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.

Introduction: Occipitocervical fusion is performed to address craniocervical and atlantoaxial instability. A screw of at least 8mm is needed for biomechanical stability. Occipital thickness of Malay ethnicity is unknown, and this study presents the optimal screw placement positions for occiput screw in this population. This was a retrospective crosssectional study of 100 Malays who underwent computed tomography (CT) scan for brain assessment. To measure the occipital bone thickness of Malay ethnicity at the area of common screw placement for occipitocervical fusion. The subject’s data was obtained from the institutional database with consent from the administrations and the patients. None of the patients had any head and neck pathology. Materials and methods: The subject’s data was obtained from the institutional database with consent from the administrations and the patients. None of the patients had any head and neck pathology. Computed tomography (CT) of 100 Malay patients who underwent head and neck CT were analysed, based on our inclusion and exclusion criteria. Measurements were taken using a specialised viewer software where 55 points were measured, followed a grid with 10mm distance using external occipital protuberance (EOP) as the reference point. Results: There were 57 males and 43 females of Malay ethnicity with a mean age of 36.7 years analysed in this study. The EOP was the thickest bone of the occiput which measured 16.15mm. There was an area of at least 8mm thickness up to 20mm on either side of the EOP, and at level 10mm inferior to the EOP. There is thickness of at least 8mm, up to 30mm inferior to the EOP at the midline. The males have significantly thicker bone especially along the midline compared to females. Conclusion: Screws of at least 8mm can be safely inserted in the Malay population at 20mm on either side of the EOP at the level 10mm inferior to the EOP and up to 30mm inferior to the EOP at the midline.

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.

Members of the genus Kocuria are commonly found in the environment and they are also commensals of the mammalian skin and oropharynx mucosa. Human infections, although rare, are increasingly being reported recently suggesting that this genus has mostly been overlooked or misidentified. Its transmission route however, is still not known. We report here the isolation and identification of a Kocuria marina isolate from the lung of a wild urban rat (Rattus rattus diardii) caught at a wet market. The isolate was susceptible to most of the commonly used antibiotics. The finding suggests a possibility that rats could be a vector for K. marina.