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.

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.

Human immunodeficiency virus (HIV)-infected individuals have greater susceptibility to infections by a myriad of microorganisms which can cause significant morbidity and mortality compared to immunocompetent individuals. Of these microbial infections, intestinal parasitic infections (IPIs) however are receiving less attention than bacterial and viral infections, hence, the lack of information of parasitic infections in HIV individuals. Prevalence of IPIs among 346 HIV-infected individuals in Malaysia was determined in this study. The overall prevalence of intestinal parasitic infections (IPIs) was 37.9% (131 of 346) with protozoa infections (18.8%) being more common compared to helminth infections (7.5%). Observed protozoa include Entamoeba histolytica/dispar (16.8%), Cryptosporidium parvum (12.4%), Isospora belli (10.1%), Cyclospora cayetanensis (4.9%) and Giardia duodenalis (intestinalis) (3.2%) whilst helminthes which were detected comprised of Ascaris lumbricoides (13.9%), Trichuris trichiura (6.4%) and hookworms (0.6%). Among those 131 infected, 50.4% had multiple infections and 48.9% had single parasitic infection. The CD4 counts were significantly lower (i.e., 200 cells/mm3) in patients harbouring IPIs. Of those individuals infected with intestinal parasites, 49% were intravenous drug users and 58% were not on any antiretroviral therapy. Most were asymptomatic and had concurrent opportunistic infections (OIs) mainly with Mycobacterium tuberculosis infection. These results confirmed that IPIs are ubiquitous among HIV-infected individuals, especially those presenting with low CD4 T cells counts, and provide useful insights into the epidemiology of these infections among HIVinfected patients in Malaysia. It is therefore recommended, that diagnosis of these intestinal parasitic pathogens should be conducted on a routine basis for better management of gastrointestinal illnesses among HIV individuals.

An analytical cross-sectional study was conducted in a public university in Kuala Lumpur among a random sample of 2665 undergraduates. The objective was to study the prevalence of breakfast skipping and its associated factors. Data collection was conducted via a self-administered pre-tested questionnaire. There were 43.5% male respondents, with Malays being the majority (58.3%). The prevalence of breakfast skipping was 29.2 (95% CI: 27.3 – 30.3) %. The factors significantly associated with breakfast skipping (p<0.05) were age, race, accommodation, faculty and skipping dinner. As the respondents’ age increased, their risk of breakfast skipping was lower (OR: 0.95; 0.89 – 0.99). Malays (OR: 1.94; 1.48 – 2.54), Indians (OR: 1.70; 1.08 – 2.66), and students from the Sabah and Sarawak indigenous communities (OR: 2.13; 1.37 – 3.33) were more likely to skip breakfast compared to their Chinese counterparts. Respondents who stayed in their own houses were also less likely to skip breakfast compared to those staying in hostel with meals catered (OR: 2.32; 1.39 – 3.84), hostel with cafeteria (OR: 2.92; 1.74 – 4.91) or in rented houses (OR: 2.08; 1.25 – 3.46). Respondents majoring in Arts & Economics had 1.40 (1.07 – 1.82) times risk of breakfast skipping compared to those majoring in Life Sciences. Those who skipped dinner too had twice the odds (1.47 – 2.77) of breakfast skipping. In conclusion the prevalence of breakfast skipping among the undergraduates of this university was moderately high. Health awareness campaigns or introduction of healthy eating guidelines should be initiated for the undergraduates as well as food caterers in campus. The policy and pricing of catered food in campus should also be reviewed.