Real-time fluorescence loop-mediated isothermal amplification assays for detection of zoonotic malaria Plasmodium parasites

BACKGROUND

Natural human infections by Plasmodium cynomolgi and P. inui have been reported recently and gain the substantial attention from Southeast Asian countries. Zoonotic transmission of non-human malaria parasites to humans from macaque monkeys occurred through the bites of the infected mosquitoes. The objective of this study is to establish real-time fluorescence loop-mediated isothermal amplification (LAMP) assays for the detection of zoonotic malaria parasites by combining real-time fluorescent technology with the isothermal amplification technique.

METHODS

By using 18S rRNA as the target gene, the primers for P. cynomolgi, P. coatneyi and P. inui were newly designed in the present study. Four novel real-time fluorescence LAMP assays were developed for the detection of P. cynomolgi, P. coatneyi, P. inui and P. knowlesi. The entire amplification process was completed in 60 min, with the assays performed at 65 °C. By using SYTO-9 as the nucleic acid intercalating dye, the reaction was monitored via real-time fluorescence signal.

RESULTS

There was no observed cross-reactivity among the primers from different species. All 70 field-collected monkey samples were successfully amplified by real-time fluorescence LAMP assays. The detection limit for P. cynomolgi, P. coatneyi and P. knowlesi was 5 × 109 copies/µL. Meanwhile, the detection limit of P. inui was 5 × 1010 copies/µL.

CONCLUSION

This is the first report of the detection of four zoonotic malaria parasites by real-time fluorescence LAMP approaches. It is an effective, rapid and simple-to-use technique. This presented platform exhibits considerable potential as an alternative detection for zoonotic malaria parasites.

Recombinase-Aided Loop-Mediated Isothermal Amplification on Human Plasmodium knowlesi

Loop-mediated isothermal amplification (LAMP) is a nucleic acid amplification technique that can amplify specific nucleic acids at a constant temperature (63-65°C) within a short period (<1 hour). In this study, we report the utilization of recombinase-aided LAMP to specifically amplify the 18S sRNA of Plasmodium knowlesi. The method was built on a conventional LAMP assay by inclusion of an extra enzyme, namely recombinase, into the master mixture. With the addition of recombinase into the LAMP assay, the assay speed was executed within a time frame of less than 28 minutes at 65°C. We screened 55 P. knowlesi samples and 47 non-P. knowlesi samples. No cross-reactivity was observed for non-P. knowlesi samples, and the detection limit for recombinase-aided LAMP was one copy for P. knowlesi after LAMP amplification. It has been reported elsewhere that LAMP can be detected through fluorescent readout systems. Although such systems result in considerable limits of detection, the need for sophisticated equipment limits their use. Hence, we used here a colorimetric detection platform for the evaluation of the LAMP assay's performance. This malachite green-based recombinase-aided LAMP assay enabled visualization of results with the naked eye. Negative samples were observed by a change in color from green to colorless, whereas positive samples remained green. Our results demonstrate that the LAMP assay developed here is a convenient, sensitive, and useful diagnostic tool for the rapid detection of knowlesi malaria parasites. This method is suitable for implementation in remote healthcare settings, where centralized laboratory facilities, funds, and clinicians are in short supply.

A visualized hybrid PCR-LAMP assay for the detection of human Plasmodium species

Combining the advantages of PCR and LAMP, we described a new technique, namely PCR-LAMP, for malaria diagnosis. The whole process of DNA amplification can be completed in 35 min. This hybrid amplification technique markedly improved the sensitivity of detection compared to the classic single PCR or LAMP assay alone. PCR-LAMP assay had a detection limit of 1 copy/µL for P. knowlesi and P. ovale, 0.1 copy/µL for P. vivax, P. falciparum and P. malariae, respectively. To facilitate the endpoint detection, xylenol orange was added. Positive samples were indicated in orange while negative reactions were violet. The inclusion of xylenol orange into the LAMP reaction mix significantly reduces the post-amplification workload. Without relying on the use of specific instruments, the color changes of the amplicons could be visualized directly through the naked eye. In conclusion, PCR-LAMP poses the potential to be developed as a new malaria molecular diagnosis tool.

Lateral Flow Recombinase Polymerase Amplification Assays for the Detection of Human Plasmodium Species

This study highlights the development of two lateral flow recombinase polymerase amplification assays for the diagnosis of human malaria. The lateral flow cassettes contained test lines that captured biotin-, 6-carboxyfluorescein, digoxigenin-, cyanine 5-, and dinitrophenyl-labeled amplicons. The overall process can be completed in 30 minutes. Recombinase polymerase amplification coupled with lateral flow had a detection limit of 1 copy/µL for Plasmodium knowlesi, Plasmodium vivax, and Plasmodium falciparum. No cross-reactivity was observed among nonhuman malaria parasites such as Plasmodium coatneyi, Plasmodium cynomolgi, Plasmodium brasilanium, Plasmodium inui, Plasmodium fragile, Toxoplasma gondii, Sarcocystis spp., Brugia spp., and 20 healthy donors. It is rapid, highly sensitive, robust, and easy to use. The result can be read without the need for special equipment and thus has the potential to serve as an effective alternative to polymerase chain reaction methods for the diagnosis of malaria.

Point-of-Care Diagnosis of Malaria Using a Simple, Purification-Free DNA Extraction Method Coupled with Loop-Mediated Isothermal Amplification-Lateral Flow

We propose a protocol suitable for point-of-care diagnosis of malaria utilizing a simple and purification-free DNA extraction method with the combination of loop-mediated isothermal amplification assay and lateral flow (LAMP-LF). The multiplex LAMP-LF platform developed here can simultaneously detect Plasmodium knowlesi, P. vivax, P. falciparum, and Plasmodium genus (for P. malariae and P. ovale). Through the capillary effect, the results can be observed by the red band signal on the test and control lines within 5 min. The developed multiplex LAMP-LF was tested with 86 clinical blood samples on-site at Hospital Kapit, Sarawak, Malaysia. By using microscopy as the reference method, the multiplex LAMP-LF showed 100% sensitivity (95% confidence interval (CI): 91.4 to 100.00%) and 97.8% specificity (95% CI: 88.2% to 99.9%). The high sensitivity and specificity of multiplex LAMP-LF make it ideal for use as a point-of-care diagnostic tool. The simple and purification-free DNA extraction protocol can be employed as an alternative DNA extraction method for malaria diagnosis in resource-limited settings. By combining the simple DNA extraction protocol and multiplex LAMP-LF approach, we aim to develop a simple-to-handle and easy-to-read molecular diagnostic tool for malaria in both laboratory and on-site settings.

Two-Stage Detection of Plasmodium spp. by Combination of Recombinase Polymerase Amplification and Loop-Mediated Isothermal Amplification Assay

We developed a combination of recombinase polymerase and loop-mediated isothermal amplification methods (RAMP) for rapid screening of five human Plasmodium spp. simultaneously. RAMP is a two-stage isothermal amplification method, which consists of a first-stage recombinase polymerase amplification and a second-stage loop-mediated isothermal amplification. Under these two isothermal conditions, five Plasmodium spp. were amplified in less than 40 minutes. We demonstrated RAMP assay with 10-fold better limit of detection than a single (loop-mediated isothermal amplification) LAMP. As compared with microscopy, RAMP assay showed 100% sensitivity (95% CI: 95.65-100.00%) and 100% specificity (95% CI: 69.15-100.00%). The end products were inspected by the color changes of neutral red. Positive reactions were indicated by pink while the negative reactions remained yellow. The combination assay established in this study can be used as a routine diagnostic method for malaria.

Clinical testing on SARS-CoV-2 swab samples using reverse-transcription loop-mediated isothermal amplification (RT-LAMP)

BACKGROUND

High cost of commercial RNA extraction kits limits the testing efficiency of SARS-CoV-2. Here, we developed a simple nucleic acid extraction method for the detection of SARS-CoV-2 directly from nasopharyngeal swab samples.

METHODS

A pH sensitive dye was used as the end point detection method. The obvious colour changes between positive and negative reactions eliminates the need of other equipment.

RESULTS

Clinical testing using 260 samples showed 92.7% sensitivity (95% CI 87.3-96.3%) and 93.6% specificity (95% CI 87.3-97.4%) of RT-LAMP.

CONCLUSIONS

The simple RNA extraction method minimizes the need for any extensive laboratory set-up. We suggest combining this simple nucleic acid extraction method and RT-LAMP technology as the point-of care diagnostic tool.

Colorimetric detection of SARS-CoV-2 by uracil-DNA glycosylase (UDG) reverse transcription loop-mediated isothermal amplification (RT-LAMP)

OBJECTIVES

Preventing reverse transcription loop-mediated isothermal amplification (RT-LAMP) carryover contamination could be solved by adding deoxyuridine triphosphate (dUTP) and uracil-DNA glycosylase (UDG) into the reaction master mix.

METHODS

RNA was extracted from nasopharyngeal swab samples by a simple RNA extraction method.

RESULTS

Testing of 77 samples demonstrated 91.2% sensitivity (95% confidence interval [CI]: 78-98.2%) and 100% specificity (95% confidence interval: 92-100%) using UDG RT-LAMP.

CONCLUSION

This colorimetric UDG RT-LAMP is a simple-to-use, fast, and easy-to-interpret method, which could serve as an alternative for diagnosis of SARS-CoV-2 infection, especially in remote hospitals and laboratories with under-equipped medical facilities.

End-point detection of loop-mediated isothermal amplification (LAMP) on malaria by direct observation with colorimetric dyes

In order to ascertain the results of the LAMP technique, different end-point detection methods can be employed. However, these methods require sophisticated equipment. To simplify current end-point detection methods for the diagnosis of malaria, we propose the incorporation of colorimetric dyes: malachite green (MG), phenol red (PR), and xylenol orange (XO) in the LAMP assay. To evaluate the optimum concentration of dyes, 5 different concentrations (50 μM, 75 μM, 100 μM, 125 μM, and 150 μM) were used with buffer pH 8.5 and pH 8.8, respectively. The results showed that 125 μM of MG at pH 8.8 produced the most obvious colour change. A total of 71 clinical blood samples of Plasmodium knowlesi, Plasmodium malariae, Plasmodium vivax, Plasmodium falciparum, and healthy donors were tested using MG-LAMP. It showed 100% sensitivity and specificity. The simplicity and affordability of this method make it ideal to be used as an end-point detection method for malaria diagnosis in resource limited settings.

Plasmodium knowlesi: the game changer for malaria eradication

Plasmodium knowlesi is a zoonotic malaria parasite that has gained increasing medical interest over the past two decades. This zoonotic parasitic infection is prevalent in Southeast Asia and causes many cases with fulminant pathology. Despite several biogeographical restrictions that limit its distribution, knowlesi malaria cases have been reported in different parts of the world due to travelling and tourism activities. Here, breakthroughs and key information generated from recent (over the past five years, but not limited to) studies conducted on P. knowlesi were reviewed, and the knowledge gap in various research aspects that need to be filled was discussed. Besides, challenges and strategies required to control and eradicate human malaria with this emerging and potentially fatal zoonosis were described.

RNA purification-free detection of SARS-CoV-2 using reverse transcription loop-mediated isothermal amplification (RT-LAMP)

BACKGROUND

Current diagnosis of SARS-CoV-2 infection relies on RNA purification prior to amplification. Typical extraction methods limit the processing speed and turnaround time for SARS-CoV-2 diagnostic testing.

METHODS

Here, we applied reverse transcription loop-mediated isothermal amplification directly onto human clinical swabs samples to amplify the RNA from SARS-CoV-2 swab samples after processing with chelating resin.

RESULTS

By testing our method on 64 samples, we managed to develop an RT-LAMP assay with 95.9% sensitivity (95% CI 86 to 99.5%) and 100% specificity (95% CI 78.2-100%).

CONCLUSION

The entire process including sample processing can be completed in approximately 50 min. This method has promising potential to be applied as a fast, simple and inexpensive diagnostic tool for the detection of SARS-CoV-2.

Two extraction-free reverse transcription loop-mediated isothermal amplification assays for detection of SARS-CoV-2

BACKGROUND

Current assays for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) rely on time consuming, costly and laboratory based methods for virus isolation, purification and removing inhibitors. To address this limitation, we propose a simple method for testing RNA from nasopharyngeal swab samples that bypasses the RNA purification step.

METHODS

In the current project, we have described two extraction-free reverse transcription loop-mediated isothermal amplification (RT-LAMP) assays for the detection of SARS-CoV-2 by using E gene and RdRp gene as the targets.

RESULTS

Here, results showed that reverse transcription loop-mediated isothermal amplification assays with 88.4% sensitive (95% CI: 74.9-96.1%) and 67.4% sensitive (95% CI: 51.5-80.9%) for E gene and RdRp gene, respectively.

CONCLUSION

Without the need of RNA purification, our developed RT-LAMP assays for direct detection of SARS-CoV-2 from nasopharyngeal swab samples could be turned into alternatives to qRT-PCR for rapid screening.

High incidence of Plasmodium knowlesi malaria compared to other human malaria species in several hospitals in Malaysia

Through the regional control programme, Malaysia has been successfully reducing the incidence of Plasmodium falciparum and Plasmodium vivax infections. However, the incidence of zoonotic malaria Plasmodium knowlesi infection is increasing and now has been the major cause of malaria in Malaysia especially Malaysian Borneo. The emergence of knowlesi infection has threatened the malaria elimination programme which the government aims to reduce the overall malaria infections by 2020. Unlike other benign human Plasmodium spp., P. knowlesi can cause fatal infections. The aim of this study was to determine the incidence and distribution of five human malaria parasites including P. knowlesi in Peninsular Malaysia and Malaysian Borneo. A total of 112 blood samples were collected from seven states and district hospitals in Peninsular Malaysia and Malaysian Borneo from year 2015 to 2016. The samples were examined by microscopy and further confirmed by nested PCR assay targeting 18S rRNA gene of Plasmodium spp. Following the nested PCR assays, a total of 54 (48.2%) samples were positive for P. knowlesi infections, 12 (10.7%) cases were positive for P. vivax infections, followed by 7 (6.3%) cases of P. falciparum and 4 (3.5%) cases of P. malariae. There were 3 cases (2.7%) of mixed infections (P. knowlesi/P. vivax). However, no cases were identified as P. ovale. A total of 32 (28.6%) cases were found as negative infections. LoopMediated Isothermal Amplification Assay (LAMP) was performed to confirm inconclusive results produced by microscopy and nested PCR. P. knowlesi showed the highest prevalence in Sarawak (n= 30), Sabah (n=13), Pulau Pinang (n=5) and Pahang (n=6). PCR and LAMP was not able to detect a large number of microscopy positive samples due to DNA degradation during storage and shipping. Among all the states involved in this study, the highest prevalence of P. knowlesi infection was found in Sabah and Sarawak.

Experimental Study on Plasmodium knowlesi Normocyte Binding Protein Xa Region II (PkNBPXaII) for Erythrocyte Binding

Normocyte binding protein Xa (NBPXa) has been implied to play a significant role in parasite invasion of human erythrocytes. Previous phylogenetic studies have reported the existence of three types of NBPXa for Plasmodium knowlesi (PkNBPXa). PkNBPXa region II (PkNBPXaII) of type 1, type 2 and type 3 were expressed on mammalian cell surface and interacted with human and macaque (Macaca fascicularis) erythrocytes. The binding activities of PkNBPXaII towards human and macaque erythrocytes were evaluated using erythrocyte-binding assay (EBA). Three parameters were evaluated to achieve the optimal protein expression of PkNBPXaII and erythrocyte binding activity in EBA: types of mammalian cells, post transfection time and erythrocyte incubation time. COS-7, HEK-293, and CHO-K1 cells showed successful expression of PkNBPXaII, despite the protein expression is weak compared to the positive control. COS-7 was used in EBA. All three types of PkNBPXaII showed rosette formation with macaque erythrocytes but not with human erythrocytes. Future studies to enhance the PkNBPXaII expression on surface of mammalian cells is indeed needed in order to elucidate the specific role of PkNBPXaII in erythrocytes invasion.

Colorimetric Reverse Transcription-Loop-Mediated Isothermal Amplification Assay for Rapid Detection of SARS-CoV-2

Coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been spreading rapidly all over the world. In the absence of effective treatments or a vaccine, there is an urgent need to develop a more rapid and simple detection technology of COVID-19. We describe a WarmStart colorimetric reverse transcription–loop-mediated isothermal amplification (RT-LAMP) assay for the detection of SARS-CoV-2. The detection limit for this assay was 1 copy/µL SARS-CoV-2. To test the clinical sensitivity and specificity of the assay, 37 positive and 20 negative samples were used. The WarmStart colorimetric RT-LAMP had 100% sensitivity and specificity. End products were detected by direct observation, thereby eliminating the need for post-amplification processing steps. WarmStart colorimetric RT-LAMP provides an opportunity to facilitate virus detection in resource-limited settings without a sophisticated diagnostic infrastructure.

Enteral myiasis causing acute dysentery: A case report

Enteral myiasis or intestinal myiasis is acquired by ingesting food or water contaminated with dipteran fly eggs or larvae. Here, we describe a patient with intestinal myiasis presenting with acute dysentery caused by the larva of Hermetia illucens. The larva was identified morphologically, and its species confirmed through molecular analysis using polymerase chain reaction and sequencing based on mitochondrial cytochrome c oxidase subunit I gene (COI).

Validation of SYBR green I based closed-tube loop-mediated isothermal amplification (LAMP) assay for diagnosis of knowlesi malaria

BACKGROUND

As an alternative to PCR methods, LAMP is increasingly being used in the field of molecular diagnostics. Under isothermal conditions at 65 °C, the entire procedure takes approximately 30 min to complete. In this study, we establish a sensitive and visualized LAMP method in a closed-tube system for the detection of Plasmodium knowlesi.

METHODS

A total of 71 malaria microscopy positive blood samples collected in blood spots were obtained from the Sarawak State Health Department. Using 18s rRNA as the target gene, nested PCR and SYBR green I LAMP assay were performed following the DNA extraction. The colour changes of LAMP end products were observed by naked eyes.

RESULTS

LAMP assay demonstrated a detection limit of 10 copies/µL in comparison with 100 copies/µL nested PCR. Of 71 P. knowlesi blood samples collected, LAMP detected 69 microscopy-positive samples. LAMP exhibited higher sensitivity than nested PCR assay. The SYBR green I LAMP assay was 97.1% sensitive (95% CI 90.2-99.7%) and 100% specific (95% CI 83.2-100%). Without opening the cap, incorporation of SYBR green I into the inner cap of the tube enabled the direct visualization of results upon completion of amplification. The positives instantaneously turned green while the negatives remained orange.

CONCLUSIONS

These results indicate that SYBR green I LAMP assay is a convenient diagnosis tool for the detection of P. knowlesi in remote settings.

Development of a reverse transcription recombinase polymerase amplification assay for rapid and direct visual detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)

Rapid diagnosis is an important intervention in managing the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) outbreak. Real time reverse transcription polymerase chain reaction (RT-qPCR) remains the primary means for diagnosing the new virus strain but it is time consuming and costly. Recombinase polymerase amplification (RPA) is an isothermal amplification assay that does not require a PCR machine. It is an affordable, rapid, and simple assay. In this study, we developed and optimized a sensitive reverse transcription (RT)-RPA assay for the rapid detection of SARS-CoV-2 using SYBR Green I and/or lateral flow (LF) strip. The analytical sensitivity and specificity of the RT-RPA assay were tested by using 10-fold serial diluted synthetic RNA and genomic RNA of similar viruses, respectively. Clinical sensitivity and specificity of the RT-RPA assay were carried out using 78 positive and 35 negative nasopharyngeal samples. The detection limit of both RPA and RT-qPCR assays was 7.659 and 5 copies/μL RNA, respectively with no cross reactivity with other viruses. The clinical sensitivity and specificity of RT-RPA were 98% and 100%, respectively. Our study showed that RT-RPA represents a viable alternative to RT-qPCR for the detection of SARS-CoV-2, especially in areas with limited infrastructure.

Elimination of contamination in loop-mediated isothermal amplification assay for detection of human malaria

The LAMP assay, amplifies the target DNA rapidly, with 10-fold greater sensitivity than conventional PCR. The greater sensitivity also comes with greater risks of contamination. To overcome this issue, the current project includes either uracil DNA glycosylase (UDG) or a mineral oil overlay in the LAMP assay. Our results indicated that UDG or a mineral oil overlay can effectively prevent carryover contamination in the LAMP assay for the detection of human malaria. By incorporating these preventative methods, contamination can be eliminated and LAMP can potentially be used in the field; and point of care diagnosis for human malaria.

Natural Plasmodium infection in wild macaques of three states in peninsular Malaysia

Zoonotic cases of Plasmodium knowlesi account for most malaria cases in Malaysia, and humans infected with P. cynomolgi, another parasite of macaques have recently been reported in Sarawak. To date the epidemiology of malaria in its natural Macaca reservoir hosts remains little investigated. In this study we surveyed the prevalence of simian malaria in wild macaques of three states in Peninsular Malaysia, namely Pahang, Perak and Johor using blood samples from 103 wild macaques (collected by the Department of Wildlife and National Parks Peninsular Malaysia) subjected to microscopic examination and nested PCR targeting the Plasmodium small subunit ribosomal RNA gene. As expected, PCR analysis yielded significantly higher prevalence (64/103) as compared to microscopic examination (27/103). No relationship between the age and/or sex of the macaques with the parasitaemia and the Plasmodium species infecting the macaques could be identified. Wild macaques in Pahang had the highest prevalence of Plasmodium parasites (89.7%), followed by those of Perak (69.2%) and Johor (28.9%). Plasmodium inui and P. cynomolgi were the two most prevalent species infecting the macaques from all three states. Half of the macaques (33/64) harboured two or more Plasmodium species. These data provide a baseline survey, which should be extended by further longitudinal investigations that should be associated with studies on the bionomics of the anopheline vectors. This information will allow an accurate evaluation of the risk of zoonotic transmission to humans, and to elaborate effective strategies to control simian malaria.

A Sensitive Reverse Transcription Loop-Mediated Isothermal Amplification Assay for Direct Visual Detection of SARS-CoV-2

A simple and rapid reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for the detection of SARS-CoV-2. The RT-LAMP assay was highly specific for SARS-CoV-2 and was able to detect one copy of transcribed SARS-CoV-2 RNA within 24 minutes. Assay validation performed using 50 positive and 32 negative clinical samples showed 100% sensitivity and specificity. The RT-LAMP would be valuable for clinical diagnosis and epidemiological surveillance of SARS-CoV-2 infection in resource-limited areas as it does not require the use of sophisticated and costly equipment.

Case report: recurrence of Plasmodium vivax malaria due to defective cytochrome P450 2D6 function in Pos Lenjang, Pahang, Malaysia

Five children in Pos Lenjang, Pahang, Malaysia were PCR-positive for vivax malaria and were admitted to the hospital from 5 to 26 July 2019. One of the patients experienced three episodes of recurrence of vivax malaria. Microsatellite analysis showed that reinfection is unlikely. Drug resistance analysis indicated that Riamet (artemether-lumefantrine) is effective. Cytochrome P450 2D6 (CYP2D6) testing showed that this patient has defective CYP2D6 function. Primaquine failure to clear the Plasmodium vivax hypnozoites may be the cause of recurring infections in this patient. This report highlights the need for the development of liver-stage curative antimalarials that do not require metabolism by the CYP2D6 enzyme.

Evaluation of WarmStart Colorimetric Loop-Mediated Isothermal Amplification Assay for Diagnosis of Malaria

The incidence of zoonotic malaria, Plasmodium knowlesi, infection is increasing and now is the major cause of malaria in Malaysia. Here, we describe a WarmStart colorimetric loop-mediated isothermal amplification (LAMP) assay for the detection of Plasmodium spp. The detection limit for this assay was 10 copies/µL for P knowlesi and Plasmodium ovale and 1 copy/µL for Plasmodium falciparum, Plasmodium vivax, and Plasmodium malariae. To test clinical sensitivity and specificity, 100 microscopy-positive and 20 malaria-negative samples were used. The WarmStart colorimetric LAMP was 98% sensitive and 100% specific. Amplification products were visible for direct observation, thereby eliminating the need for post-amplification processing steps. Therefore, WarmStart colorimetric LAMP is suitable for use in resource-limited settings.

Detection of Plasmodium knowlesi using recombinase polymerase amplification (RPA) combined with SYBR Green I

In this study, recombinase polymerase amplification (RPA) combined with SYBR Green I was developed for the detection of Plasmodium knowlesi. Positive samples were indicated with a green color while negative samples were orange. To increase the efficiency of amplification, an interval mixing step of samples after 3 to 6 min incubation was recommended. Different sets of reaction volumes from 6.25 to 50 µL were tested and the results indicated no differences in detection. RPA's combination with SYBR Green I is fast and easy to perform, hence this method is suitable for use in resource-limited settings.

Real-time reverse transcription loop-mediated isothermal amplification for rapid detection of SARS-CoV-2

Background

Highly sensitive real-time reverse transcription polymerase chain reaction (RT-qPCR) methods have been developed for the detection of SARS-CoV-2. However, they are costly. Loop-mediated isothermal amplification (LAMP) assay has emerged as a novel alternative isothermal amplification method for the detection of nucleic acid.

Methods

A rapid, sensitive and specific real-time reverse transcription LAMP (RT-LAMP) assay was developed for SARS-CoV-2 detection.

Results

This assay detected one copy/reaction of SARS-CoV-2 RNA in 30 min. Both the clinical sensitivity and specificity of this assay were 100%. The RT-LAMP showed comparable performance with RT-qPCR. Combining simplicity and cost-effectiveness, this assay is therefore recommended for use in resource resource-limited settings.

Detection of Toxoplasma gondii by Loop-mediated Isothermal Amplification in Blood and Urine Samples from Women in Saudi Arabia

Introduction: Toxoplasmosis is the disease which is caused by the protozoan parasite Toxoplasma gondii (T. gondii), which has the ability to infect all warm-blooded animals. Several molecular techniques for the diagnosis of Toxoplasma gondii includes normal and Real Time Polymerase Chain Reaction (RT-PCR), and gene sequencing. Aim: To apply Loop-Mediated Isothermal Amplification (LAMP) for the diagnosis of T. gondii infections in urine and blood samples from female population in Saudi Arabia. Materials and Methods: In this cross-sectional study, genomic DNA was extracted from 22 blood and urine samples (11 each), two LAMP assays based on B1 and Surface Antigen 2 (SAG2) genes of T. gondii was performed. Conventional PCR was done for the LAMP product followed by sequencing to confirm the specificity of LAMP method. Statistical Package for the Social Sciences (SPSS) version 20.0 was used to summarise continuous and categorical variables. Results: From 22 samples, 17 samples were LAMP positive in both urine and blood samples, four were negative in blood and positive in urine samples, and one was positive in blood and negative in urine. Sequencing of PCR product confirm the specificity of the method used. Conclusion: LAMP detection of T. gondii DNA is an appropriate, sensitive and specific method for diagnosis of toxoplasmosis from urine and blood specimens in humans.

Comparison of three molecular methods for the detection and speciation of five human Plasmodium species

In this study, three molecular assays (real-time multiplex polymerase chain reaction [PCR], merozoite surface antigen gene [MSP]-multiplex PCR, and the PlasmoNex Multiplex PCR Kit) have been developed for diagnosis of Plasmodium species. In total, 52 microscopy-positive and 20 malaria-negative samples were used in this study. We found that real-time multiplex PCR was the most sensitive for detecting P. falciparum and P. knowlesi. The MSP-multiplex PCR assay and the PlasmoNex Multiplex PCR Kit were equally sensitive for diagnosing P. knowlesi infection, whereas the PlasmoNex Multiplex PCR Kit and real-time multiplex PCR showed similar sensitivity for detecting P. vivax. The three molecular assays displayed 100% specificity for detecting malaria samples. We observed no significant differences between MSP-multiplex PCR and the PlasmoNex multiplex PCR kit (McNemar's test: P = 0.1489). However, significant differences were observed comparing real-time multiplex PCR with the PlasmoNex Multiplex PCR Kit (McNemar's test: P = 0.0044) or real-time multiplex PCR with MSP-multiplex PCR (McNemar's test: P = 0.0012).

Stepwise self-assembly of C₆₀ mediated by atomic scale moiré magnifiers

Self-assembly of atoms or molecules on a crystal surface is considered one of the most promising methods to create molecular devices. Here we report a stepwise self-assembly of C₆₀ molecules into islands with unusual shapes and preferred sizes on a gold-indium-covered Si(111) surface. Specifically, 19-mer islands prefer a non-compact boomerang shape, whereas hexagonal 37-mer islands exhibit extraordinarily enhanced stability and abundance. The stepwise self-assembly is mediated by the moiré interference between an island with its underlying lattice, which essentially maps out the adsorption-energy landscape of a C₆₀ on different positions of the surface with a lateral magnification factor and dictates the probability for the subsequent attachment of C₆₀ to an island's periphery. Our discovery suggests a new method for exploiting the moiré interference to dynamically assist the self-assembly of particles and provides an unexplored tactic of engineering atomic scale moiré magnifiers to facilitate the growth of monodispersed mesoscopic structures.

Broken even-odd symmetry in self-selection of distances between nanoclusters due to the presence or absence of topological solitons

Depositing particles randomly on a 1D lattice is expected to result in an equal number of particle pairs separated by even or odd lattice units. Unexpectedly, the even-odd symmetry is broken in the self-selection of distances between indium magic-number clusters on a Si(100)-2×1 reconstructed surface. Cluster pairs separated by even units are less abundant because they are linked by silicon atomic chains carrying topological solitons, which induce local strain and create localized electronic states with higher energy. Our findings reveal a unique particle-particle interaction mediated by the presence or absence of topological solitons on alternate lattices.

Simultaneous detection of methicillin-resistant Staphylococcus aureus, Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa by multiplex PCR

A PCR-based assay that can simultaneously detect and differentiate five different types of nosocomial bacterial pathogens was developed. Six pairs of selected primers targeting femA (132 bp) and mecA (310 bp) of methicillin-resistant Staphylococcus aureus, gltA (722 bp) of Acinetobacter baumannii, phoA (903 bp) of Escherichia coli, mdh (364 bp) of Klebsiella pneumoniae and oprL (504 bp) of Pseudomonas aeruginosa were used in this study. The conditions were optimized for the multiplex PCR to ensure specific amplification of the selected targets. Sensitivity and specificity tests were also carried out using a blind test approach on 50 bacterial cultures and resulted in 100% for both positive and negative predictive values.

Inhibition of 12-lipoxygenase during baicalein-induced human lung nonsmall carcinoma H460 cell apoptosis

Baicalein is known as a 12-lipoxygenase (12-LOX) inhibitor. The 12-LOX is found to be involved in the progression of human cancers and the inhibitor of 12-LOX offers a target for the prevention cancer. We demonstrated the inhibitory effect of baicalein on the gene and protein expression of 12-LOX in H460 human lung nonsmall carcinoma cell line. Treatment of baicalein inhibited the growth of H460 cells in a dose-dependent manner. Following 24h exposure to 50muM baicalein, cell cycle analysis revealed an increase in the cell population in S-phase. During the S-phase arrest, baicalein decreased the protein levels of cdk1 and cyclin B1, which are the regulating proteins of S-phase transition to G2/M-phase, in this study. Furthermore, baicalein induced the most of H460 cell apoptosis after treatment for 48h. H460 cells formed vesicles and apoptotic body, and then floated after treatment with baicalein. Baicalein-induced H460 cell apoptosis was confirmed by DNA condensation and fragmentation. Baicalein-induced apoptosis were also accompanied by decreasing in Bcl-2 and proform of caspase-3 and increasing p53 and Bax protein levels. Pretreatment with a specific caspase-3 inhibitor, Ac-DEVD-CHO, partially reduced baicalein-induced cell death, indicating baicalein induces apoptosis is partially dependent on caspase-3 pathway in H460 cells. These data suggest that baicalein, a 12-LOX inhibitor, inhibits the proliferation of H460 cells via S-phase arrest and induces apoptosis in association with the regulation of molecules in the cell cycle and apoptosis-related proteins.

Successful Treatment of Hepatitis B Virus Infection With Lamivudine After Heart Transplantation

Patients with hepatitis B virus (HBV) infection have a higher morbidity and mortality after heart transplantation (HT). HBV infection is endemic in Taiwan. We studied the effect of lamivudine treatment of HBV infection after HT. From July 1987 to July 2005, 252 patients underwent HT. All recipients and donors underwent routine screening of hepatitis B surface antigen (HBsAg), hepatitis B e antigen, antibody to hepatitis B surface antigen, antibody to hepatitis B core antigen, antibody to hepatitis B e antigen, and an alanine aminotransferase (ALT) level before HT. When ALT was two times greater than the upper limit of normal or serum bilirubin was higher than 3 mg/dL in HBsAg-positive patients, HBV-DNA were checked by a branched DNA assay or polymerase chain reaction. When HVB-DNA was greater than 100,000 copies/mL, lamivudine (100 mg per day) was prescribed indefinitely. There were 14 patients under lamivudine treatment after HT, among whom, none suffered severe adverse reactions from lamivudine. Four patients died: one due to end-stage cirrhosis while awaiting liver transplantation at 14 months after HT. Two died of sudden death at 54 months and 138 months after HT. Another died of diffuse B cell lymphoma at 62 months after HT. All the survivors have normal ALT and undetectable HBV-DNA after lamivudine treatment. But the YMDD mutant was detected in two patients. With successful treatment of HBV infection in HT, it is not necessary to exclude HBV infection patients from HT.

Structure determination of surface magic clusters

The structure of a type of surface magic cluster is determined by a combination of scanning tunneling microscopy, density-functional calculations, and dynamical low energy electron diffraction. The diffraction method is applicable because these clusters created through hierarchical self-organization of Ga deposited onto a Si(111)-7x7 surface have identical size and structure and form an ordered array with exact translational symmetry. The unprecedented detailed structure information provided by the diffraction measurement is consistent with direct microscopic imaging and theoretical calculations.

Molecular epidemiology of hepatitis B viral serotypes and genotypes in taiwan

Subtypes of hepatitis B virus (HBV) have specific geographic distributions and can serve as epidemiological markers. The relationship of HBV serotypes and genotypes in Taiwan and their correlation with the domiciles of origin in 122 patients with chronic HBV infection were investigated. The serotype of HBV was determined by comparing the surface gene encoding amino acids 22-148 of the major surface protein with published sequences. Genotyping of HBV was performed by polymerase chain reaction-restriction fragment length polymorphism. Serotype adw accounted for 70% (85/122) of all HBVs, with the remaining belonging to serotype adr. All adr HBVs were genotype C, regardless of the patient's domicile. Of the 85 adw HBVs, 69 (81%) were genotype B, 10 (12%) were genotype C, 5 (6%) were genotype F and only 1 (1%) was genotype A. In the 31 patients originating from mainland China, the prevalence of adr/genotype C was higher than in the 91 Taiwanese patients (15/31 vs. 22/91; p < 0.05). The distribution of the HBV serotypes and genotypes was not significantly different between 17 patients born in Taiwan (6 adw/genotype B, 2 adw/genotype C, 1 adw/genotype F and 8 adr/genotype C) and 14 patients born in mainland China (5 adw/genotype B, 2 adw/genotype C and 7 adr/genotype C). Our results indicate that in Taiwan, most HBVs of serotype adw are genotype B, and all HBVs of serotype adr are genotype C. Patients with origins in mainland China have a higher proportion of serotype adr/genotype C infection.

Meta-analysis: ribavirin-induced haemolytic anaemia in patients with chronic hepatitis C

AIM

To use meta-analysis to study the risk of anaemiarelated to ribavirin therapy for chronic hepatitisC.

METHODS

The MEDLINE database up to January 2001 was searched for randomized controlled trials of ribavirin (monotherapy or combined with interferon) for chronic hepatitis C. The outcomes evaluated were withdrawal from the study due to anaemia, ribavirin dosage reduction due to a decrease in haemoglobin and haemoglobin levels below 10 g/dL.

RESULTS

Based on 17 studies, the overall risk difference (ribavirin vs. no ribavirin) for anaemia was 0.09 [95% confidence interval (CI), 0.04-0.13]. Two Asian studies reported risk differences of 0.29 and 0.22, greater than the pooled risk difference of 0.07 (95% CI, 0.03-0.12) for 15 non-Asian studies. The risk associated with 1 g or more of ribavirin per day was higher (risk difference, 0.09; 95% CI, 0.04-0.14) than that for 0.8 g of ribavirin per day (risk difference, 0.01; 95% CI, - 0.04-0.06).

CONCLUSIONS

Chronic hepatitis C patients treated with 1 g or more of ribavirin per day were at a higher risk of developing anaemia. Reported risks were higher among Asian studies, which may be due to differences in study entrance criteria, dosage titration strategy or ethnic vulnerability.

Molecular epidemiology of hepatitis B viral serotypes and genotypes in taiwan

Subtypes of hepatitis B virus (HBV) have specific geographic distributions and can serve as epidemiological markers. The relationship of HBV serotypes and genotypes in Taiwan and their correlation with the domiciles of origin in 122 patients with chronic HBV infection were investigated. The serotype of HBV was determined by comparing the surface gene encoding amino acids 22-148 of the major surface protein with published sequences. Genotyping of HBV was performed by polymerase chain reaction-restriction fragment length polymorphism. Serotype adw accounted for 70% (85/122) of all HBVs, with the remaining belonging to serotype adr. All adr HBVs were genotype C, regardless of the patient's domicile. Of the 85 adw HBVs, 69 (81%) were genotype B, 10 (12%) were genotype C, 5 (6%) were genotype F and only 1 (1%) was genotype A. In the 31 patients originating from mainland China, the prevalence of adr/genotype C was higher than in the 91 Taiwanese patients (15/31 vs. 22/91; p < 0.05). The distribution of the HBV serotypes and genotypes was not significantly different between 17 patients born in Taiwan (6 adw/genotype B, 2 adw/genotype C, 1 adw/genotype F and 8 adr/genotype C) and 14 patients born in mainland China (5 adw/genotype B, 2 adw/genotype C and 7 adr/genotype C). Our results indicate that in Taiwan, most HBVs of serotype adw are genotype B, and all HBVs of serotype adr are genotype C. Patients with origins in mainland China have a higher proportion of serotype adr/genotype C infection.

Probable reinfection with hepatitis C virus in a chronic hepatitis C patient with a sustained response to combination therapy

Superinfection with hepatitis C virus (HCV) in already chronically infected subjects has been documented. Whether a complete response to antiviral therapy is associated with protective immunity against reinfection with HCV remains unknown. We describe a patient who had a sustained biochemical and virologic response with loss of intrahepatic HCV RNA after a course of combination therapy using interferon plus ribavirin. Histopathologically, the chronic hepatitis was in remission on follow-up biopsy 6 months post-therapy. Unfortunately, 34 weeks post-therapy, a flare of hepatitis with reappearance of hepatitis C viremia was noted 2 months after he received injections from a non-licensed medical provider. Analysis of the core gene sequences showed a 95% homology between the HCV strains isolated before antiviral treatment and during the hepatitis flare. The data indicated that the hepatitis flare after a period of sustained response to combination therapy in this patient could have been caused by reinfection with homotypic HCV. Our observation indicates the lack of protective immunity against reinfection with HCV in patients with chronic hepatitis C, even after successful clearance of the virus. Therefore, reinforcing the education of these subjects to avoid HCV reinfection should be stressed.

Functional measurement of hepatitis C virus core-specific CD8(+) T-cell responses in the livers or peripheral blood of patients by using autologous peripheral blood mononuclear cells as targets or stimulators

As is widely recognized, CD8(+) cytotoxic T lymphocytes (CTLs) play a crucial role in hepatitis C virus (HCV) infection, both in pathogenesis of liver injury and in clearing the virus. CTL studies with HCV-infected patients have been difficult because of the relatively low frequency of CTL precursors in the peripheral blood and because the targeted epitopes vary depending on the human leukocyte antigen (HLA) types of the individuals. This study attempts to overcome these problems by assessing the feasibility of using autologous peripheral blood mononuclear cells (PBMCs) expressing viral antigens as stimulators or targets in order to monitor the CTL responses. Primary PBMCs were transduced using a retroviral vector pseudotyped with a vesicular stomatitis virus G glycoprotein expressing the HCV core gene. Additionally, the vector-transduced PBMCs were used as targets of CTL assays to measure the HCV core-specific CTL activities from the liver-infiltrating lymphocytes of six different HLA-type patients with chronic HCV infection. The core-expressing PBMCs also served as stimulators, allowing us to measure core-specific CD8(+) T-cell responses by intracellular gamma interferon staining of the peripheral blood of hepatitis C patients who had received treatment with alpha interferon plus ribavirin. This approach provides an efficient means of measuring antigen-specific CTL responses without HLA constraints.

Ribavirin enhances interferon-gamma levels in patients with chronic hepatitis C treated with interferon-alpha

Some patients with chronic hepatitis C respond to interferon (IFN)-alpha treatment, and the efficiency can be improved by combining it with ribavirin. The mechanism of this improvement is unknown. To investigate the effects of these two regimens on the immune responses in 51 patients with chronic hepatitis C, we examined the hepatitis C core antigen-specific proliferative response and cytokine production profiles, natural killer (NK) cell cytotoxicity and cytotoxic T cell function during treatment. The results are as follows: (1) both viral clearance and biochemical normalization occurred more frequently in patients receiving combination therapy; (2) the function of NK cells increased after treatment in the responders of both groups (p < 0.05); (3) the level of IFN-gamma produced by hepatitis C core antigen-stimulated peripheral blood mononuclear cells was higher in patients receiving combination therapy, especially in responders; (4) the core antigen-specific proliferative response decreased after treatment, and (5) in addition, the core-specific cytotoxic T cell activities of five responder patients also increased significantly after therapy. In conclusion, enhancement of immune responses, especially those related to type-1 T helper cell activity, may contribute to better efficacy in combining ribavirin with IFN-alpha for treatment of chronic hepatitis C.

Acute exacerbations of chronic hepatitis B are rarely associated with superinfection of hepatitis B virus

There are 7 genotypes of hepatitis B virus (HBV). Whether superinfection of HBV carriers with different HBV genotypes occurs remains unknown. We therefore determined the HBV genotype and association between superinfection and acute exacerbation of disease in a cohort of 244 patients with chronic HBV infection who had elevated serum aminotransferase levels for at least 1 year. Within this group, 103 patients experienced acute exacerbation with an annual incidence of 13%, and 20 of the 103 patients had IgM antibody to hepatitis B core antigen (IgM anti-HBc). These 20 patients had a higher prevalence of genotype C infection (65%) than the remaining 83 anti-core IgM-negative patients (40%) who also had acute exacerbations (P <.05). Detailed analysis of HBV genotypes and sequences of the variable pre-S gene were determined in serial samples from 20 patients with IgM anti-HBc-positive acute exacerbations (group A), 20 patients with IgM anti-HBc-negative acute exacerbations (group B), and 20 patients without exacerbations (group C). Two (10%) of the group A patients had virologic evidence of HBV superinfection during acute exacerbation, one superinfected with heterotypic virus and the other with homotypic virus. The newly introduced virus disappeared after the exacerbation and the original virus resumed thereafter. The calculated prevalence of HBV superinfection in the hepatitis B carriers and those with acute exacerbations was 0.8% (2 of 244) and 1.9% (2 of 103), respectively. In conclusion, superinfection of HBV on hepatitis B carriers indeed occurs and may cause acute exacerbations, albeit at a low frequency even in hyperendemic areas of HBV infection.

Dietary heterocyclic amines and microsatellite instability in colon adenocarcinomas

Microsatellite instability (MSI) is now an accepted and important pathway in colon tumorigenesis, occurring in 10-15% of sporadic colon cancers and almost all hereditary nonpolyposis colon cancers. Little is known about possible environmental influences on MSI status in colon cancer. We conducted an epidemiological study of 276 colon cancer cases in Los Angeles County that was designed to determine the population prevalence of MSI(+) colon cancer and to identify environmental influences in the development of MSI(+) tumors. Our results support the cigarette smoking and MSI(+) association recently reported [Slattery,M.L., Curtin,K., Anderson,K. et al. (2000) J. Natl Cancer Inst., 92, 1831-1836]. Risk of MSI(+) colon cancers increased with increasing dose (number of cigarettes per day) and increasing duration (years of smoking) of smoking. Compared with never-smokers, those who smoked 1-20 pack-years and >20 pack-years showed odds ratios of 1.39 and 1.64, respectively (P for trend = 0.03). In addition, our results show, for the first time, that after adjustment for cigarette smoking habits and red meat intake, patients with MSI(+) colon cancers had significantly higher dietary exposure to heterocyclic aromatic amines (HAA) as determined by two surrogates of high dietary HAA exposure: preference for well-done red meat and high frequencies of certain cooking practices (frying, barbecuing, broiling and using meat drippings). The risk of MSI(+) colon cancer was increased 3-fold (smoking/red meat intake adjusted OR = 3.03, 95% CI = 1.06, 8.63) among patients who preferred to eat red meat that was very well-done and was increased >2-fold (smoking/red meat adjusted OR = 2.33, 95% CI = 1.00, 5.25) among those who frequently fried/barbecued/broiled their meats or used meat drippings. The risk of MSI(+) colon cancer associated with cigarette smoking remained statistically significant after adjustment for high dietary HAA exposure. The significant association between cigarette smoking and dietary HAA with a specific subset of colon cancers may explain, at least in part, inconsistencies in results linking these two exposures to colon cancers. These results provide a potential mechanism of linking HAA exposure and cigarette smoking to a specific subset of colon cancers.

Prolonged interferon treatment after combination interferon and ribavirin therapy in patients with chronic hepatitis C: a clinical trial of interferon relapsers and non-responders

BACKGROUND AND PURPOSE

For the retreatment of chronic hepatitis C patients relapsing after, or non-responsive to, previous interferon therapy, the efficacy of combination therapy with interferon alfa plus ribavirin is superior to interferon alone. The aim of this study was to determine whether prolonged interferon alfa treatment after 24-week combination therapy can further increase the efficacy of combination therapy.

METHODS

Nineteen interferon relapsers and 17 interferon non-responders were randomly assigned to receive either interferon alfa 5 million units (MU) thrice weekly plus oral ribavirin 1,200 mg daily for 24 weeks (regimen A) or interferon alfa 5 MU thrice weekly plus oral ribavirin 1,200 mg daily for 24 weeks followed by interferon alfa 3 MU thrice weekly for another 24 weeks (regimen B). Efficacy was assessed by normalization of serum aminotransferase concentrations and disappearance of serum hepatitis C virus (HCV) RNA at the end of treatment and at 24 weeks after stopping treatment.

RESULTS

Overall, 67% of relapsers receiving regimen A and 80% of those receiving regimen B had sustained virologic responses 24 weeks after stopping treatment. In contrast, 45% of non-responders receiving regimen A and 63% of those receiving regimen B had sustained responses. The sustained response was more common in relapsers with non-1b HCV genotypes. The sustained response rate to combination therapy was 50% or more in patients with genotype 1b infection.

CONCLUSIONS

Prolonged interferon treatment after combination therapy has a comparable efficacy to combination therapy alone for the retreatment of chronic hepatitis C patients relapsing after, or non-responsive to, previous interferon therapy.

Lamivudine treatment for hepatitis B reactivation in HBsAg carriers after organ transplantation: a 4-year experience

BACKGROUND

Reactivation of hepatitis B after organ transplantation in hepatitis B surface antigen (HBsAg) carriers may be fatal. In this study, we reported our experience of lamivudine treatment in HBsAg carriers who had post-transplant reactivation of hepatitis B.

METHODS

The patients were 15 men and one woman. Nine received kidney transplants, six received heart transplants, and one received a lung transplant. They developed a reactivation of hepatitis B 1-101 months (median, 14 months) after transplantation. They received lamivudine 100 mg daily on a compassionate-use basis, and had regular follow ups. The median pretreatment total serum bilirubin level was 3.0 mg/dL, and the alanine aminotransferase level was 357 U/L. Four of the 16 patients were positive for HBeAg. The serum hepatitis B virus (HBV) DNA levels were > 3000 pg/mL in 13 (81%) patients. Three were coinfected with hepatitis C virus.

RESULTS

The overall survival rate was 75%. All four fatal cases had a pretreatment total serum bilirubin level of > or = 3 mg/dL. Serum HBV-DNA soon became undetectable in 12 survivors. Of the 12 survivors, after a median treatment period of 101 weeks, a lamivudine-resistant strain with variation in the YMDD motif of the HBV polymerase gene developed in three (25%). None had significant adverse reactions to lamivudine treatment.

CONCLUSIONS

These results indicated that lamivudine is effective in the treatment of post-transplant hepatitis B reactivation, including patients with dual chronic hepatitis B and C. Early recognition of HBV reactivation and prompt lamivudine treatment are important to prevent mortality.