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.

The present study aimed at exploring whether sunlight exposure might account for the relative difference in COVID-19-related morbidity and mortality between tropical and non-tropical countries. A retrospective observational study was designed and data from the World Health Organization weekly COVID-19 epidemiological update was compiled. We examined the total number of confirmed COVID-19 cases per 100 000 population, as well as the total number of COVID-19-related mortalities per 100 000 population. Solar variables data were obtained from the Global Solar Atlas website (https://globalsolaratlas.info/). These data were analyzed to determine the association of sunlight exposure to COVID-19-related morbidity and mortality in tropical and non-tropical countries. Results revealed a statistically significant decrease in the number of confirmed COVID-19 cases per 100 000 population (P<0.001), as well as the number of COVID-19-related mortalities per 100 000 population (P<0.001) between tropical and non-tropical countries. Analyses of sunlight exposure data found that specific photovoltaic power output, global horizontal irradiation, diffuse horizontal irradiation and global tilted irradiation at optimum angle were significantly inversely correlated to COVID-19-related morbidity and mortality. This suggests that stronger sunlight exposure potentially leads to lower COVID-19-related morbidity and mortality. Findings from this study suggest that the relatively low COVID-19-related morbidity and mortality in tropical countries were possibly due to better sunlight exposure that translates into adequate vitamin D status.

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.

The recommended test guidelines for Zika virus (ZIKV) include using both molecular and serological tools. While the molecular tools are useful for detecting acute infection, the serological tools are useful for the detection of previous infections. Nevertheless, detection of ZIKV-specific antibodies remains a challenge due to the high cross-reactivity between ZIKV and other flaviviruses such as dengue virus (DENV) and Japanese encephalitis virus (JEV). The objective of this study is to evaluate the commercially available enzyme-linked immunosorbent assay (ELISA) for the detection of ZIKV IgG. In this study, we evaluated 6 commercially available anti-ZIKV IgG ELISA kits. Pre-characterized serum panels consisting of 70 sera were selected for the evaluation. The diagnostic accuracy of each ELISA kits was determined and compared to the gold standard, Foci Reduction Neutralization Test (FRNT). The present study established that the performance of the NS1-based anti-ZIKV IgG ELISA kit was superior to that which uses of the E protein as antigen. Overall, commercial ZIKV IgG ELISA showed varying test performances, with some achieving moderate to high test sensitivities and specificities. When compared against the FRNT, the test sensitivities ranged from 7.1% to 78.6%, whereas, the test specificities ranged from 40.0% to 100%. Limitation to the study includes the cross reactivity between flavivirus and specificity of the kit in addressing the cross reactivity.

Three genomic regions, VP4 capsid, VP1 capsid and 3D RNA polymerase of human enterovirus 71 (EV-71) and coxsackievirus A16 (CV-A16) were sequenced to understand the evolution of these viruses in Malaysia. A total of 42 EV-71 and 36 CV-A16 isolates from 1997-2008 were sequenced. Despite the presence of many EV-71 subgenotypes worldwide, only subgenotypes B3, B4, B5, C1 and C2 were present in Malaysia. Importation of other subgenotypes such as C3, C4/D and C5 from other countries was infrequent. For CV-A16, the earlier subgenotype B1 was replaced by subgenotypes B2a and the recent B2c. Subgenotype B2a was present throughout the study while B2c only emerged in 2005. No genetic signatures could be attributed to viral virulence suggesting that host factors have a major role in determining the outcome of infection. Only three EV-71 B3 isolates showed non-consistent phylogeny in the 3D RNA polymerase region which indicated occurrence of recombination in EV-71. High genetic diversity was observed in the Malaysian EV-71 but Malaysian CV-A16 showed low genetic diversity in the three genomic regions sequenced. EV-71 showed strong purifying selection, but that occurred to a lesser extent in CV-A16.