Emerging and re-emerging viruses in Malaysia, 1997-2007

Interactive effects of meteorological factors and air pollutants on hand, foot, and mouth disease in Chengdu, China: a time-series study

OBJECTIVES

Hand, foot, and mouth disease (HFMD) is a viral infectious disease that poses a substantial threat in the Asia-Pacific region. It is widely reported that meteorological factors are associated with HFMD. However, the relationships between air pollutants and HFMD are still controversial. In addition, the interactive effects between meteorological factors and air pollutants on HFMD remain unknown. To fill this research gap, we conducted a time-series study.

DESIGN

A time-series study.

SETTING AND PARTICIPANTS

Daily cases of HFMD as well as meteorological and air pollution data were collected in Chengdu from 2011 to 2017. A total of 184 610 HFMD cases under the age of 15 were included in our study.

OUTCOME MEASURES

Distributed lag nonlinear models were used to investigate the relationships between HFMD and environmental factors, including mean temperature, relative humidity, SO₂, NO₂, and PM₁₀. Then, the relative excess risk due to interaction (RERI) and the proportion attributable to interaction were calculated to quantitatively evaluate the interactions between meteorological factors and air pollutants on HFMD. Bivariate response surface models were used to visually display the interactive effects.

RESULTS

The cumulative exposure-response curves of SO₂ and NO₂ were inverted 'V'-shaped and 'M'-shaped, respectively, and the risk of HFMD gradually decreased with increasing PM₁₀ concentrations. We found that there were synergistic interactions between mean temperature and SO₂, relative humidity and SO₂, as well as relative humidity and PM₁₀ on HFMD, with individual RERIs of 0.334 (95% CI 0.119 to 0.548), 0.428 (95% CI 0.214 to 0.642) and 0.501 (95% CI 0.262 to 0.741), respectively, indicating that the effects of SO₂ and PM₁₀ on HFMD were stronger under high temperature (>17.3°C) or high humidity (>80.0%) conditions.

CONCLUSIONS

There were interactive effects between meteorological factors and air pollutants on HFMD. Our findings could provide guidance for targeted and timely preventive and control measures for HFMD.

Assessment on Hand Hygiene Knowledge and Practices Among Pre-school Children in Klang Valley

Background. Pre-school children are at a higher risk to acquire infectious diseases such as hand, foot and mouth disease due to their immature immune system. Good hand hygiene prevents transmission of infectious diseases. This study aimed to determine the knowledge and practices of hand hygiene among pre-schoolers. Methods. In this prospective, multi-center study, the pre-schools were selected according to the selection criteria. A questionnaire consisting of socio-demographics, knowledge and practices of hand hygiene were administered via face-to-face interview during the pre- and post-intervention period. A total of 435 pre-schoolers aged 5 and 6 years old from 2 pre-schools within Klang Valley, School P (test group) and School C (control group) were involved in this study. The test group was provided with comprehensive hand hygiene education including video on proper handwashing technique during the 2 months intervention period, whereas the control group did not receive any form of intervention. The data were statistically analyzed using descriptive analysis and independent t-test. Results. Majority of pre-schoolers gained knowledge of handwashing from their parents. However, only 63% demonstrated good handwashing technique. Test group were significantly better (P < 0.05) in handwashing technique and hand hygiene routine score. Conclusion. A comprehensive hand hygiene education program should include proper handwashing facilities, resources, and awareness of the care-givers in instilling and sustaining good hand hygiene behavior.

Alanine scanning mutagenesis of SP70 epitope in characterizing species‑specific antibodies induced by enterovirus 71‑based antigens

The enterovirus 71 (EV71) SP70 epitope, derived from amino acids 208‑222 of VP1, is a neutralizing epitope. The present study aimed to assess the inter‑species differences of the antibodies induced by EV71‑based antigens in responses to SP70 mutant peptides. BALB/c mice and Lou/C rats were immunized with EV71 SP70. Monoclonal antibodies (Mabs) were produced by hybridoma clones. Serum polyclonal antibodies (Pabs) were produced from BALB/c mice and New Zealand white rabbits immunized with recombinant EV71 VP1 (rEV71‑VP1) protein or inactivated EV71. Micro‑neutralization and immunofluorescence assays were used to evaluate the capacity of the antibodies to bind to EV71. Reactivity of Mabs and Pabs to mutated SP70 were determined by alanine scanning mutagenesis. Furthermore, serums from EV71‑infected patients were collected to examine the affinity of SP70 antibody in the serum to mutated SP70, using competitive ELISA. The binding affinity of mouse Mabs to the SP70 epitope was increased by alanine substitution at sites of 210, 212, 213, 214, and 221. The binding affinity of rat Mabs to the SP70 epitope was increased by alanine substitution at sites 210, 217, 219, and 221. Mouse serum Pabs elicited by inactivated EV71 bound wild‑type SP70, but lost affinity for mutated peptides. Conversely, rabbit serum Pabs elicited by inactivated EV71 robustly recognized SP70 mutants. Mouse serum Pabs elicited by rEV71‑VP1 presented the same trend as mouse Mabs. Mutations at sites 214, 215, and 217 led to loss of recognition by rabbit Pabs elicited by rEV71‑VP1, while most mutations did not influence antibody binding. Compared with the wild‑type, mutations at the sites 209, 219 and 221 of SP70 lead to increased affinity with the serum antibodies produced by the EV71‑infected patients. Antibody responses triggered by inactivated EV71, rEV71‑VP1 and EV71 SP70 differed among species in neutralizing capacity and affinity for SP70 mutant peptides.

Pathogenicity of H5N8 highly pathogenic avian influenza viruses isolated from a wild bird fecal specimen and a chicken in Japan in 2014

Poultry outbreaks caused by H5N8 highly pathogenic avian influenza viruses (HPAIVs) occurred in Japan between December 2014 and January 2015. During the same period; H5N8 HPAIVs were isolated from wild birds and the environment in Japan. The hemagglutinin (HA) genes of these isolates were found to belong to clade 2.3.4.4 and three sub-groups were distinguishable within this clade. All of the Japanese isolates from poultry outbreaks belonged to the same sub-group; whereas wild bird isolates belonged to the other sub-groups. To examine whether the difference in pathogenicity to chickens between isolates of different HA sub-groups of clade 2.3.4.4 could explain why the Japanese poultry outbreaks were only caused by a particular sub-group; pathogenicities of A/chicken/Miyazaki/7/2014 (Miyazaki2014; sub-group C) and A/duck/Chiba/26-372-48/2014 (Chiba2014; sub-group A) to chickens were compared and it was found that the lethality of Miyazaki2014 in chickens was lower than that of Chiba2014; according to the 50% chicken lethal dose. This indicated that differences in pathogenicity may not explain why the Japanese poultry outbreaks only involved group C isolates.

Bat-man disease transmission: zoonotic pathogens from wildlife reservoirs to human populations

Bats are natural reservoir hosts and sources of infection of several microorganisms, many of which cause severe human diseases. Because of contact between bats and other animals, including humans, the possibility exists for additional interspecies transmissions and resulting disease outbreaks. The purpose of this article is to supply an overview on the main pathogens isolated from bats that have the potential to cause disease in humans.

Cyclical Patterns of Hand, Foot and Mouth Disease Caused by Enterovirus A71 in Malaysia

Enterovirus A71 (EV-A71) is an important emerging pathogen causing large epidemics of hand, foot and mouth disease (HFMD) in children. In Malaysia, since the first EV-A71 epidemic in 1997, recurrent cyclical epidemics have occurred every 2–3 years for reasons that remain unclear. We hypothesize that this cyclical pattern is due to changes in population immunity in children (measured as seroprevalence). Neutralizing antibody titers against EV-A71 were measured in 2,141 residual serum samples collected from children ≤12 years old between 1995 and 2012 to determine the seroprevalence of EV-A71. Reported national HFMD incidence was highest in children <2 years, and decreased with age; in support of this, EV-A71 seroprevalence was significantly associated with age, indicating greater susceptibility in younger children. EV-A71 epidemics are also characterized by peaks of increased genetic diversity, often with genotype changes. Cross-sectional time series analysis was used to model the association between EV-A71 epidemic periods and EV-A71 seroprevalence adjusting for age and climatic variables (temperature, rainfall, rain days and ultraviolet radiance). A 10% increase in absolute monthly EV-A71 seroprevalence was associated with a 45% higher odds of an epidemic (adjusted odds ratio, aOR1.45; 95% CI 1.24–1.69; P<0.001). Every 10% decrease in seroprevalence between preceding and current months was associated with a 16% higher odds of an epidemic (aOR = 1.16; CI 1.01–1.34 P<0.034). In summary, the 2–3 year cyclical pattern of EV-A71 epidemics in Malaysia is mainly due to the fall of population immunity accompanying the accumulation of susceptible children between epidemics. This study will impact the future planning, timing and target populations for vaccine programs.

Enterovirus A71 (EV-A71) is a major cause of hand, foot, and mouth disease (HFMD) in children. Since the first outbreak in Malaysia in 1997, EV-A71 epidemics have occurred every 2–3 years, in 2000, 2003, 2006, 2008/2009, and 2012. As the reasons for this cyclical pattern are not known, we hypothesize that it is due to changes in population immunity in children. In this study, we measured the EV-A71 neutralizing antibody prevalence in serum collected from children ≤12 years old between 1995 and 2012, covering 18 years and 6 epidemics. HFMD incidence was highest in children <2 years, and seroprevalence increased with age, and was higher during epidemics compared to non-epidemic periods. Peaks in EV-A71 genetic diversity coincided with reported EV-A71 epidemics. Decreases in EV-A71 seroprevalence over time were significantly associated with subsequent epidemic periods. This suggests that epidemics lead to high levels of population seroprevalence; but during the 2–3 years between epidemics, the population of young children with no immunity is replenished and increases, making it more likely that a new epidemic will occur. This is the first study to show that the cyclical pattern of EV-A71 epidemics is associated with changes in EV-A71 seroprevalence.

Characterization of the enterovirus 71 P1 polyprotein expressed in Pichia pastor as a candidate vaccine

Human enterovirus 71 (EV71) plays an important role in hand, foot, and mouth disease (HFMD), which recently caused the death of hundreds of children in the Asia-Pacific region. However, there are no specific treatments available for EV71 infections; thus, a safe and effective vaccine is needed urgently. In this study, we developed an effective and economical method for producing EV71 polyprotein (P1 protein) in Pichia pastoris. Furthermore, we evaluated the potential of P1 protein as a candidate vaccine against EV71 virus. The data revealed that P1 protein induced persistent high cross-neutralization antibodies for different EV71 subtypes, and elicited significant splenocyte proliferation. The high levels of interleukin-10(IL-10) and interferon-gamma (IFN-γ) showed that P1 protein induced Th1 and Th2 immune responses. Interestingly, vaccinating female mice with the P1 protein conferred cross-protection against different EV71 subtypes to their neonatal offspring.Compared with heat-inactivated EV71, the P1 protein elicited improved humoral and cellular immune responses and showed good cross-protection with different EV71 subtypes. Therefore, the EV71-P1 protein produced by P. pastoris is a promising candidate vaccine against EV71.

The prevalence and distribution of Brucella melitensis in goats in Malaysia from 2000 to 2009

A study was conducted to describe the prevalence and distribution of zoonotic Brucella melitensis in goats in Peninsular Malaysia. Using serosurveillance data of the last decade (2000-2009) involving 119,799 goats and 3555 farms, the seroprevalence of brucellosis among goats was 0.91% (95% CI=0.86-0.96) and among farms was 7.09% (95% CI=6.27-7.98). The odds of brucellosis was significantly (P<0.05) higher in the later part of the decade, in larger herd size and among the states located in the peninsula as compared to eastern Malaysia. The infection was detected throughout Malaysia but at generally low seroprevalences with states like Perlis that border neighbouring countries having higher seroprevalence of brucellosis than other non-border states.

Antivirals against enteroviruses: a critical review from a public-health perspective

The enteroviruses (EVs) of the Picornaviridae family are the most common viral pathogens known. Most EV infections are mild and self-limiting but manifestations can be severe in children and immunodeficient individuals. Antiviral development is actively pursued to benefit these high-risk patients and, given the alarming problem of antimicrobial drug resistance, antiviral drug resistance is a public-health concern. Picornavirus antivirals can be used off-label or as part of outbreak control measures. They may be used in the final stages of poliovirus eradication and to mitigate EV-A71 outbreaks. We review the potential emergence of drug-resistant strains and their impact on EV transmission and endemic circulation. We include non-picornavirus antivirals that inhibit EV replication, for example, ribavirin, a treatment for infection with HCV, and amantadine, a treatment for influenza A. They may have spurred resistance emergence in HCV or influenza A patients who are unknowingly coinfected with EV. The public-health challenge is always to find a balance between individual benefit and the long-term health of the larger population.

A Review of Hendra Virus and Nipah Virus Infections in Man and Other Animals

Hendra virus (HeV) and Nipah virus (NiV) emerged in the last decade of the twentieth century. They were the cause of a number of outbreaks of respiratory and neurological disease infecting horses and pigs respectively. Transmission from infected domestic animal species resulted in human infections as well, with high case fatality rates a feature. Today they continue to cause outbreaks of human and animal disease. NiV causes yearly disease outbreaks in humans in Bangladesh, and HeV causes sporadic disease outbreaks in horses in north eastern Australia. Due to their zoonotic nature, they have been ideal candidates for collaborative projects in the One Health space, bringing public health and animal health professionals together. This has lead to insightful epidemiological studies, which has resulted in practical disease prevention solutions including a horse vaccine for HeV and NiV spill-over prevention interventions in the field. As more surveillance is undertaken, their known distributions have expanded, as has the range of reservoir host species. The majority of bat species for which there is evidence of henipavirus infection belong to the group known as the Old World family of fruit and nectar feeding bats (Family Pteropodidae, Suborder Megachiroptera). This review of the bat borne henipaviruses discusses the epidemiology, pathology, transmission and disease symptoms in these closely related viruses which belong to the Genus Henipavirus, Family Paramyxoviridae.

Characterization of the enterovirus 71 VP1 protein as a vaccine candidate

Enterovirus 71 (EV71) is an important agent responsible for hand-foot-and-mouth disease (HFMD), which can cause severe neurological complications and death in children. However, there is no specific treatment for EV71 infection, and a safe and effective vaccine is needed urgently. In this study, an effective and economical method for the production of EV71-VP1 protein was developed, and the VP1 protein was evaluated in humoral and cellular immune responses as an EV71 vaccine. The results revealed that the VP1 protein induced high titers of cross-neutralizing antibodies for different EV71 subtypes, and elicited significant splenocyte proliferation. The high levels of IFN-r and IL-10 showed the VP1 protein induced a mixed Th1 and Th2 immune response. Vaccinated female mice could confer protection in their neonatal offspring. Compared with the inactivated EV71, the VP1 protein elicited similar humoral and cellular responses, but the engineered protein is safer, less expensive and can be produced more efficiently. Therefore, EV71-VP1 protein can induce effective immunologic protection against EV71 and is an ideal candidate against EV71 infection.

Enterovirus 71 viral capsid protein linear epitopes: identification and characterization

Background

To characterize the human humoral immune response against enterovirus 71 (EV71) infection and map human epitopes on the viral capsid proteins.

Methods

A series of 256 peptides spanning the capsid proteins (VP1, VP2, VP3) of BJ08 strain (genomic C4) were synthesized. An indirect enzyme-linked immunosorbent assay (ELISA) was carried out to detect anti-EV71 IgM and IgG in sera of infected children in acute or recovery phase. The partially overlapped peptides contained 12 amino acids and were coated in the plate as antigen (0.1 μg/μl). Sera from rabbits immunized with inactivated BJ08 virus were also used to screen the peptide panel.

Results

A total of 10 human anti-EV71 IgM epitopes (vp1-14 in VP1; vp2-6, 21, 40 and 50 in VP2 and vp3-10, 12, 15, 24 and 75 in VP3) were identified in acute phase sera. In contrast, only one anti-EV71 IgG epitope in VP1 (vp1-15) was identified in sera of recovery stage. Four rabbit anti-EV71 IgG epitopes (vp1-14, 31, 54 and 71) were identified and mapped to VP1.

Conclusion

These data suggested that human IgM epitopes were mainly mapped to VP2 and VP3 with multi-epitope responses occurred at acute infection, while the only IgG epitope located on protein VP1 was activated in recovery phase sera. The dynamic changes of humoral immune response at different stages of infection may have public health significance in evaluation of EV71 vaccine immunogenicity and the clinical application of diagnostic reagents.

Host specificity and niche partitioning in flea-small mammal networks in Bornean rainforests

The diversity of ectoparasites in Southeast Asia and flea-host associations remain largely understudied. We explore specialization and interaction patterns of fleas infesting non-volant small mammals in Bornean rainforests, using material from a field survey carried out in two montane localities in northwestern Borneo (Sabah, Malaysia) and from a literature database of all available interactions in both lowland and montane forests. A total of 234 flea individuals collected during our field survey resulted in an interaction network of eight flea species on seven live-captured small mammal species. The interaction network from all compiled studies currently includes 15 flea species and 16 small mammal species. Host specificity and niche partitioning of fleas infesting diurnal treeshrews and squirrels were low, with little difference in specialization among taxa, but host specificity in lowland forests was found to be higher than in montane forests. By contrast, Sigmactenus alticola (Siphonaptera: Leptopsyllidae) exhibited low host specificity by infesting various montane and lowland nocturnal rats. However, this species exhibited low niche partitioning as it was the only commonly recorded flea from rats on Borneo. Overall complementary specialization was of intermediate intensity for both networks and differed significantly from random association; this has important implications for specific interactions that are also relevant to the potential spread of vector-borne diseases.

Development and evaluation of reverse transcription-loop-mediated isothermal amplification assay for rapid detection of enterovirus 71

Background

Hand, foot, and mouth disease (HFMD) caused by enterovirus 71 (EV71) is very common in China. It is difficult to distinguish between EV71 and coxsackievirus A16 (CVA16) infections in clinical HFMD patients. Routine laboratory diagnosis of EV71 infection is time-consuming and requires expensive instruments. In this study, we have developed a one-step, single tube, reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay for rapid and sensitive detection of EV71.

Methods

Six primers that can recognize 6 distinct regions on the VP2 gene of EV71 were designed for RT-LAMP assay. The amplification was completed by incubating all reagents in a single tube with reverse transcriptase and Bst DNA polymerase under the isothermal condition (60°C) for 60 min, and could be evaluated by using GoldView staining under a handheld ultraviolet torch lamp or electrophoresis analysis.

Results

A total of 123 specimens collected from suspicious patients with HFMD were simultaneously detected by RT-LAMP and PCR fluorescence probing assay. The RT-LAMP amplified products containing EV71 were digested by HinfI and TaqI restriction endonucleases; in contrast, non-specific products with CVA16, coxsackievirus A4 and coxsackievirus B3 could not be detected in RT-LAMP assay. Meanwhile, RT-LAMP assay could amplify EV71 virus with a detection limit of 1 PFU/ml within 60 min. Compared with PCR fluorescence probing assay, RT-LAMP assay exhibited 98.4% identity during the detection of EV71 viral RNA without the missing of positive samples.

Conclusion

Our results indicated that RT-LAMP is a rapid, sensitive, specific and accurate method for the detection of EV71 in clinical specimens. Therefore, this developed method has potential application for rapid and comprehensive surveillance for EV71 infection, especially in developing country.

Hendra and nipah infection: pathology, models and potential therapies

The Paramyxoviridae family comprises of several genera that contain emerging or re-emerging threats for human and animal health with no real specific effective treatment available. Hendra and Nipah virus are members of a newly identified genus of emerging paramyxoviruses, Henipavirus. Since their discovery in the 1990s, henipaviruses outbreaks have been associated with high economic and public health threat potential. When compared to other paramyxoviruses, henipaviruses appear to have unique characteristics. Henipaviruses are zoonotic paramyxoviruses with a broader tropism than most other paramyxoviruses, and can cause severe acute encephalitis with unique features among viral encephalitides. There are currently no approved effective prophylactic or therapeutic treatments for henipavirus infections. Although ribavirin was empirically used and seemed beneficial during the biggest outbreak caused by one of these viruses, the Nipah virus, its efficacy is disputed in light of its lack of efficacy in several animal models of henipavirus infection. Nevertheless, because of its highly pathogenic nature, much effort has been spent in developing anti-henipavirus therapeutics. In this review we describe the unique features of henipavirus infections and the different strategies and animal models that have been developed so far in order to identify and test potential drugs to prevent or treat henipavirus infections. Some of these components have the potential to be broad-spectrum antivirals as they target effectors of viral pathogenecity common to other viruses. We will focus on small molecules or biologics, rather than vaccine strategies, that have been developed as anti-henipaviral therapeutics.

Comparative pathogenesis of epidemic and enzootic Chikungunya viruses in a pregnant Rhesus macaque model

Since 2004, an East African genotype of Chikungunya virus (CHIKV) has emerged, causing significant epidemics of an arthralgic syndrome. In addition, this virus has been associated for the first time with neonatal transmission and neurological complications. In the current study, pregnant Rhesus macaques were inoculated with an enzootic or epidemic strain of CHIKV to compare pathogenesis and transplacental transmission potential. Viremias were similar for both strains and peaked at 2-3 days post-inoculation (dpi). Viral RNA was detected at necropsy at 21 dpi in maternal lymphoid, joint-associated, and spinal cord tissues. The absence of detectable viral RNA and the lack of germinal center development in fetuses indicated that transplacental transmission did not occur. Neutralizing antibodies were detected in all dams and fetuses. Our study establishes a non-human primate model for evaluating vaccines and antiviral therapies and indicates that Rhesus macaques could serve as a competent enzootic reservoir.

Development and evaluation of a reverse transcription-loop-mediated isothermal amplification assay for rapid detection of enterovirus 71

Human enterovirus 71 (EV71) is the major etiological agent of hand, foot, and mouth disease (HFMD), which is a common infectious disease in young children and infants. EV71 can cause various clinical manifestations and has been associated with severe neurological complications; it has resulted in fatalities during recent outbreaks in Asian-Pacific regions since 1997. The early and rapid detection is critical for prevention and control of EV71 infection, since no vaccine or antiviral drugs are currently available. In this study, a simple and sensitive reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay was developed for rapid detection of EV71. The detection limit of the RT-LAMP assay was approximately 0.01 PFU per reaction mixture, and no cross-reactive amplification with other enteroviruses was observed. The assay was evaluated further with 40 clinical specimens and exhibited 92.9% sensitivity and 100% specificity. This RT-LAMP assay may become a useful alternative in clinical diagnosis of EV71, especially in resource-limited hospitals or rural clinics of China and other countries in the Asian-Pacific region.

Performance of detecting IgM antibodies against enterovirus 71 for early diagnosis

Enterovirus 71 (EV71) infection is more likely to induce severe complications and mortality than other enteroviruses. Methods for detection of IgM antibody against EV71 had been established for years, however, the performance of the methods in the very early diagnosis of EV71 infection had not been fully evaluated, which is especially meaningful because of the short incubation period of EV71 infection. In this report, the performance of an IgM anti-EV71 assay was evaluated using acute sera collected from 165 EV71 infected patients, 165 patients infected with other enteroviruses, and more than 2,000 sera from healthy children or children with other infected diseases. The results showed a 90% sensitivity in 20 patients who were in their first illness day, and similar sensitivity remained till 4 days after onset. After then the sensitivity increased to 95% to 100% for more than one month. The specificity of the assay in non-HFMD children is 99.1% (95% CI: 98.6–99.4), similar as the 99.9% specificity in healthy adults. The cross-reaction rate in patients infected with other non-EV71 enteroviruses was 11.4%. In conclusion, the data here presented show that the detection of IgM anti-EV71 by ELISA affords a reliable, convenient, and prompt diagnosis of EV71 infection.

A(H5N1) Virus Evolution in South East Asia

Highly Pathogenic Avian Influenza (HPAI) H5N1 virus is an ongoing public health and socio-economic challenge, particularly in South East Asia. H5N1 is now endemic in poultry in many countries, and represents a major pandemic threat. Here, we describe the evolution of H5N1 virus in South East Asia, the reassortment events leading to high genetic diversity in the region, and factors responsible for virus spread. The virus has evolved with genetic variations affecting virulence, drug-resistance, and adaptation to new host species. The constant surveillance of these changes is of primary importance in the global efforts of the scientific community.

Estimating the date of origin of an HIV-1 circulating recombinant form

HIV is capable of frequent genetic exchange through recombination. Despite the pandemic spread of HIV-1 recombinants, their times of origin are not well understood. We investigate the epidemic history of a HIV-1 circulating recombinant form (CRF) by estimating the time of the recombination event that lead to the emergence of CRF33_01B, a recently described recombinant descended from CRF01_AE and subtype B. The gag, pol and env genes were analyzed using a combined coalescent and relaxed molecular clock model, implemented in a Bayesian Markov chain Monte Carlo framework. Using linked genealogical trees we calculated the time interval between the common ancestor of CRF33_01B and the ancestors it shares with closely related parental lineages. The recombination event that generated CRF33_01B (t(rec)) occurred sometime between 1991 and 1993, suggesting that recombination is common in the early evolutionary history of HIV-1. The proof-of-concept approach provides a new tool for the investigation of HIV molecular epidemiology and evolution.