Central Epidemic Command Center (CECC) was assembled to combat the COVID- 19 pandemic in Taiwan on 20 January, 2020. The CECC executed several strategies to reduce disease transmission and its government guided strategies may have contributed to mitigating the disease’s spread. Taiwan’s first confirmed case was detected on 21 January 2020, and by mid-March there were 49 cases. With the last reported locally transmitted case on 12 April by 21 November 2020, Taiwan has marked its 222nd consecutive day without a locally transmitted case. During these past 7 months, 148 new confirmed imported cases but no indigenous case was reported in Taiwan. However, there are several hospital cluster infections and community outbreaks in 2021. Based the data reported by CECC, a total of 16,588 cases were reported during the period from 2020 to November 28, 2021. Of the 16,588 confirmed cases, 1,944 are imported; 14,590 are indigenous cases; 36 are naval crew members aboard the Panshi fast combat support ship; 3 are infections on an aircraft; 1 case has unknown sources of infection; 14 cases' sources of infection are being investigated. There has been a cumulative total of 848 COVID-19 deaths since 2020; of the 848 deaths, 836 are from indigenous cases and the other 12 are from imported cases.

At the early of 2020, the LDT real time RT-PCR method for diagnosis of SARS-CoV-2 infection was first established by the National Laboratory located at the Centers for Disease Control (CDC), Taiwan. In order to reduce the capacity of work load and turnaround time, CDC delivered the reagents to the 8 contracted clinical virology laboratory in medical centers. After obtained good proficiency results, CDC authorized these 8 contracted laboratories to receive the clinical samples for running the nucleic acid test (NAT) of SARS-CoV-2 virus. As the end of November 2021, total number of authorized laboratories for doing NAT test are 247.

In addition to NAT, the virus isolation, rapid antigen test and antibody detection are also established in many clinical laboratories. In order to accelerate the performance of laboratory diagnosis, as the end of October 2021, the numbers of imported EUA (TFDA) for COVID-19 NAT, antigen detection and antibody detection reagents are 53, 40 and 33 respectively and the domestic manufacture diagnostic reagents (EUA, TFDA) for COV-19 NAT, antigen and antibody tests are 21, 23 and 13 respectively. Regarding virus culture, it is only allowed to perform in the laboratory with BSL-3 facility.

The harmonization and proficiency test of laboratory diagnosis of COVID-19 should be established in future.

Objective: We aim to develop a phylogenomic database coupled with geospatial information system to unveil the transmission linkage of COVID-19 cases in Hong Kong.

Result: Phylogenomic analysis enabled us to identify an asymptomatic patient as the source of the first superspreading event of COVID-19 (Buddhist worship hall cluster) happened in late February 2020.After months of relative quiescence, a large COVID-19 outbreak (third wave) occurred in Hong Kong in July 2020. The phylogeny of some early cases indicated that the outbreak was attributed to a single lineage B.1.1.63, which was identical to viral genomes isolated from marine crew and aircrew who were exempted from mandatory quarantine.

In early October 2020, before the onset of the fourth wave, we identified a novel viral genome (lineage B.1.36.27) among local cases, which was most closely related to imported cases from Nepal. We highlighted flaws in hotel quarantine arrangements, under which travellers could still receive visitors. The Government later implemented the policy that inbound travellers should be quarantined at designated hotels and not be allowed visitors.

In December 2020, the United Christian Hospital experienced a large outbreak of SARS-CoV-2 in a palliative care and medicine ward. Later in January 2021, two healthcare workers from North District Hospital tested positive after taking care of COVID-19 patients. In both cases, we conducted phylogenomic analysis, enabling the hospitals to trace the transmission chain and prevent further cases.

In April 2021, we used rapid phylogenomic analysis to identify the transmission link between Filipino domestic helpers and an Indian businessman who had travelled from Dubai and tested positive for a SARS-CoV-2 VOC Beta. The genomic data enabled us to trace the entire transmission chain and their close contacts. Eventually, we identified an inbound traveller, who had stayed in the adjacent hotel room to the Indian businessman during quarantine, was the source of the transmission.

Recently we developed a phylogeographical information system which integrated the genomic, epidemiological, spatial and temporal information of COVID-19 cases in Hong Kong. Data visualizations are combined with the cartographic display to yield a clear view of the genomic diversity of SARS-CoV-2 variants and their distributions across Hong Kong districts, with a focus on the clustering of cases based on phylogenetic proximity.

Conclusion: Continued genomic surveillance of the imported cases is pivotal in detecting novel lineages that enters Hong Kong.

Ten days after dose 1, 67.6% (48/71)/69.0% (49/71) were T-Ab/IgG positive; only 15.5% (11/71)/14.1% (10/71) were N-Ab/IgM positive. While all (100%) subjects had brisk T-Ab, IgG and N-Ab antibody responses 20 days after complete vaccination, only 79.1% (53/67) were IgM positive. At 180 days (n = 8), T-Ab/IgG/N-Ab were still reactive (lowest T-Ab 186 U/mL, IgG 617 AU/mL, N-Ab 0.39 μg/mL), but IgM was negative in all samples. Spike antibody thresholds of T-Ab 74.1 U/mL (r = 0.95) and IgG 916 AU/mL (r = 0.95) corresponded to N-Ab reactivity (>0.3 μg/mL).

Post-vaccination spike IgM responses are less robust than that of spike total and IgG antibodies and sero-reversion occurs earlier. There is good correlation between spike antibodies (T-Ab, IgG) and N-Ab (r=0.95) suggesting that spike Ab may be a good surrogate for N-Ab. While the spike antibody (T-Ab & IgG ) and N-Ab responses remain detectable at 180 days, its durability and levels needed to confer sufficient protection is not known. One of our subjects with a spike T-Ab of 600 U/mL and N-Ab of 0.6 ug/mL (@ 6 months post-vaccination) experienced a re-infection 3 weeks thereafter; this suggests that N-Ab levels higher than 0.6 ug/mL is required for protection. Emerging data from Israel noted that a spike T-Ab (Roche) of 930 was not sufficient to forestall a breakthrough infection.

Clearly needed are larger studies on correlates of protection against CoVID and durability of these protective antibodies.