SARS-CoV-2 lineage B.6 was the major contributor to early pandemic transmission in Malaysia

Chong, Yoong Min; Sam, I‐Ching; Chong, Jennifer; Bador, Maria Kahar; Ponnampalavanar, Sasheela; Omar, Sharifah Faridah Syed; Kamarulzaman, Adeeba; Munusamy, Vijayan; Wong, Chee Kuan; Jamaluddin, Fadhil Hadi; Chan, Yoke Fun

doi:10.1371/journal.pntd.0008744

Cited by 35 publications

(36 citation statements)

References 18 publications

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“…The phylogenetic analysis demonstrated that most of circulating viruses in Iran belong to the lineage B.4 that is compatible with the other reports (8,26). B.1 is the most prevalent lineages in the world, although some reports from other countries show that other lineages are more frequent circulating variants (27). Furthermore, just as all other reports, we found that all the D614G mutations are related to the sequences belong to B.1 lineages (28).…”

Section: Discussionsupporting

confidence: 91%

Variation analysis of SARS-CoV-2 complete sequences from Iran

Moradi

Moghoofei

et al. 2021

Preprint

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The SARS-CoV-2 is a new emerging coronavirus initially reported in China at the late December 2019 and rapidly spread to the whole of the world. To date, 1261903 total case and 55830 deaths are reported from Iran as 8 January. In this study, we investigated all the complete sequences of SARS-CoV-2 that publicly reported from Iran. Twenty-four sequences between March to September 2020 were analyzed to identify genome variations and phylogenetic relationships. Furthermore, we assessed the amino acid changes related to the spike glycoprotein as an important viral factor associated with the entry to the host cells and as a vaccine target. Most of the variations are occurred in the ORF1ab, S, N, intergenic and ORF7 regions. The analysis of spike protein mutations demonstrated that D614G mutation could be detected from the May and beyond. Phylogenetic analysis showed that most of the circulated viruses in Iran are belong to the B.4 lineage. Although, we found a limited number of variants associated to the B.1 lineage carrying D614G mutation. Furthermore, we detected a variant characterize as the B.1.36 lineage with sixteen mutations in the spike protein region. This study showed the frequency of the viral populations in Iran as September, therefore, there is an emergent need to genomic surveillance to track viral lineage shift in the country beyond the September. These data would help to predict future situation and apply better strategy to control of the pandemic.

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Section: Discussionsupporting

confidence: 91%

Variation analysis of SARS-CoV-2 complete sequences from Iran

Moradi

Moghoofei

et al. 2021

Preprint

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“…In a study conducted in Northern California from late January to mid-March 2020, using samples from 36 patients spanning nine counties and the Grand Princess cruise ship, phylogenetic analyses revealed the cryptic introduction of at least seven different SARS-CoV-2 lineages into California (Deng et al, 2020). Genetic surveillance of COVID-19 studies in Malaysia and other Asian countries highlighted the presence of B.6 lineage in the Asia Pacific region (representing 95% of the world cases of B.6 strains) (Chong et al, 2020). The genomic based surveillance of COVID-19 cases in Beijing, China till May 2020 revealed transmission of SARS-CoV-2 in the city via three routes including Wuhan exposure group, foreigner imported cases, and locally transmitted cases (Du et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Surveillance of genetic diversity and evolution in locally transmitted SARS-CoV-2 in Pakistan during the first wave of the COVID-19 pandemic

Shakeel

Irfan

Nisa

et al. 2021

Preprint

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Surveillance of genetic diversity in the SARS-CoV-2 is extremely important to detect the emergence of more infectious and deadly strains of the virus. In this study, we monitored mutational events in the SARS-CoV-2 genome through whole genome sequencing. The samples (n=48) were collected from the hot spot regions of the metropolitan city Karachi, Pakistan during the four months (May 2020 to August 2020) of first wave of the COVID-19 pandemic. The data analysis highlighted 122 mutations, including 120 single nucleotide variations (SNV), and 2 deletions. Among the 122 mutations, there were 71 singletons, and 51 recurrent mutations. A total of 16 mutations, including 5 nonsynonymous mutations, were detected in spike protein. Notably, the spike protein missense mutation D614G was observed in 31 genomes. The phylogenetic analysis revealed majority of the genomes (36) classified as B lineage, where 2 genomes were from B.6 lineage, 5 genomes from B.1 ancestral lineage and remaining from B.1 sub-lineages. It was noteworthy that three clusters of B.1 sub-lineages were observed, including B.1.36 lineage (10 genomes), B.1.160 lineage (11 genomes), and B.1.255 lineage (5 genomes), which represent independent events of SARS-CoV-2 transmission within the city. The sub-lineage B.1.36 had higher representation from the Asian countries and the UK, B.1.160 correspond to the European countries with highest representation from the UK, Denmark, and lesser representation from India, Saudi Arabia, France and Switzerland, and the third sub-lineage (B.1.255) correspond to the USA. Collectively, our study provides meaningful insight into the evolution of SARS-CoV-2 lineages in spatio-temporal local transmission during the first wave of the pandemic.

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“…SARS-CoV-2 is an RNA virus from the family of Coronaviridae and genus Betacoronavirus [ 14 ]. RNA viruses have high rates of mutation.…”

Section: Introductionmentioning

confidence: 99%

“…Then, it is critical to monitor the dynamics of SARS-CoV-2 mutation in order to understand its infectivity, virulence, and pathogenicity for a vaccine development [ 13 ]. In [ 14 ], the genetic epidemiology of SARS-CoV-2 in Malaysia was studied by sequencing four genomes from the country during the second wave of infection. The lineage B.6 strain was found to be predominant, implying a local evolution [ 14 ].…”

Section: Introductionmentioning

confidence: 99%

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Impact of control interventions on COVID-19 population dynamics in Malaysia: a mathematical study

Abidemi

Zainuddin²,

Aziz³

2021

Eur. Phys. J. Plus

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Coronavirus disease 2019 (COVID-19) pandemic has posed a serious threat to both the human health and economy of the affected nations. Despite several control efforts invested in breaking the transmission chain of the disease, there is a rise in the number of reported infected and death cases around the world. Hence, there is the need for a mathematical model that can reliably describe the real nature of the transmission behaviour and control of the disease. This study presents an appropriately developed deterministic compartmental model to investigate the effect of different pharmaceutical (treatment therapies) and non-pharmaceutical (particularly, human personal protection and contact tracing and testing on the exposed individuals) control measures on COVID-19 population dynamics in Malaysia. The data from daily reported cases of COVID-19 between 3 March and 31 December 2020 are used to parameterize the model. The basic reproduction number of the model is estimated. Numerical simulations are carried out to demonstrate the effect of various control combination strategies involving the use of personal protection, contact tracing and testing, and treatment control measures on the disease spread. Numerical simulations reveal that the implementation of each strategy analysed can significantly reduce COVID-19 incidence and prevalence in the population. However, the results of effectiveness analysis suggest that a strategy that combines both the pharmaceutical and non-pharmaceutical control measures averts the highest number of infections in the population.

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SARS-CoV-2 lineage B.6 was the major contributor to early pandemic transmission in Malaysia

Cited by 35 publications

References 18 publications

Variation analysis of SARS-CoV-2 complete sequences from Iran

Variation analysis of SARS-CoV-2 complete sequences from Iran

Surveillance of genetic diversity and evolution in locally transmitted SARS-CoV-2 in Pakistan during the first wave of the COVID-19 pandemic

Impact of control interventions on COVID-19 population dynamics in Malaysia: a mathematical study

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