Id |
Subject |
Object |
Predicate |
Lexical cue |
T9 |
0-61 |
Sentence |
denotes |
Timely implementation of molecular diagnostics for SARS-CoV-2 |
T10 |
62-461 |
Sentence |
denotes |
In connection with the ongoing outbreak of a novel coronavirus in the province Hubei and surrounding areas in China, it was expected that Europe would also be confronted with the emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as infections in travellers in several Asian countries outside of China were confirmed shortly after the announcement of the outbreak in Wuhan [1-4]. |
T11 |
462-628 |
Sentence |
denotes |
Therefore, it was necessary to rapidly implement adequately quick and sensitive diagnostic assays for outbreak management of SARS-CoV-2 in public health laboratories. |
T12 |
629-800 |
Sentence |
denotes |
As soon as the World Health Organization (WHO) published the first protocols for real-time RT-PCR assays, the Bavarian Food and Health Authority started to implement them. |
T13 |
801-939 |
Sentence |
denotes |
We ordered control material and oligonucleotides (see details below) in week 4 and ran our first SARS-CoV-2 assays on 27 January (week 5). |
T14 |
940-1047 |
Sentence |
denotes |
On the same day, the first German case of coronavirus disease 2019 (COVID-19) was diagnosed in Bavaria [1]. |
T15 |
1048-1209 |
Sentence |
denotes |
In the following days, health authorities implemented comprehensive measures to prevent further transmission of SARS-CoV-2, including testing of contact persons. |
T16 |
1210-1375 |
Sentence |
denotes |
We initially used the protocol based on the E gene and RdRp gene developed by the German Consiliary Laboratory for Coronaviruses hosted at the Charité in Berlin [5]. |
T17 |
1376-1573 |
Sentence |
denotes |
Real-time RT-PCR was initially performed with the QuantiTect Virus +Rox Vial kit (QIAGEN, Hilden, Germany) on the Bio-Rad CFX96 Touch Real-Time PCR Detection System (Bio-Rad, Feldkirchen, Germany). |
T18 |
1574-1696 |
Sentence |
denotes |
The kit was chosen for its frequent and successful use in our laboratory with other assays and its immediate availability. |
T19 |
1697-1789 |
Sentence |
denotes |
Primers and probes were used as described [5] and provided by TIB Molbiol (Berlin, Germany). |
T20 |
1790-2016 |
Sentence |
denotes |
Control material was ordered from the European Virus Archive (EVAg) and consisted of synthetic Wuhan coronavirus 2019 E gene control (reference number 026N-03866) and SARS-CoV Frankfurt 1 RNA (reference number 004N-02005) [6]. |
T21 |
2017-2155 |
Sentence |
denotes |
In addition, the control of LightMix Modular Wuhan CoV RdRP-gene (TibMolbiol, Berlin, Germany) was used for the SARS-CoV-2 specific assay. |
T22 |
2156-2257 |
Sentence |
denotes |
Respiratory samples (nasopharyngeal swabs or sputum) were obtained from patients and contact persons. |
T23 |
2258-2326 |
Sentence |
denotes |
Sputum samples were diluted in 2 mL phosphate buffered saline (PBS). |
T24 |
2327-2446 |
Sentence |
denotes |
RNA was extracted using the QIAamp Bio Robot kit (QIAGEN) on a Hamilton Microlab Star (Hamilton, Bonaduz, Switzerland). |
T25 |
2447-2765 |
Sentence |
denotes |
Each sample was tested by three PCRs: the screening assay for the E gene and two confirmatory assays targeting the RdRp gene, all performed as recommended in [5], with either both probes (RdRP_SARSr-P1 and RdRP_SARSr-P2), detecting SARS-CoV and SARS-CoV-2, or only with the SARS-CoV-2-specific probe RdRP_SARSr-P2 [5]. |
T26 |
2766-2822 |
Sentence |
denotes |
We used human RNAse P as control for RNA extraction [7]. |
T27 |
2823-2890 |
Sentence |
denotes |
The cumulative numbers of all tested samples are shown in Figure 1. |
T28 |
2891-3039 |
Sentence |
denotes |
Two weeks after starting the SARS-CoV-2 diagnostics, we had analysed 669 respiratory samples at the Bavarian Health and Food Safety Authority (LGL). |
T29 |
3040-3101 |
Sentence |
denotes |
Among them, seven showed positive results for SARS CoV-2 RNA. |
T30 |
3102-3165 |
Sentence |
denotes |
By 11 February, 14 COVID-19 cases had been detected in Bavaria. |
T31 |
3166-3275 |
Sentence |
denotes |
Figure 1 Cumulative numbers of suspected COVID-19 samples tested during week 5 and 6 2020, Bavaria (n = 675) |
T32 |
3276-3365 |
Sentence |
denotes |
COVID: coronavirus disease; PHEIC: public health emergency of international concern; LGL: |
T33 |
3366-3413 |
Sentence |
denotes |
Bavarian Health and Food Safety Authority; WHO: |
T34 |
3414-3440 |
Sentence |
denotes |
World Health Organization. |
T35 |
3441-3580 |
Sentence |
denotes |
The figure shows all samples tested at LGL, negative and positive, as well as six positive samples tested in other laboratories in Bavaria. |
T36 |
3581-3649 |
Sentence |
denotes |
All data are cumulative, with a final total of positive tests of 13. |