| Literature DB >> 33923720 |
Shiori Sano1, Shuetsu Fukushi2, Souichi Yamada2, Shizuko Harada2, Hitomi Kinoshita2, Satoko Sugimoto2, Tomoki Yoshikawa2, Takeshi Kurosu2, Yuki Takamatsu2, Masayuki Shimojima2, Shoichi Toda3, Yuka Hamada4, Naoki Fujisawa5, Takayuki Sugimoto6, Masayuki Saijo2.
Abstract
Detection of severe fever with thrombocytopenia syndrome (SFTS) virus (SFTSV) during the early phase of the disease is important for appropriate treatment, infection control, and prevention of further transmission. The reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a nucleic acid amplification method that amplifies the target sequence under isothermal conditions. Here, we developed an RT-LAMP with a novel primer/probe set targeting a conserved region of the SFTSV L segment after extraction of viral RNA (standard RT-LAMP). Both the Chinese and Japanese SFTSV strains, including various genotypes, were detected by the standard RT-LAMP. We also performed RT-LAMP using the same primer/probe set but without the viral RNA extraction step (called simplified RT-LAMP) and evaluated the diagnostic efficacy. The sensitivity and specificity of the simplified RT-LAMP were 84.9% (45/53) and 89.5% (2/19), respectively. The simplified RT-LAMP can detect SFTSV in human sera containing >103.5 copies/mL viral RNA. The two RT-LAMP positive but quantitative real-time reverse transcription-polymerase chain reaction (RT-PCR) negative samples were positive in the conventional RT-PCR, suggesting that there was no false positive reaction in the RT-LAMP. Both the standard and simplified RT-LAMP are useful for detecting the SFTSV genome in patients during the early phase of the disease.Entities:
Keywords: RT-LAMP; SFTS virus; simplified method
Year: 2021 PMID: 33923720 PMCID: PMC8073756 DOI: 10.3390/v13040693
Source DB: PubMed Journal: Viruses ISSN: 1999-4915 Impact factor: 5.048
Figure 1Alignment of SFTSV L segment sequences and positions of the primers used for RT-LAMP assay. The Genbank accession numbers for the L segment sequences of SFTSV strains are as follows, YG1: AB817979; SPL010: AB817983; SPL035: AB817986; SPL057: AB983500; SPL100:AB983519; SPL004:AB817981; SPL230; LC620253, JS4: HQ141604; SD4: HM802202, 2012YSH105: KF711869; WJ: HQ171186, and HB29: HM745930; SPL193; LC620254, SPL238; LC620252, SPL179; LC620255.
Primer/probe sets used for the SFTSV RT-LAMP assay.
| Name | Primer Sequence (5′-3′) | Position | Final Conc. |
|---|---|---|---|
| SFTS_L_F3 | GATGGAGATGGGACTAGCAAC | 5231–5251 | 5 |
| SFTS_L_B3-1 | CTTGATCTTGAACCCACTCAG | 5384–5404 | 2.5 |
| SFTS_L_B3-2 | CTTGATCTTGAATCCACTCAG | 5384–5404 | 2.5 |
| SFTS_L_FIP-1 | CTTCGGATGGATTCAATGAC-TGGCTTGAGGAGATCAGG | 5297–5316(F1c) + 5252–5269 (F2) | 60 |
| SFTS_L_FIP-2 | CTCCGGATCGATTCAATGAC-TGGCTTGAGGAGATCAGG | 5297–5316(F1c) + 5252–5269 (F2) | 40 |
| SFTS_L_BIP-1 | GTGACGACCTTGGGATCAA-CCTAACCATGCAATGACCTC | 5322–5339(B1c) + 5364–5384(B2) | 60 |
| SFTS_L_BIP-2 | GTGATGACCTTGGGATCA-CCTAACCATGCAATGACCTC | 5322–5340(B1c) + 5364–5384(B2) | 40 |
| SFTS_L_LF | CATAAAGCCTGGCATCACTAC | 5274–5294 | 20 |
| SFTS_L_LB-1 | TAACAGGGTGGCATCTGC | 5341–5358 | 10 |
| SFTS_L_LB-2 | CAACAGGGTAGCATCTGC | 5341–5358 | 10 |
| SFTS_L_QProbe | CATAAAGCCTGGCATCACTACTGAGCC | 5268–5294 | 1 |
Results of three independent standard RT-LAMP assays designed to detect various SFTSV strains. Experiments were performed in triplicate.
| Genotype | Strain | Viral RNA Copy Numbers/Reaction | ||
|---|---|---|---|---|
| 100 | 10 | 1 | ||
| J1 | YG1 | +/+/+ | +/+/− | +/−/− |
| SPL010 | +/+/+ | −/−/− | −/−/− | |
| SPL035 | +/+/+ | +/+/+ | −/−/− | |
| J2 | SPL100 | +/+/+ | +/+/− | −/−/− |
| SPL057 | +/+/+ | +/−/− | −/−/− | |
| J3 | SPL004 | +/+/+ | +/−/− | +/−/− |
| SPL230 | +/+/+ | +/−/− | −/−/− | |
| C3 | HB29 | +/+/+ | +/+/+ | −/−/− |
| C4 | SPL193 | +/+/+ | +/−/− | −/−/− |
| C5 | SPL087 | +/+/+ | +/−/− | +/−/− |
| SPL179 | +/+/+ | +/+/+ | +/+/− | |
| SPL238 | +/+/+ | −/−/− | −/−/− | |
+: detected; −: undetected.
Cross reactivity of the SFTSV RT-LAMP with viruses belonging to the Phenuiviridae, Nairoviridae, and Arenaviridae families, and with Nipah virus, Zika virus, SARS-related CoV, and MERS-related CoV.
| Family | Species | Virus Titer (Log10 TCID50 or FFU/mL) | Standard RT-LAMP |
|---|---|---|---|
| Phenuiviridae | SFTSV SPL004 | 8.0 | + |
| Heartland bandavirus | 7.8 | − | |
| Palma virus (Bhanja bandavirus) | 7.3 | − | |
| Forecariah virus (Bhanja bandavirus) | 7.1 | − | |
| Rift Valley fever phlebovirus (MP−12) * | 6.4 | − | |
| Nairoviridae | Soft tick bunyavirus (Keterah orthonairovirus) | 5.5 | − |
| Issyk-Kul virus (Keterah orthonairovirus) | 5.5 | − | |
| Hazara orthonairovirus | 5.9 | − | |
| Dugbe orthonairovirus | 6.1 | − | |
| Arenaviridae | Mobala mammarenavirus | 6.0 | − |
| Mopeia mammarenavirus | 8.4 | − | |
| Argentinian mammarenavirus (Candid#1 **) | 6.7 | − | |
| Lymphocytic choriomeningitis mammarenavirus | 5.0 | − | |
| Paramyxoviridae | Nipah henipavirus | 7.6 | − |
| Flaviviridae | Zika virus | 6.9 | − |
| Coronaviridae | SARS-related CoV | 7.6 | − |
| MERS-related CoV | 7.5 | − |
+: detected; −: undetected. * Attenuated vaccine strain of Rift Valley fever phlebovirus. ** Attenuated vaccine strain of Junin virus.
Detection limits of the standard and the simplified RT-LAMP assays. Experiments were performed in triplicate.
| Genotype (L Segment) | Strain | LAMP Method | Viral Titer (FFU/mL) | |||
|---|---|---|---|---|---|---|
| 1000 | 100 | 10 | 1 | |||
| J1 | SPL010 | Standard | +/+/+ | +/+/− | −/−/− | −/−/− |
| Simplified | +/+/+ | +/−/− | −/−/− | −/−/− | ||
| J2 | SPL100 | Standard | +/+/+ | +/+/+ | +/−/− | −/−/− |
| Simplified | +/+/+ | −/−/− | −/−/− | −/−/− | ||
| J3 | SPL230 | Standard | +/+/+ | +/+/+ | +/−/− | −/−/− |
| Simplified | +/+/+ | +/+/+ | −/−/− | −/−/− | ||
| C5 | SPL238 | Standard | +/+/+ | +/+/+ | +/−/− | −/−/− |
| Simplified | +/+/+ | +/−/− | −/−/− | −/−/− | ||
+: detected; −: undetected.
Comparison of SFTSV detection by RT-LAMP and qRT-PCR.
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| LAMP method | Standard | Positive | 49 | 2 * |
| Negative | 4 | 17 | ||
| Simplified | Positive | 45 | 2 * | |
| Negative | 8 | 17 | ||
* Conventional RT-PCR positive.
Figure 2qPCR measurement of RNA copy numbers in serum samples that were positive and negative in the simplified RT-LAMP assay. There was a significant difference (p < 0.01) in RNA copy number in the positive and negative samples.