los Alamos National Laboratory HIV international sequences followed by estimation of the time to the most recent common ancestor (tMRCA), effective reproductive number (Re), effective viral population size (Ne), relative migration rates and geographic spread of CRF01_AE with BEAST. Re and Ne were compared between CRF01_AE and B. Most CRF01_AE sequences formed a single clade with a tMRCA of 1999 [95% HPD: 1996, 2001]. Exponential growth of Ne was observed from 1999 to 2013. The Re reached peaks of 3.71 [95% HPD: 1.71, 6.14] in 2009 and 2.87 [95% HPD: 1.78, 4.22] between 2012 and 2015. A transient decrease to 0.398 [95% HPD: 0.0105, 2.28] occurred between 2010 and 2012. The epidemic most likely started in Luzon in the National Capital Region, which then spread diffusely to the rest of the country. Both CRF01_AE and subtype B exhibited similar but unsynchronized patterns of Re over time. These results characterize the subtype-specific phylodynamic history of the CRF01_AE epidemic in the Philippines, which contextualizes and may inform past, present, and future public health measures toward controlling the HIV epidemic in the Philippines.