Covid-19 variants: Impact on transmissibility and virulence.

The genetic evolution of SARS-CoV-2 began in February 2020, with G614 spike protein strains superseding D614 strains globally. Since then with each subsequent mutations, the SARS-CoV-2 variants of concern, namely Alpha, Beta, Gamma, Delta and Omicron, superseded the previous one to become the dominant strain during the pandemic. By the end of November 2022, the Omicron variant and its descendent lineages account for 99.9% of sequences reported globally. All five VOCs have mutations located in the RBD of the spike protein, resulting in increased affinity of the spike protein to the ACE2 receptors resulting in enhanced viral attachment and its subsequent entry into the host cells. In vitro studies showed the mutations in spike protein help increase the viral fitness, enhancing both transmissibility and replication. In general, Alpha, Beta, Gamma, and Delta variants, were reported with higher transmissibility of 43-90%, around 50%, 170-240%, or 130-170% than their co-circulating VOCs, respectively. The Omicron however was found to be 2.38 times and 3.20 times more transmissible than Delta among the fully-vaccinated and boostervaccinated households. Even the SARS-Cov-2 Omicron subvariants appear to be inherently more transmissible than the ones before. With the broader distribution, enhanced evasion, and improved transmissibility, SARS-CoV-2 variants infection cause severe diseases due to immune escape from host immunity and faster replication. Reports have shown that each subsequent VOC, except Omicron, cause increased disease severity compared with those infected with other circulating variants. The Omicron variant infection however, appears to be largely associated with a lower risk of hospitalisation, ICU admission, mechanical ventilation, and even a shorter length of hospital stay. It has been shown that the relatively much slower replication of the Omicron variants in the lung, resulted in a less severe disease.

Properties of Coronavirus and SARS-CoV-2.

were identified beginning with the discovery of SARS-CoV in 2002. With the recent detection of SARS-CoV-2, there are now seven human coronaviruses. Those that cause mild diseases are the 229E, OC43, NL63 and HKU1, and the pathogenic species are SARS-CoV, MERS-CoV and SARS-CoV-2 Coronaviruses (order Nidovirales, family Coronaviridae, and subfamily Orthocoronavirinae) are spherical (125nm diameter), and enveloped with club-shaped spikes on the surface giving the appearance of a solar corona. Within the helically symmetrical nucleocapsid is the large positive sense, single stranded RNA. Of the four coronavirus genera (α,ß,γ,δ), human coronaviruses (HCoVs) are classified under α-CoV (HCoV-229E and NL63) and ß-CoV (MERS-CoV, SARS-CoV, HCoVOC43 and HCoV-HKU1). SARS-CoV-2 is a ß-CoV and shows fairly close relatedness with two bat-derived CoV-like coronaviruses, bat-SL-CoVZC45 and bat-SL-CoVZXC21. Even so, its genome is similar to that of the typical CoVs. SARS-CoV and MERS-CoV originated in bats, and it appears to be so for SARS-CoV-2 as well. The possibility of an intermediate host facilitating the emergence of the virus in humans has already been shown with civet cats acting as intermediate hosts for SARS-CoVs, and dromedary camels for MERS-CoV. Human-to-human transmission is primarily achieved through close contact of respiratory droplets, direct contact with the infected individuals, or by contact with contaminated objects and surfaces. The coronaviral genome contains four major structural proteins: the spike (S), membrane (M), envelope (E) and the nucleocapsid (N) protein, all of which are encoded within the 3' end of the genome. The S protein mediates attachment of the virus to the host cell surface receptors resulting in fusion and subsequent viral entry. The M protein is the most abundant protein and defines the shape of the viral envelope. The E protein is the smallest of the major structural proteins and participates in viral assembly and budding. The N protein is the only one that binds to the RNA genome and is also involved in viral assembly and budding. Replication of coronaviruses begin with attachment and entry. Attachment of the virus to the host cell is initiated by interactions between the S protein and its specific receptor. Following receptor binding, the virus enters host cell cytosol via cleavage of S protein by a protease enzyme, followed by fusion of the viral and cellular membranes. The next step is the translation of the replicase gene from the virion genomic RNA and then translation and assembly of the viral replicase complexes. Following replication and subgenomic RNA synthesis, encapsidation occurs resulting in the formation of the mature virus. Following assembly, virions are transported to the cell surface in vesicles and released by exocytosis.

Naturally occurring hepatitis B virus surface antigen mutant variants in Malaysian blood donors and vaccinees.

Hepatitis B virus surface mutants are of enormous importance because they are capable of escaping detection by serology and can infect both vaccinated and unvaccinated populations, thus putting the whole population at risk. This study aimed to detect and characterise hepatitis B-escaped mutants among blood donors and vaccinees. One thousand serum samples were collected for this study from blood donors and vaccinees. Hepatitis B surface antigen, antibodies and core antibodies were tested using a commercial enzyme-linked immunosorbent assay (ELISA) kit. DNA detection was performed via nested polymerase chain reaction (PCR), and the S gene was sequenced and analysed using bioinformatics. Of the 1,000 samples that were screened, 5.5% (55/1,000) were found to be HBsAg-negative and anti-HBc- and HBV DNA-positive. All 55 isolates were found to belong to genotype B. Several mutations were found across all the sequences from synonymous and non-synonymous mutations, with the most nucleotide mutations occurring at position 342, where adenine was replaced by guanine, and cytosine at position 46 was replaced by adenine in 96.4% and 98% of the isolates, respectively. Mutation at position 16 of the amino acid sequence was found to be common to all the Malaysian isolates, with 85.7% of the mutations occurring outside the major hydrophilic region. This study revealed a prevalence of 5.5% for hepatitis B-escaped mutations among blood donors and vaccinated undergraduates, with the most common mutation being found at position 16, where glutamine was substituted with lysine.

Molecular phylogeny of modern coxsackievirus A16.

A phylogenetic analysis of VP1 and VP4 nucleotide sequences of 52 recent CVA16 strains demonstrated two distinct CVA16 genogroups, A and B, with the prototype strain being the only member of genogroup A. CVA16 G-10, the prototype strain, showed a nucleotide difference of 27.7-30.2% and 19.9-25.2% in VP1 and VP4, respectively, in relation to other CVA16 strains, which formed two separate lineages in genogroup B with nucleotide variation of less than 13.4% and less than 16.3% in VP1 and VP4, respectively. Lineage 1 strains circulating before 2000 were later displaced by lineage 2 strains.

Field efficacy of a new repellent, KBR 3023, against Aedes albopictus (SKUSE) and Culex quinquefasciatus (SAY) in a tropical environment.

Two new repellent formulations, KBR 3023 10% and 20% from Bayer AG, Germany, were evaluated together with DEET 10% and 20% as standard repellent formulations. Evaluation was based on two separate field studies: a daytime study (0900-1700 hr) in a forested orchard on Penang Island and a nighttime study (2100-0100 hr) in a squatter residential area on the adjacent mainland of peninsular Malaysia. Both studies were carried out by exposing humans with bare arms and legs to mosquitoes landing/biting for an eight hour period. Right arms and legs of the human baits were treated with different repellent formulations (KBR 3023 10%, 20% and DEET 10%, 20%) and the left limbs were left untreated to act as controls. The daytime study indicated that all four formulations were equally effective (P < 0.05) as repellents against the predominant Aedes albopictus with greater than 88.5% reduction in landing/biting in the first four hours and not less than 65.0% in the next four hours of the assessment period. In the night study, all four formulations were also found to be equally effective (P < 0.05) in repelling Culex quinquefasciatus, the predominant species. All four formulations provided complete protection against Cx. quinquefasciatus in the first two hours of exposure. The percentage reduction values were maintained above 90.0% for the next six hours of the assessment period. In conclusion, both the KBR 3023 and DEET formulations were found to be equally effective (P < 0.05) in providing a long-lasting reduction in human-mosquito contact in both the day and night field studies.

Performance of ULV formulations (Pesguard 102/Vectobac 12AS) against three mosquito species.

Adulticidal and larvicidal performances of a water-based pyrethroid microemulsion Pesguard PS 102 (AI d-allethrin and d-phenothrin, both at 5.0% w/w) and Vectobac 12AS, an aqua-suspension Bacillus thuringiensis israelensis (B.t.i.) formulation (AI 1,200 ITU/mg) were assessed against mosquitoes Aedes aegypti, Aedes albopictus, and Culex quinquefasciatus using a Leco ULV Fog Generator Model 1600 and a Scorpion 20 ULV AirBlast Sprayer. Laboratory-cultured mosquito adults and larvae were used for efficacy assessment. For trials using Leco, both pyrethroid and bacterial formulations were dispersed both singly and in combination with Pesguard PS 102 at a dosage of 0.2 liters/ha and B.t.i. at a dosage of 1.0 liter/ha. Similar trials with the Scorpion were also conducted with Pesguard PS 102 at a dosage of 0.2 liters/ha and a higher dosage of B.t.i. (1.5 liters/ha). Experiments were conducted in a football field (200 x 100 m) where five check points at 10, 25, 50, 75, and 100 m downwind from the spray nozzle were chosen for efficacy assessments. Knockdown and mortality were scored at 1 and 24 h postspraying. Results from both trials showed that mortality values varied with distance from spray nozzle. For trials with Leco, fogging with the combination of Pesguard PS 102 and B.t.i. provided larvicidal mortality of > 80% for both Aedes species and of > 60% for Cx. quinquefasciatus larvae at several check points, depending on wind conditions. Complete mortality of adult Aedes mosquitoes at 24 h posttreatment was also achieved, while mortality values for Culex adults reached > 90% under strong wind conditions. As for trials with the Scorpion 20, high adult and larval mortalities were also achieved, with > 90% mortality at some check points. The above study demonstrated the possibility of achieving both larvicidal and adulticidal effects when using a combination of B.t.i. and Pesguard PS 102 in ULV space spray.