Establishing an early warning surveillance system in jails in Calabarzon, the Philippines, 2021

@#The Philippines’ Republic Act 11332 (2020) mandates prisons, jails and detention centres to participate in disease surveillance, but currently no surveillance system exists in these facilities. This report aims to describe the piloting of an early warning disease surveillance system in 21 selected jails in Calabarzon from July to September 2021. Sites were selected based on congestion, proximity to health facilities and logistical capacity. Data sources, collection mechanisms and reporting tools were determined and health personnel were trained in the operation of the system. During the implementation period, the system detected 10 health events, with influenza-like illness and foodborne illness being the most common. Nine of these events were reported within 24 hours. The local health unit provided medications for clinical management and instructed jail nurses on infection prevention and control measures, including active case finding, the isolation of cases and the inspection of food handling. Twelve sites reported over 8 of the 10 weeks, with all sites reporting zero cases promptly. The challenges identified included insufficient workforce, slow internet speed and multitasking. It was concluded that the jail-based early warning surveillance system is feasible and functional, but the perceived benefits of jail management are crucial to the acceptability and ownership of the system. It is recommended to replicate the surveillance system in other penitentiaries nationwide.

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

We report the sequencing and detection of 39 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 (UK variant) in the Philippines.

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

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.