Epidemic Surveillance Models for Containing the Spread of SARS-CoV-2 Variants: Taiwan Experience

Abstract

Objectives: Two kinds of epidemic surveillance models are presented for containing the spread of SARS-CoV-2 variants so as to avert and stamp out a community-acquired outbreak (CAO) with non-pharmaceutical interventions (NPIs), tests, and vaccination. Design: The surveillance of domestic cluster infections transmitted from imported cases with one-week time lag assessed by the Poisson model and the surveillance of whether, how and when NPIs and test contained the CAO with the SEIR model. Settings: Border and Community of Taiwan. Main Outcome Measurements: The expected number and the upper bound of the 95% credible interval (CrI) of weekly covid-19 cases compared with the observed number for assessing the threshold of a CAO; effective reproductive number (Rt) and the effectiveness of NPIs for containing a CAO. Results: For the period of January-September 2020 when the wild type and the D614G period were prevailing, an increase in one imported case prior to one week would lead to 9.54% (95% CrI 6.44% to 12.59%) higher risk of domestic cluster infection that provides a one-week prior alert signal for more stringent NPIs and active testing locally. Accordingly, there was an absence of CAO until the Alpha VOC period of February 2021. However, given level one of NPI alert the risk of domestic cluster infections was gradually elevated to 14.14% (95% CrI 5.41% to 25.10%), leading to the Alpha VOC CAOs of six hotspots around mid-May 2021. It took two-and-half months for containing this CAO mainly with level three of NPI alert and rapid test and partially by the rolling out of vaccination. By applying the SEIR model, the Rt decreased from 4.0 at beginning to 0.7 on 31 July 2021 in parallel with the escalating NPIs from 30% to 90%. Containing a small outbreak of Delta VOC during this CAO period was also evaluated and demonstrated. After controlling the CAO, it again returned to imported-domestic transmission for Delta VOC from July until September 2021, giving an estimate of 10.16% (95% CrI: 7.01% to 13.59%) for the risk of several small cluster infections. However, there was an absence of CAO that resulted from the effectiveness of NPIs and tests, and the rapid expansion of vaccination. Conclusions: Averting and containing CAOs of SARS-CoV-2 variants are demonstrated by two kinds of epidemic surveillance models that have been applied to Taiwan scenario. These two models can be accommodated to monitor the epidemic of forthcoming emerging SARS-CoV-2 VOCs with various circumstances of vaccine coverage, NPIs, and tests in countries worldwide.

Emergency SARS-CoV-2 Variants of Concern: Novel Multiplex Real-Time RT-PCR Assay for Rapid Detection and Surveillance

“…With the emergence of the B.1.1.7 lineage, Taiwan confronted a COVID-19 flare-up in May 2021 ( 12 ) and later in June 2021. The first imported B.1.617.2 cases were reported by Taiwan Central Epidemic Command Center (CECC), which later led to outbreaks of community transmission ( 13 ). To meet this challenge, assays for the detection of SARS-CoV-2 VOCs were designed and implemented in our hospital.…”

Investigating the Current Status of SARS-CoV-2 Antibodies in Hospital Staff

“…Taiwan experienced a COVID-19 outbreak in May 2021 and later in June 2021 due to the emergence of the Alpha-lineage (B.1.1.7) [ 37 ]. The first cases of the Delta-lineage B.1.617.2 were later reported by the Taiwan Central Epidemic Command Center (CECC), which then led to community transmission outbreaks [ 38 ].…”

Primary and booster vaccination in reducing severe clinical outcomes associated with Omicron Naïve infection

“…In Taiwan, as there has not been a large-scale community-acquired outbreak before the emergence of Omicron BA.2 [11] , the Taiwanese cohort together with naïve Omicron infection provides an opportunity of evaluating pure effectiveness of primary and booster vaccination in reducing the severity of and death from COVID-19 without being largely confounded by prior infection resulting from the antecedent large-scale community-acquired outbreaks.…”