COVID-19 Sample Pooling: From RNA Extraction to Quantitative Real-time RT-PCR

The COVID-19 pandemic requires mass screening to identify those infected for isolation and quarantine. Individually screening large populations for the novel pathogen, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is costly and requires a lot of resources. Sample pooling methods improve the efficiency of mass screening and consume less reagents by increasing the capacity of testing and reducing the number of experiments performed, and are therefore especially suitable for under-developed countries with limited resources. Here, we propose a simple, reliable pooling strategy for COVID-19 testing using clinical nasopharyngeal (NP) and/or oropharyngeal (OP) swabs. The strategy includes the pooling of 10 NP/OP swabs for extraction and subsequent testing via quantitative real-time reverse transcription polymerase chain reaction (RT-qPCR), and may also be applied to the screening of other pathogens.

Detection of Zika virus RNA in Aedes aegypti and Aedes albopictus larvae in Klang Valley, Peninsular Malaysia

We report the presence of Zika virus RNA in naturally infected field captured Aedes aegypti and Ae. albopictus mosquito larvae in Malaysia from May 2016 to April 2017. Zika virus RNA was detected (n = 30) in the larvae of both Aedes mosquito species. Phylogenetic analysis of the NS5 partial sequence of all positive samples shows that the circulating Zika virus in the field collected larvae are of the Asian lineage.

Parasites in soil samples from Signy island, Antarctica

Studies on parasite populations in Antarctic soils are scarce and thus little is known about the threat of these parasites towards either the natural fauna or human visitors. However, human presence in Antarctica, mainly through research and tourism, keeps increasing over time, potentially exposing visitors to zoonotic infections from Antarctic wildlife and environment. Most available literature to date has focused on faecal samples from Antarctic vertebrates. Therefore, this study addressed the possible presence of parasites in Antarctic soil that may be infectious to humans. Soil samples were obtained from five locations on Signy Island (South Orkney Islands, maritime Antarctic), namely North Point and Gourlay Peninsula (penguin rookeries), Pumphouse (relic coal-powered pump house), Jane Col (barren high altitude fellfield) and Berntsen Point (low altitude vegetated fellfield close to current research station). Approximately 10% of the soil samples (14/135) from 3 out of the 5 study sites had parasites which included Diphyllobotridae spp. eggs, Cryptosporidium sp., an apicomplexan protozoa (gregarine), Toxoplasma gondii, helminths (a cestode, Tetrabothrius sp., and a nematode larva) and mites. The presence of parasites in the 3 sites are most likely due to the presence of animal and human activities as two of these sites are penguin rookeries (North Point and Gourlay Peninsula) while the third site (Pumphouse Lake) has human activity. While some of the parasite species found in the soil samples appear to be distinctive, there were also parasites such as Cryptosporidium and Toxoplasma gondii that have a global distribution and are potentially pathogenic.

Detection of dengue viruses and Wolbachia in Aedes aegypti and Aedes albopictus larvae from four urban localities in Kuala Lumpur, Malaysia

Dengue fever (DF) is currently one of the most important mosquito-borne diseases that affects humans. Dengue fever (DF) and dengue hemorrhagic fever (DHF) are caused by four serotypes of dengue viruses (DENV-1 to DENV-4). The main vector transmitting dengue is Aedes aegypti while Aedes albopictus acts as a secondary vector. As treatment is unavailable and the first dengue vaccine approved in Mexico, Dengvaxia® has yet to be accepted worldwide, prevention of the disease relies heavily on surveillance and control of mosquito vectors. A transgene driver, Wolbachia was found to limit the transmission of dengue virus in Aedes mosquitoes. Wolbachia alone was able to inhibit viral replication, dissemination and transmission in A. aeygpti mosquitoes in experimental studies. In A. albopictus, Wolbachia did not affect the replication of dengue virus but was able to reduce the viral infection of mosquito salivary glands and limit transmission. Studies on Wolbachia have all been carried out in adult Aedes mosquitoes, hence this study was conducted to determine the presence of dengue virus serotypes and Wolbachia in A. aegypti and A. albopictus larvae collected from ovitraps in four localities in Kuala Lumpur viz. Happy Gardens, IMU Bukit Jalil, Ampang and Taman Yarl. Another objective of this study was to determine the association between dengue virus serotypes and the presence of Wolbachia in A. aegypti and A. albopictus larvae. A total of 300 mosquito larvae was collected; 99 (Happy Gardens), 85 (Bukit Jalil), 73 (Ampang) and 43 (Taman Yarl). Out of 300 larvae collected, 284 were identified as A. albopictus and 16 others were identified as A. aegypti. Of the 284 A. albopictus larvae collected, 211 (74.3%) and 73 (25.7%) were found to be negative and positive for dengue virus respectively. The dengue serotypes detected were 2 DENV-2 (2.7%), 58 DENV-3 (79.5%) and 13 DENV-4 (17.8%). DENV-1 was not detected in any of the A. albopictus larvae. For A. aegypti, out of 16 A. aegypti larvae collected, 12 (75%) were found to be negative and 4 (25%) were positive for DENV-2. For the detection of Wolbachia in A. albopictus, 71 out of 284 (25%) and 213 (75%) larvae were found to be positive and negative for Wolbachia respectively. For A. aegypti, 4 (25%) and 12 (75%) out of 16 larvae were positive and negative for Wolbachia respectively. This is the first report of Wolbachia in A. albopictus and A. aegypti larvae in Malaysia. A chisquare test analysis to determine the association between dengue virus and Wolbachia in A. albopictus and A. aegypti larvae collected from the four localities in Kuala Lumpur showed that there was no association (χ² = 3.080; df = 1; P > 0.05).

Isolation and identification of mites associated with raw and commercial farm edible bird nests

The global demand for edible bird nests (EBNs) is high, especially from Hong Kong and Peoples Republic of China. Recently, this industry was greatly affected when China banned the import of all the EBNs from Malaysia (except for canned version) due to detection of high levels of nitrites. Several cases of anaphylaxis following ingestion of EBNs were reported. The source(s) of these allergens remain unknown. Mites have been reported to trigger allergic responses. Hence, this study was designed to quantify, isolate and identify the mites that are associated with EBNs. The raw EBNs were purchased from swiftlet farms in five locations in Peninsular Malaysia while the commercial nests were purchased from five different Chinese traditional medicinal shops. The average mite density of all the raw nests was 285 ± 603 mites per gram of EBN while the commercial nests had a much lower mean value of 21 ± 32 mites per gram of EBN (p = 0.082). Among the raw EBNs, the nests from Kajang had the highest average mite density (946 ± 1443 mites/g of EBN) whereas the nests from Kuala Sanglang had the lowest (54 ± 34 mites/g of EBN). Among the commercial EBNs, the nests from Company D had the highest average mite density (76 ± 18 mites/g of EBN) whereas the nests from Company A were free of mites. Overall, the average densities of mites in the raw nests obtained from southern regions of Malaysia (Selangor and Johor) were higher than those nests obtained from the northern regions (Kedah and Kelantan). Thirty types of mites were isolated from both the raw and commercial nests. Among these, some are probably feather mites (Eustathia cultrifer, Pteroherpus garrulacis, Pterodectes amaurochalinus, Laminalloptes sp., Berlesella alata and Neochauliacia sp.), house dust and storage mites (Suidasia sp., Austroglycyphagus sp., and Aleuroglyphus ovatus), mesostigmatid mites (Dermanyssus sp.), prostigmatid mites (Cheyletus sp., tarsonemid and cunaxid mites), astigmatid mites (Collocalidectes sp., Streetacarus sp. and Hemisarcoptes sp.) and oribatid mites. This study provides baseline information on the density and type of mites that are probably associated with EBNs. This study also heightens the importance of mites as a possible source of EBN-associated anaphylaxis.

Field evaluation of a rapid diagnostic test to detect antibodies in human toxocariasis

Human toxocariasis which is caused mainly by the larvae of Toxocara canis and Toxocara cati, is a worldwide zoonotic disease that can be a potentially serious human infection. The enzyme-linked immunosorbent assay (ELISA) using T. canis excretory-secretory (TES) antigens harvested from T. canis larvae is currently the serological test for confirming toxocariasis. An alternative to producing large amounts of Toxocara TES and improved diagnosis for toxocariasis is through the development of highly specific recombinant antigens such as the T. canis second stage larva excretory-secretory 30 kDa protein (recTES-30). The aim of this study was to evaluate the sensitivity and specificity of a rapid diagnostic kit (RDT, named as iToxocara kit) in comparison to recTES-30 ELISA in Serendah Orang Asli village in Selangor, Malaysia. A total of 133 subjects were included in the study. The overall prevalence rates by ELISA and RDT were 29.3% and 33.1%, respectively, with more positive cases detected in males than females. However, no association was found between toxocariasis and gender or age. The percentage sensitivity, specificity, positive predictive value and negative predictive value of RDT were 85.7%, 90.1%, 80% and 93.2%, respectively. The prevalence for toxocariasis in this population using both ELISA and RDT was 27.1% (36/133) and the K-concordance test suggested good agreement of the two tests with a Cohen's kappa of 0.722, P<0.01. In addition, the followed-up Spearman rank correlation showed a moderately high correlation at R=0.704 and P<0.01. In conclusion, the RDT kit was faster and easier to use than an ELISA and is useful for the laboratory diagnosis of hospitalized cases of toxocariasis.