Dengue virus type 4 (DENV-4) circulates in tropical and subtropical countries from Asia and the Americas. Despite the importance of dengue virus distribution, little is known about the worldwide viral spread. Following a Bayesian phylogenetic approach we inferred the evolutionary history of 310 isolates sampled from 37 countries during the time period 1956-2008 and the spreading dynamics for genotypes I and II. The region (tropical rainforest biome) comprised by Malaysia-Thailand was the most likely ancestral area from which the serotype has originated and spread. Interestingly, cross-correlation analysis on demographic time series with the Asian sequences showed a statistically significant negative correlation that could be suggestive of competition among genotypes within the same serotype.
About two-thirds of the world's population live in areas infested with dengue vectors, mainly Aedes aegypti. All four dengue viruses are circulating, sometimes simultaneously, in most of these areas. It is estimated that up to 80 million persons become infected annually although marked underreporting results in the notification of much smaller figures. Currently dengue is endemic in all continents except Europe and epidemic dengue haemorrhagic fever (DHF) occurs in Asia, the Americas and some Pacific islands. The incidence of DHF is much greater in the Asian countries than in other regions. In Asian countries the disease continues to affect children predominantly although a marked increase in the number of DHF cases in people over 15 years old has been observed in the Philippines and Malaysia during recent years. In the 1990's DHF has continued to show a higher incidence in South-East Asia, particularly in Viet Nam and Thailand which together account for more than two-thirds of the DHF cases reported in Asia. However, an increase in the number of reported cases has been noted in the Philippines, Lao People's Democratic Republic, Cambodia, Myanmar, Malaysia, India, Singapore and Sri Lanka during the period 1991-1995 as compared to the preceding 5-year period. In the Americas, the emergence of epidemic DHF occurred in 1981 almost 30 years after its appearance in Asia, and its incidence is showing a marked upward trend. In 1981 Cuba reported the first major outbreak of DHF in the Americas, during which a total of 344,203 cases of dengue were notified, including 10,312 severe cases and 158 deaths. The DHF Cuban epidemic was associated with a strain of dengue-2 virus and it occurred four years after dengue-1 had been introduced in the island causing epidemics of dengue fever. Prior to this event suspected cases of DHF or fatal dengue cases had been reported by five countries but only a few of them fulfilled the WHO criteria for diagnosis of DHF. The outbreak in Cuba is the most important event in the history of dengue in the Americas. Subsequently to it, in every year except 1983, confirmed or suspected cases of DHF have been reported in the Region. The second major outbreak in the Americas occurred in Venezuela in 1989 and since then this country has suffered epidemics of DHF every year. Between 1981 and 1996 a total of 42,246 cases of DHF and 582 deaths were reported by 25 countries in the Americas, 53% of which originated from Venezuela and 24% from Cuba. Colombia, Nicaragua and Mexico have each reported over 1,000 cases during the period 1992-1996. About 74% of the Colombian cases and 97% of the Mexican cases were reported during 1995-1996. A main cause of the emergence of DHF in the Americas was the failure of the hemispheric campaign to eradicate Aedes aegypti. Following a successful period that resulted in the elimination of the mosquito from 18 countries by 1962, the programme began to decline and as a result there was a progressive dissemination of the vector so that by 1997 with the exception of Canada, Chile and Bermuda, all countries in the Americas are infested. Other factors contributing to the emergence/re-emergence of dengue/DHF include the rapid growth and urbanization of populations in Latin America and the Caribbean, and increased travel of persons which facilitates dissemination of dengue viruses. Presently, all four dengue serotypes are circulating in the Americas, thus increasing the risk for DHF in this region.
The widespread severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continuously impacts our economic and public health. The potential of emerging variants to increase transmissibility and evade vaccine-induced immunity lets us put more effort to research on viral mutations and explore the pathogenic haplotypes. In this study, we characterized the haplotype and sub-haplotype diversity of SARS-CoV-2 global variants in January-March and the areas with low and high COVID19 vaccination rates in May 2021 by analyzing viral proteome of complete genome sequences published. Phylogenetic tree analysis of the proteomes of SARS-CoV-2 variants with Neighbor-Joining and Maximum Parsimony methods indicated that haplotype 2 variant with nsp12 P323L and Spike D614G was dominant (98.81%), including new sub-haplotypes 2A_1 to 2A_3, 2B_1 to 2B_3, and 2C_1 to 2C_2 emerged post-one-year COVID-19 outbreak. In addition, the profiling of sub-haplotypes indicated that sub-haplotype 2A_1 with the mutations at N501Y, A570D, D614G, P681H, T716I, S982A, and D118H in Spike was over 58% in May 2021 in the high partly vaccinated rate group (US, Canada, and Germany). Meanwhile, the new haplotype 2C_3 bearing the mutations at EFR156-158del, T19R, A222V, L452R, T478K, and D614G in Spike occupied over 54.8% in May 2021 in the low partly vaccinated rate group (India, Malaysia, Taiwan, and Vietnam). Sub-haplotypes 2A_1 and 2C_3 had a meaningful alternation of ACE2-specific recognition site, neutralization epitopes, and furin cleavage site in SARS-CoV-2 Spike protein. The results discovered the haplotype diversity and new sub-haplotypes of SARS-CoV-2 variants post one-year pandemic in January-March 2021, showing the profiles of sub-haplotypes in the groups with low and high partly vaccinated rates in May 2021. The study reports the emergence of new SARS-CoV-2 sub-haplotypes during ongoing pandemic and vaccination in early 2021, which might help inform the response to vaccination strategies.
The environmental bacterium Burkholderia pseudomallei causes an estimated 165,000 cases of human melioidosis per year worldwide and is also classified as a biothreat agent. We used whole genome sequences of 469 B. pseudomallei isolates from 30 countries collected over 79 years to explore its geographic transmission. Our data point to Australia as an early reservoir, with transmission to Southeast Asia followed by onward transmission to South Asia and East Asia. Repeated reintroductions were observed within the Malay Peninsula and between countries bordered by the Mekong River. Our data support an African origin of the Central and South American isolates with introduction of B. pseudomallei into the Americas between 1650 and 1850, providing a temporal link with the slave trade. We also identified geographically distinct genes/variants in Australasian or Southeast Asian isolates alone, with virulence-associated genes being among those over-represented. This provides a potential explanation for clinical manifestations of melioidosis that are geographically restricted.