Mosquito-borne arboviral diseases such as dengue and chikungunya have continuously been a major global public health concern. Introducing the intracellular bacterial endosymbiont Wolbachia into mosquito populations has been proven to reduce dengue virus transmission, and its broader efficacy against other arboviruses has also been investigated. Several Wolbachia strains have been successfully propagated in insect cell lines, highlighting the utility of in vitro systems for studying microbial-host interactions under controlled conditions. This study investigated the initial establishment and replication kinetics of a flea-derived Wolbachia strain (wCfe), which was originally isolated from Malaysian Ctenocephalides felis and maintained in the Ixodes scapularis tick-derived cell line (IDE8), and then transferred into an Aedes albopictus-derived cell line (C6/36). The wCfe strain was semi-purified from IDE8 cultures and inoculated into C6/36 cells in 24-well plates. Replication dynamics were monitored by quantitative real-time PCR targeting the Wolbachia pipientis 16S rRNA gene. Following infection, a lag phase was observed at day 0 to 5 days post-infection (d.p.i.), followed by exponential growth from 6 d.p.i. after which Wolbachia levels remained relatively stable until the end of the observation period at 12 d.p.i. Overall, a 25.30-fold increase in Wolbachia density was detected relative to 0 d.p.i. Across replicates, the estimated generation time of wCfe in C6/36 cells ranged from 1.7 to 2.5 days. These results demonstrate successful initial establishment and replication of the flea-derived Wolbachia strain in the Aedes mosquito cell line. However, longer-term in vivo studies will be necessary to determine the persistence of wCfe infection in C6/36 cells and within the mosquito host.

Reverse transcription-polymerase chain reaction (RT-PCR) cycle threshold (Ct) value in detecting the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection is inversely proportionate to the virus load in the patient’s specimen. These values could be beneficial in the epidemic trajectory at the population level. The SARS-CoV-2 B.1.617.2 (Delta) variant which emerged in late 2020, caused an unprecedented exponential increase in SARS-CoV-2 infection cases worldwide. In Malaysia, the surge in coronavirus disease 2019 (COVID-19) cases and the inclining positivity rate contributed to the epidemic waves in late May 2021. Sudden surge in cases was suggested to be associated with increased transmission caused by the emergence of the B.1.617.2 variant. In the present study, Ct value distribution of the positive COVID-19 samples from 2020 and 2021 was tabulated against SARS-CoV-2 genomic variants determined from genomic sequencing. A significant decreasing pattern of median Ct values from overall 2020 and 2021 samples was evident (p<0.01). However, notable variability was observed in the Ct values between 2020 and 2021, which samples showing lower median Ct values in 2021. The percentages of SARS-CoV-2 genomic variants B.1.36 and B.1.524 were 31.6% and 68.4%, respectively, for samples obtained in October and December 2020. Whereas samples obtained in June and July 2021 were 100% of the B.1.617.2 variant. The population neutralizing antibody against SARS-CoV-2 during the initial peak of B.1.617.2 was low, however, increased during the B.1.617.2 wave. A decreasing trend in the Ct value distribution from samples tested in our laboratory correlated well with the increasing weekly COVID-19 cases reported by the Malaysia national data, which was subsequently attributed to the emergence of B.1.617.2 variant. This study proposes that analyzing Ct value distribution in screened SARS-CoV-2 samples could reveal population-level transmission dynamics and emerging variants. Coupled with genomic sequencing, it supports early control strategies against new SARS-CoV-2 strains.

Various methods have been developed for rapid and high throughput full genome sequencing of SARS-CoV-2. Here, we described a protocol for targeted multiplex full genome sequencing of SARS-CoV-2 genomic RNA directly extracted from human nasopharyngeal swabs using the Ion Personal Genome Machine (PGM). This protocol involves concomitant amplification of 237 gene fragments encompassing the SARS-CoV-2 genome to increase the abundance and yield of viral specific sequencing reads. Five complete and one near-complete genome sequences of SARS-CoV-2 were generated with a single Ion PGM sequencing run. The sequence coverage analysis revealed two amplicons (positions 13 751-13 965 and 23 941-24 106), which consistently gave low sequencing read coverage in all isolates except 4Apr20-64Hu. We analyzed the potential primer binding sites within these low covered regions and noted that the 4Apr20-64-Hu possess C at positions 13 730 and 23 929, whereas the other isolates possess T at these positions. The genome nucleotide variations observed suggest that the naturally occurring variations present in the actively circulating SARS-CoV-2 strains affected the performance of the target enrichment panel of the Ion AmpliSeq™ SARS CoV 2 Research Panel. The possible impact of other genome nucleotide variations warrants further investigation, and an improved version of the Ion AmpliSeq™ SARS CoV 2 Research Panel, hence, should be considered.