A large-scale COVID-19 TPR is often used globally to control the pandemic as the SARS-CoV-2 transmission indicator and may estimate COVID-19 prevalence, predicting health care requirements, and monitoring the severity of cases in a country (12–14). Here we determined the COVID-19 q-RT-PCR TPR in West Sumatra Province of Indonesia from April 2020 to March 2021 by using large retrospective data from the two labs. Our analysis showed that the TPR of West Sumatra in the first year period was surpassing WHO recommendation of 5%. The COVID-19 TPR in cities reached above 10%, two times compared to regencies, indicating that SARS-CoV-2 transmission was still out of control especially in these regions. In some districts, nearly one of four samples tested was positive in a monthly period. TPR trends also increased over time although some short declines were recorded but never far beyond recommendation.
Our study result demonstrated that the TPR in West Sumatra was high (> recommendation of 5%) in the first-year period of COVID-19 pandemic entered the province, especially in cities. There was a significant difference in the TPR between cities and regencies, where the annual TPR of cities was two times higher. This finding may be related to urban or rural types of regions based on population density where the cities were mostly had higher densities than regencies (15). West Sumatra had an average population density of 131 people/ square kilometers, with a high average density in cities of 1,219 people/ square kilometers compared to regencies with only 100 people/ square kilometers (10, 11). The highest number of population densities was Kota Bukittinggi of 4,795 people/ square kilometers and Kota Padang Panjang of 2,448 people/ square kilometers, in line with the TPR of these cities as the highest among other districts in the province. Some studies had highlighted the population density as the main factor of viral spreading in a region due to the increase of contact rates (16–18). Further analysis should be performed to find other confounding factors that affect a high TPR in cities, such as testing capability, health care capacity, transportation, behavioral factors, and government policy.
Although many districts in the province had a higher annual TPR than the global recommendation to control the pandemic, 6 of 19 (35%) districts were not. Dharmasraya, Kepulauan Mentawai, Pasaman, Solok Selatan, Padang Pariaman, and Pasaman Barat regencies were the six districts in the province that have annual TPR below 5%, showing that the SARS-CoV-2 transmission was under control during the one-year period. These findings may be explained by the relatively low population density in these regencies with an average of 109 people/ square kilometers. Furthermore, our results showed a significant difference in TPR between the cities and the regencies (p < 0.001). Thus, the density level appeared to be an important factor to TPR. However, none of the six regencies had TPR < 5% in their all quarter or month in a whole one-year period. In the third quarter, especially in October 2020, the TPR(s) were sharply rose to their highest peak, as similar as provincial TPR. The annual TPR of West Sumatra seemed to fell in December 2020 before rearose in the next three months. This data is in line with a cumulative number of COVID-19 new cases recorded in West Sumatra at the same time (3). However, daily TPR might predict the number of hospitalized patients after 15 days, much longer than daily incidence cases with only 4 days, so further research is needed to confirm (13).
Using TPR as an epidemiological indicator of COVID-19 growth should be more beneficial to estimate viral transmission than using the cumulative number of new cases. Incidence number might be informative in the early epidemic phase, but when the number of new cases is surpassing testing capacity, it would create bias and subsequently, the curve of epidemic growth will continue to be constant. When the testing rate is increased, the cumulative cases also exponentially surges, but the TPR will fall significantly (19). Since the number of COVID-19 testing in West Sumatra was high in the third quarter while the TPR was increased, we predicted that the actual cumulative cases were far higher than recorded and the testing capacity is not yet adequate. This hypothesis also comes from our findings in January 2021 where the TPR was declining to 5.79% after testing was increased to its largest capacity. Our data also showed that in March 2021 when the testing rate declined, the TPR increased significantly. Therefore, consistent massive testing and appropriate treatment are necessary to find new cases and reducing the health public burden due to COVID-19 pandemic.
Based on the period, a fluctuated trend of TPR and the surge in the third quarter especially October 2020 in West Sumatra might be related to not only density level, but also due to changes in mobility and people’s behavior. At the beginning of the epidemic, COVID-19 TPR of West Sumatra recorded 6.76%, slightly higher than the control threshold. The national government responded to enforce a large-scale social distancing policy (PSBB) to lock down the provincial border and to close any public activities in schools, offices, houses of worship, and other social events. West Sumatra government applied PSBB on 20 April 2020 (20). As the result, the TPR trends fell to reach their lowest point of 0.75% since the pandemic in June 2020. This finding was in line with some studies that found public mobility restriction was related with declining of SARS-CoV-2 transmission (21–23). However, when national and provincial governments replace PSBB with a new normal policy (TNBPAC) at the end of June 2020 where the public spaces slowly opened with the implementation of health protocols such as washing hands, wearing a mask, and physical distancing, the TPR increased to 10 times in September 2020 and reached its peak on October 2020 (24). It is assumed that disinformation about COVID-19 in West Sumatra community also contributed to the TPR surge by affecting public behavior in which the health protocols were not applied effectively and consequently (25, 26). Therefore, it is believed that government policies and public cooperation are vital in controlling pandemics.
The TPR trends on the cities-regencies level periodically were similar to provincial trend. However, the higher TPR in cities might be mainly related to population density and their mobility. Besides, the regencies tended to have a monthly late TPR trend following cities especially from September 2020. For example, City of Kota Padang was having a peak of 22.66% in October 2020 while the neighboring regencies of Solok and Padang Pariaman just reached the peak in November 2020, one month later when the TPR of Kota Padang was declined. From this data, we assumed that the transmission rate in regencies was lower than in cities. We also hypothesized that the surge of infection in regencies is mainly due to high epidemic transmission in cities followed by regencies-cities-regencies migration, although the source of infection might come from both regions (27). It is important to control the regional border to prevent COVID-19 outbreak in an area during pandemic situation due to its high spreading potential.
The limitation of this study is that the data on the origin of the sample is available only from the location of the health facility sending the specimen, not from the individual's domicile origin. However, assuming that the patient was in the location at the time of sampling, it should represent the presence of the virus in the district at the same time. Further research is suggested to use domicile data to get a better and more representative picture. Finally, this study should be helpful to enhance information about TPR as a useful indicator to estimate and predict COVID-19 transmission and severity in a country.