Dynamics and Dispersal of Local HIV Epidemics Within San Diego and Across The San Diego-Tijuana Border

Phylodynamics for Human Immunodeficiency Virus Prevention: A Miami-Dade County Case Study

BACKGROUND

To date, human immunodeficiency virus (HIV) molecular epidemiology has been primarily used to identify clusters of related infections (cluster detection and response) and then address interventions to these clusters. Community groups have raised concern regarding cluster detection and response related to privacy and ethical concerns. Here we demonstrate how an alternative approach to HIV molecular epidemiology can provide public health benefit.

METHODS

A limited data set for Miami-Dade County provided by the Florida Department of Health was curated and annotated by neighborhood health district (NBHD) and genetic linkage (using a genetic distance threshold of ≤0.5%) and phylodynamic analyses were performed. Phylodynamic analyses were used to infer viral transmissions into Miami-Dade County and between NBHDs within the county.

RESULTS

A total of 7274 HIV sequences from unique persons collected between 1 January 2015 and 31 December 2021 were analyzed, including 50% of the 7894 new diagnoses during this period. The proportion of sequences in local clusters increased over time. Higher ratios of local introductions, compared to viral egress (ie, source of local clusters in other NBHDs) were observed in 3 NBHDs in North Miami (range, 1.9-2.5), suggesting earlier diagnosis, but high numbers of susceptible persons not receiving preexposure prophylaxis. South Dade/Homestead had a low ratio (0.3) of local introductions compared with egress, suggesting later diagnosis and less durable suppression.

CONCLUSIONS

Phylodynamic and genetic linkage analyses can highlight populations and geographic regions that might benefit more from particular types of HIV prevention interventions. These findings will need to be explored by evaluating the impact of scaling up interventions informed by these analyses.

Sexual Networks and Behavioral Characteristics of HIV-Positive Male Military Members, Female Sex Workers, and Male Civilians

Military members and female sex workers (FSWs) may be more likely to acquire or transmit HIV. Mapping HIV transmission across these high-risk populations and identifying behaviors associated with sexual network clustering are needed for effective HIV prevention approaches. A cross-sectional study recruited participants newly diagnosed with HIV among militaries, civilians, and FSWs in Zambia, Senegal, and Democratic Republic of the Congo (DRC). Participants were interviewed on behaviors and provided blood samples for HIV-1 partial pol sequencing. Genetic-distance based network analyses inferred putative relationships between HIV-1 partial pol sequences. Bivariate logistic regression models identified variables associated with clustering in a sexual network. 908 participants were included (n = 313 FSWs, n = 297 military, n = 298 civilians). 311 blood samples were sequenced and had survey data, of which 93 (29.9%) were genetically linked, forming 36 transmission clusters. All but one cluster were comprised of participants from the same country, including one large cluster (n = 12; 9 FSWs and 3 civilians) from DRC. A large mixed-country cluster (n = 9) including 7 men (4 civilians, 3 military) and 2 FSWs was observed. The odds of clustering in a sexual network were elevated for DRC participants, FSWs, and those cohabitating with a sexual partner. Findings underscore the importance of identifying linkages in high-risk populations to develop tailored HIV prevention strategies. Linkages across risk groups and countries illustrate the potential role of mobile populations in HIV transmission and acquisition. Larger studies including HIV recency testing may better elucidate biological and behavioral interactions between military, civilians, and FSWs.

Characterizing HIV-1 transmission by genetic cluster analysis among newly diagnosed patients in the China-Myanmar border region from 2020 to 2023

Cluster analysis of HIV sequence can provide insights into viral transmission patterns in border regions. This study aims to illuminate the HIV-1 subtype distribution and transmission dynamics among newly diagnosed individuals in Dehong prefecture, a region along the China-Myanmar border. Among 948 participants with pol gene sequences, 36 HIV-1 subtypes were identified, with URFs (18.8%, 178/948) being the dominant strain, followed by CRF01_AE (18.5%, 175/948) and CRF07_BC (10.9%, 103/948). Additionally, 287 sequences (30.3%, 287/948) were grouped into 91 clusters, 31 of which contained both Chinese and Burmese individuals. Multivariable logistic regression indicated that men who have sex with men (MSM), CD4 + cell count of 200∼499, and 500 cells/μl and above, and CRF01_AE were risk factors for entering the network. Through the Chord diagram, we found frequent transmission relationships among heterosexual China male group, especially those over 35 years of age. Additionally, the correlation between heterosexual Myanmar female group and heterosexual China male group among cross-risk groups deserved to be emphasized. Furthermore, the network exhibited a growing trend over time, with the largest active transmission cluster identified in Ruili county. In conclusion, the HIV-1 subtype landscape in Dehong has become increasingly complex, and the region has faced risks of transmission from both domestic and international sources. Targeted intervention strategies should be implemented for MSM, heterosexual Chinese middle-aged and elderly men, and heterosexual Burmese young adults to mitigate these risks. These findings provided evidence-based insights for local government to formulate coordinated transnational intervention approaches.

HIV pre-exposure prophylaxis programmatic preferences among people who inject drugs: findings from a discrete choice experiment

BACKGROUND

Pre-exposure prophylaxis (PrEP) holds promise for decreasing new HIV infections among people who inject drugs (PWID), yet daily oral PrEP use is low, and PrEP modality and delivery strategy preferences in this population remain understudied.

METHODS

From May 2022-June 2023, we conducted a discrete choice experiment (DCE) with PWID in San Diego, California. Participants viewed 18 PrEP program scenarios in sets of three and chose their preferred scenario within each set. Scenarios consisted of various combinations of five characteristics: PrEP modality (injectable, implantable, oral), frequency of use (annual, bi-monthly, daily), service location (community-based organization, clinic, telemedicine), prescription access location (on-site, street outreach, mail), and adherence supports (social support, outreach worker, phone/text reminder). Multinomial logit regression estimated probabilities of choosing PrEP program scenarios as a function of the five characteristics to estimate part-worth utility scores (PWUS; reflecting relative preferences for specific characteristic values) and relative importance scores (RIS; reflecting the relative influence of each characteristic on program choice). We also explored differences by hypothesized modifiers of preferences (i.e., sex assigned at birth, housing status, injection frequency, prior PrEP awareness).

RESULTS

Among 262 participants, mean age was 43.1 years, and most reported male sex assigned at birth (69.5%), identified as non-Hispanic (60.3%), and were previously unaware of PrEP (75.2%). Frequency of use (RIS: 51.5) and PrEP modality (RIS: 35.3) had the greatest influence on PrEP program choice. Within these characteristics, participants had relative preferences for annual use (PWUS: 0.83) and oral PrEP (PWUS: 0.57), and relative aversions to daily use (PWUS: -0.76) and implantable PrEP (PWUS: -0.53). Generally, participants did not indicate preferences for specific service or prescription access locations, or adherence supports; however, among those with prior PrEP awareness, prescription access location and adherence supports had a slightly greater influence on PrEP program choices.

CONCLUSION

Our study considered diverse PrEP scenarios and highlighted potential preferences for long-acting oral modalities. Although not currently available, renewed investment in long-acting oral PrEP formulations may facilitate PrEP care engagement among PWID. Additional delivery and implementation strategy research is needed to support PrEP uptake and persistence in this population.

Long-acting Injectable PrEP Interest and General PrEP Awareness among People who Inject Drugs in the San Diego-Tijuana Border Metroplex

Long-acting injectable HIV pre-exposure prophylaxis (LAI-PrEP) could help overcome multilevel challenges to HIV prevention for people who inject drugs (PWID), including those in the binational San Diego-Tijuana metroplex. Yet, general PrEP awareness and interest in LAI-PrEP remain underexplored among PWID. From 2020 to 2021, 562 HIV-negative PWID in San Diego and Tijuana completed surveys assessing general PrEP awareness and interest in oral and LAI-PrEP. Modified Poisson regression examined factors associated with general PrEP awareness. Multinomial logistic regression assessed factors associated with interest in both oral and LAI-PrEP, oral PrEP only, LAI-PrEP only, or neither. General PrEP awareness was low (18%) and associated with experiencing unsheltered homelessness (adjusted prevalence ratio [APR] = 1.50, 95% confidence interval [CI]: 0.96-2.33), past 6-month fentanyl injection (APR = 1.53, 95% CI: 1.04-2.25), and transactional sex (APR = 1.71, 95% CI: 1.06-2.76). Interest in oral PrEP only was most common (44%), followed by LAI-PrEP only (25%) and neither (16%). Compared to the odds of being interested in LAI-PrEP only, the odds of being interested in oral PrEP only were lower among those who were stopped by police (AOR = 0.38, 95% CI: 0.22-0.65), reported past 6-month fentanyl injection (AOR = 0.33, 95% CI: 0.20-0.56), polydrug use (AOR = 0.48, 95% CI: 0.27-0.86), injecting multiple times daily (AOR = 0.26, 95% CI: 0.14-0.46), receptive syringe use (AOR = 0.30, 95% CI: 0.19-0.49), and higher perceived HIV risk (AOR = 0.24, 95% CI: 0.15-0.39). Interest in LAI-PrEP was more common among PWID reporting social and structural factors that could interfere with oral PrEP adherence, suggesting LAI-PrEP implementation could increase PrEP coverage among those most vulnerable to HIV.

Phylodynamic evolution of HIV-1 A6 sub-subtype epidemics in Poland

The human immunodeficiency virus type 1 (HIV-1) A6 sub-subtype is highly prevalent in Eastern Europe. Over the past decade, the dissemination of the A6 lineage has been expanding in Poland. The recent Russian invasion of Ukraine may further escalate the spread of this sub-subtype. While evolutionary studies using viral sequences have been instrumental in identifying the HIV epidemic patterns, the origins, and dynamics of the A6 sub-subtype in Poland remain to be explored. We analyzed 1185 HIV-1 A6 pol sequences from Poland, along with 8318 publicly available sequences from other countries. For analyses, phylogenetic tree construction, population dynamics inference, Bayesian analysis, and discrete phylogeographic modeling were employed. Of the introduction events to Poland, 69.94% originated from Ukraine, followed by 29.17% from Russia. Most A6 sequences in Poland (53.16%) formed four large clades, with their introductions spanning 1993-2008. Central and Southern Polish regions significantly influenced migration events. Transmissions among men who have sex with men (MSM) emerged as the dominant risk group for virus circulation, representing 72.92% of migration events. Sequences from migrants were found primarily outside the large clades. Past migration from Ukraine has fueled the spread of the A6 sub-subtype and the current influx of war-displaced people maintains the growing national epidemic.

Willingness to use and distribute HIV self-testing kits among people who inject drugs in the San Diego-Tijuana border region

BACKGROUND

HIV self-testing (HIVST) could increase HIV testing access among people who inject drugs (PWID), and secondary distribution (i.e., peer-delivery) of HIVST kits in PWID social networks could further expand coverage. We assessed willingness to use and distribute HIVST kits among PWID in the San Diego-Tijuana border region.

METHODS

From 2020 to 2021, HIV-negative PWID in San Diego, USA, and Tijuana, Mexico, completed surveys and provided data on individual (N = 539) and social network (N = 366) characteristics. We used modified Poisson regression to examine the effects of individual and social network characteristics on willingness to use and distribute HIVST kits.

RESULTS

Most participants were willing to use (81%) and distribute (81%) HIVST kits. At the individual level, prior HIV testing was positively associated with willingness to use (adjusted prevalence ratio [aPR] = 1.24, 95% confidence interval [CI] 1.10-1.40) and distribute (aPR = 1.27, 95% CI 1.12-1.43) HIVST kits, while perceiving oneself to be at higher HIV risk than others was negatively associated with willingness to use HIVST kits (aPR = 0.83, 95% CI 0.74-0.93). At the network level, willingness to distribute HIVST kits was positively associated with network size (aPR = 1.04 per member, 95% CI 1.01-1.08) and greater proportions of one's network encouraging them to use drugs (aPR = 1.29, 95% CI 1.16-1.44) and having a history of homelessness (aPR = 1.51, 95% CI 1.31-1.74) or detention/arrest (aPR = 1.57, 95% CI 1.36-1.82), and negatively associated with a greater proportion of one's network including "very close" persons (aPR = 0.80, 95% CI 0.69-0.94).

CONCLUSIONS

We found high potential for HIVST kits and their secondary distribution to increase HIV testing among PWID who face the greatest barriers to facility-based testing.

Dispersal history and bidirectional human-fish host switching of invasive, hypervirulent Streptococcus agalactiae sequence type 283

Human group B Streptococcus (GBS) infections attributable to an invasive, hypervirulent sequence type (ST) 283 have been associated with freshwater fish consumption in Asia. The origin, geographic dispersion pathways and host transitions of GBS ST283 remain unresolved. We gather 328 ST283 isolate whole-genome sequences collected from humans and fish between 1998 and 2021, representing eleven countries across four continents. We apply Bayesian phylogeographic analyses to reconstruct the dispersal history of ST283 and combine ST283 phylogenies with genetic markers and host association to investigate host switching and the gain and loss of antimicrobial resistance and virulence factor genes. Initial dispersal within Asia followed ST283 emergence in the early 1980s, with Singapore, Thailand and Hong Kong observed as early transmission hubs. Subsequent intercontinental dispersal originating from Vietnam began in the decade commencing 2001, demonstrating ST283 holds potential to expand geographically. Furthermore, we observe bidirectional host switching, with the detection of more frequent human-to-fish than fish-to-human transitions, suggesting that sound wastewater management, hygiene and sanitation may help to interrupt chains of transmission between hosts. We also show that antimicrobial resistance and virulence factor genes were lost more frequently than gained across the evolutionary history of ST283. Our findings highlight the need for enhanced surveillance, clinical awareness, and targeted risk mitigation to limit transmission and reduce the impact of an emerging pathogen associated with a high-growth aquaculture industry.

Phylogeographic reconstruction of the emergence and spread of Powassan virus in the northeastern United States

Powassan virus is an emerging tick-borne virus of concern for public health, but very little is known about its transmission patterns and ecology. Here, we expanded the genomic dataset by sequencing 279 Powassan viruses isolated from Ixodes scapularis ticks from the northeastern United States. Our phylogeographic reconstructions revealed that Powassan virus lineage II was likely introduced or emerged from a relict population in the Northeast between 1940 and 1975. Sequences strongly clustered by sampling location, suggesting a highly focal geographical distribution. Our analyses further indicated that Powassan virus lineage II emerged in the northeastern United States mostly following a south-to-north pattern, with a weighted lineage dispersal velocity of ~3 km/y. Since the emergence in the Northeast, we found an overall increase in the effective population size of Powassan virus lineage II, but with growth stagnating during recent years. The cascading effect of population expansion of white-tailed deer and I. scapularis populations likely facilitated the emergence of Powassan virus in the northeastern United States.

Variant-specific introduction and dispersal dynamics of SARS-CoV-2 in New York City - from Alpha to Omicron

Since the latter part of 2020, SARS-CoV-2 evolution has been characterised by the emergence of viral variants associated with distinct biological characteristics. While the main research focus has centred on the ability of new variants to increase in frequency and impact the effective reproductive number of the virus, less attention has been placed on their relative ability to establish transmission chains and to spread through a geographic area. Here, we describe a phylogeographic approach to estimate and compare the introduction and dispersal dynamics of the main SARS-CoV-2 variants - Alpha, Iota, Delta, and Omicron - that circulated in the New York City area between 2020 and 2022. Notably, our results indicate that Delta had a lower ability to establish sustained transmission chains in the NYC area and that Omicron (BA.1) was the variant fastest to disseminate across the study area. The analytical approach presented here complements non-spatially-explicit analytical approaches that seek a better understanding of the epidemiological differences that exist among successive SARS-CoV-2 variants of concern.

Phylodynamics of HIV in the Mexico City Metropolitan Region

Evolutionary analyses of viral sequences can provide insights into transmission dynamics, which in turn can optimize prevention interventions. Here, we characterized the dynamics of HIV transmission within the Mexico City metropolitan area. HIV pol sequences from persons recently diagnosed at the largest HIV clinic in Mexico City (between 2016 and 2021) were annotated with demographic/geographic metadata. A multistep phylogenetic approach was applied to identify putative transmission clades. A data set of publicly available sequences was used to assess international introductions. Clades were analyzed with a discrete phylogeographic model to evaluate the timing and intensity of HIV introductions and transmission dynamics among municipalities in the region. A total of 6,802 sequences across 96 municipalities (5,192 from Mexico City and 1,610 from the neighboring State of Mexico) were included (93.6% cisgender men, 5.0% cisgender women, and 1.3% transgender women); 3,971 of these sequences formed 1,206 clusters, involving 78 municipalities, including 89 clusters of ≥10 sequences. Discrete phylogeographic analysis revealed (i) 1,032 viral introductions into the region, over one-half of which were from the United States, and (ii) 354 migration events between municipalities with high support (adjusted Bayes factor of ≥3). The most frequent viral migrations occurred between northern municipalities within Mexico City, i.e., Cuauhtémoc to Iztapalapa (5.2% of events), Iztapalapa to Gustavo A. Madero (5.4%), and Gustavo A. Madero to Cuauhtémoc (6.5%). Our analysis illustrates the complexity of HIV transmission within the Mexico City metropolitan area but also identifies a spatially active transmission area involving a few municipalities in the north of the city, where targeted interventions could have a more pronounced effect on the entire regional epidemic. IMPORTANCE Phylogeographic investigation of the Mexico City HIV epidemic illustrates the complexity of HIV transmission in the region. An active transmission area involving a few municipalities in the north of the city, with transmission links throughout the region, is identified and could be a location where targeted interventions could have a more pronounced effect on the entire regional epidemic, compared with those dispersed in other manners.

Long-Acting Injectable Human Immunodeficiency Virus Pre-Exposure Prophylaxis Preferred Over Other Modalities Among People Who Inject Drugs: Findings from a Qualitative Study in California

People who inject drugs (PWID) have extraordinarily low uptake of human immunodeficiency virus (HIV) pre-exposure prophylaxis (PrEP) despite high levels of need. Long-acting PrEP modalities hold promise for HIV prevention among PWID, but product preferences remain poorly understood. From September to November 2021, we conducted qualitative interviews with 28 HIV-negative, adult (≥18 years) PWID in San Diego County, CA, to explore their perspectives on daily oral PrEP pills and long-acting PrEP modalities (i.e., injections, implants, intravaginal rings, and broadly neutralizing antibodies), which we explained using standard scripts. Thematic analysis identified variations in PrEP modality interest and acceptability. We identified three key factors across the 28 interviews that appeared to influence PrEP modality preferences: perceived convenience of use, invasiveness, and familiarity (based on past experience). Overall, most participants preferred injectable PrEP over other modalities because they viewed injectable medications as convenient, noninvasive, and familiar. While injectable PrEP was recently approved for use in the United States and was most the acceptable PrEP modality in this sample, our findings suggest that intervention and implementation research is urgently needed to improve our understanding of strategies that could support access, uptake, and sustained adherence to longer-acting PrEP for PWID.

Transmission networks of SARS-CoV-2 in Coastal Kenya during the first two waves: A retrospective genomic study

Background

Detailed understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) regional transmission networks within sub-Saharan Africa is key for guiding local public health interventions against the pandemic.

Methods

Here, we analysed 1139 SARS-CoV-2 genomes from positive samples collected between March 2020 and February 2021 across six counties of Coastal Kenya (Mombasa, Kilifi, Taita Taveta, Kwale, Tana River, and Lamu) to infer virus introductions and local transmission patterns during the first two waves of infections. Virus importations were inferred using ancestral state reconstruction, and virus dispersal between counties was estimated using discrete phylogeographic analysis.

Results

During Wave 1, 23 distinct Pango lineages were detected across the six counties, while during Wave 2, 29 lineages were detected; 9 of which occurred in both waves and 4 seemed to be Kenya specific (B.1.530, B.1.549, B.1.596.1, and N.8). Most of the sequenced infections belonged to lineage B.1 (n = 723, 63%), which predominated in both Wave 1 (73%, followed by lineages N.8 [6%] and B.1.1 [6%]) and Wave 2 (56%, followed by lineages B.1.549 [21%] and B.1.530 [5%]). Over the study period, we estimated 280 SARS-CoV-2 virus importations into Coastal Kenya. Mombasa City, a vital tourist and commercial centre for the region, was a major route for virus imports, most of which occurred during Wave 1, when many Coronavirus Disease 2019 (COVID-19) government restrictions were still in force. In Wave 2, inter-county transmission predominated, resulting in the emergence of local transmission chains and diversity.

Conclusions

Our analysis supports moving COVID-19 control strategies in the region from a focus on international travel to strategies that will reduce local transmission.

Funding

This work was funded by The Wellcome (grant numbers: 220985, 203077/Z/16/Z, 220977/Z/20/Z, and 222574/Z/21/Z) and the National Institute for Health and Care Research (NIHR), project references: 17/63/and 16/136/33 using UK Aid from the UK government to support global health research, The UK Foreign, Commonwealth and Development Office. The views expressed in this publication are those of the author(s) and not necessarily those of the funding agencies.

Frequently Transmission and Close Relationship Among Immigrants in the China-Myanmar Border Region Indicated by Molecular Transmission Analysis From a Cross-Sectional Data

Background

Accurate identification of molecular transmission clusters (MTCs) and understanding the dynamics of human immunodeficiency virus (HIV) transmission are necessary to develop targeted interventions to prevent HIV transmission. We evaluated the characteristics of antiretroviral therapy-naïve individuals who belonged to HIV-1 MTCs in the China-Myanmar border region to inform targeted effective HIV intervention.

Methods

Phylogenetic analyses were undertaken on HIV-1 pol sequences to characterize subtypes or circulating recombinant forms and identify MTCs. MTCs were defined as those with 2 or more sequences having bootstrap support > 80% and a pairwise gene distance less than or equal to 0.03. Factors correlated with MTCs were evaluated using logistic regression analysis. The chi-square test was used to compare differences between Chinese and Burmese participants belonging to MTCs.

Results

A total of 900 people had their pol gene successfully sequenced. Twenty-one MTCs were identified and included 110 individuals (12.2%). Individuals in MTCs were more likely to be Burmese [aOR = 2.24 (95% CI: 1.33, 3.79), P = 0.003], be younger [aOR = 0.34 (95% CI: 0.20, 0.58), P < 0.001 for age 26-50 vs. 25 years or younger], have a lower CD4 T cell count [aOR = 2.86 (95% CI: 1.34, 6.11), P = 0.007 for < 200 vs. 350 or greater], and have subtypes CRF07_BC or C [CRF07_BC: aOR = 7.88 (95% CI: 3.55, 17.52), P < 0.001; C: aOR = 2.38 (95% CI: 1.23, 4.62), P = 0.010 compared to CRF01_AE]. In MTCs, Burmese were younger (89.7 vs. 57.7% for age 25 years or younger), had a lower education level (41.0 vs. 8.5% for illiterate), were more likely to be infected through injection drug use (35.9 vs. 12.7%), and had a higher proportion of subtype BC (33.3 vs. 15.5%) and CRF01_AE (20.5 vs. 8.5%) compared to Chinese (P < 0.05 for all).

Conclusion

Burmese participants were more likely to belong to MTCs, and most MTCs had both Burmese and Chinese participants. These data highlight the bidirectional transmission of HIV-1 frequently transmission and close relationship among immigrants in the China-Myanmar border region. Local health departments should pay more attention to HIV screening and intervention to immigrants Burmese with the characteristics of younger age, having lower CD4 T cell count and infected with HIV subtypes CRF07_ BC or C.

Phylodynamic Dispersal of SARS-CoV-2 Lineages Circulating across Polish-German Border Provinces

Introduction: The emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has evolved into a worldwide outbreak, with significant molecular evolution over time. Large-scale phylodynamic studies allow to map the virus spread and inform preventive strategies. Aim: This study investigates the extent of binational dispersal and dynamics of SARS-CoV-2 lineages between seven border provinces of the adjacent countries of Poland and Germany to reconstruct SARS-CoV-2 transmission networks. Methods: Following three pandemic waves from March 2020 to the end of May 2021, we analysed a dataset of 19,994 sequences divided into B.1.1.7|Alpha and non-Alpha lineage groups. We performed phylogeographic analyses using the discrete diffusion models to identify the pathways of virus spread. Results: Based on population dynamics inferences, in total, 673 lineage introductions (95% HPD interval 641−712) for non-Alpha and 618 (95% HPD interval 599−639) for B.1.1.7|Alpha were identified in the area. For non-Alpha lineages, 5.05% binational, 86.63% exclusively German, and 8.32% Polish clusters were found, with a higher frequency of international clustering observed for B.1.1.7|Alpha (13.11% for binational, 68.44% German and 18.45% Polish, p < 0.001). We identified key transmission hubs for the analysed lineages, namely Saxony, West Pomerania and Lower Silesia. Conclusions: Clustering patterns between Poland and Germany reflect the viral variant transmission dynamics at the international level in the borderline area. Tracing the spread of the virus between two adjacent large European countries may provide a basis for future intervention policies in cross-border cooperation efforts against the spread of the pandemics.

Assessing the impact of COVID-19 border restrictions on dengue transmission in Yunnan Province, China: an observational epidemiological and phylogenetic analysis

BACKGROUND

In response to the COVID-19 pandemic, China implemented strict restrictions on cross-border travel to prevent disease importation. Yunnan, a Chinese province that borders dengue-endemic countries in Southeast Asia, experienced unprecedented reduction in dengue, from 6840 recorded cases in 2019 to 260 in 2020.

METHODS

Using a combination of epidemiological and virus genomic data, collected from 2013 to 2020 in Yunnan and neighbouring countries, we conduct a series of analyses to characterise the role of virus importation in driving dengue dynamics in Yunnan and assess the association between recent international travel restrictions and the decline in dengue reported in Yunnan in 2020.

FINDINGS

We find strong evidence that dengue incidence between 2013-2019 in Yunnan was closely linked with international importation of cases. A 0-2 month lag in incidence not explained by seasonal differences, absence of local transmission in the winter, effective reproductive numbers < 1 (as estimated independently using genetic data) and diverse cosmopolitan dengue virus phylogenies all suggest dengue is non-endemic in Yunnan. Using a multivariate statistical model we show that the substantial decline in dengue incidence observed in Yunnan in 2020 but not in neighbouring countries is closely associated with the timing of international travel restrictions, even after accounting for other environmental drivers of dengue incidence.

INTERPRETATION

We conclude that Yunnan is a regional sink for DENV lineage movement and that border restrictions may have substantially reduced dengue burden in 2020, potentially averting thousands of cases. Targeted testing and surveillance of travelers returning from high-risk areas could help to inform public health strategies to minimise or even eliminate dengue outbreaks in non-endemic settings like southern China.

FUNDING

Funding for this study was provided by National Key Research and Development Program of China, Beijing Science and Technology Planning Project (Z201100005420010); Beijing Natural Science Foundation (JQ18025); Beijing Advanced Innovation Program for Land Surface Science; National Natural Science Foundation of China (82073616); Young Elite Scientist Sponsorship Program by CAST (YESS) (2018QNRC001); H.T., O.P.G. and M.U.G.K. acknowledge support from the Oxford Martin School. O.J.B was supported by a Wellcome Trust Sir Henry Wellcome Fellowship (206471/Z/17/Z). Chinese translation of the abstract (Appendix 2).

Dispersal dynamics of SARS-CoV-2 lineages during the first epidemic wave in New York City

During the first phase of the COVID-19 epidemic, New York City rapidly became the epicenter of the pandemic in the United States. While molecular phylogenetic analyses have previously highlighted multiple introductions and a period of cryptic community transmission within New York City, little is known about the circulation of SARS-CoV-2 within and among its boroughs. We here perform phylogeographic investigations to gain insights into the circulation of viral lineages during the first months of the New York City outbreak. Our analyses describe the dispersal dynamics of viral lineages at the state and city levels, illustrating that peripheral samples likely correspond to distinct dispersal events originating from the main metropolitan city areas. In line with the high prevalence recorded in this area, our results highlight the relatively important role of the borough of Queens as a transmission hub associated with higher local circulation and dispersal of viral lineages toward the surrounding boroughs.

Things must not fall apart: the ripple effects of the COVID-19 pandemic on children in sub-Saharan Africa

Zero to 19 year-old children in sub-Saharan Africa bear a disproportionate proportion of the global burden of communicable and non-communicable diseases. Significant public health gains have been made in the fight against these diseases, however, factors such as underequipped health systems, disease outbreaks, conflict, and political instability continue to challenge prevention and control. The novel coronavirus disease (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) introduces new challenges to public health programs in sub-Saharan Africa. Of particular concern are programs targeting major conditions among children, such as undernutrition, vaccine-preventable pneumonia and diarrhea, malaria, tuberculosis, HIV, and sickle cell disease. This article focuses on the impact of the COVID-19 pandemic on child health in sub-Saharan Africa. We review the epidemiology of major pediatric diseases and, referencing modeling projections, discuss the short- and long-term impact of the pandemic on major disease control. We deliberate on potential complications of SARS-CoV-2 co-infections/co-morbidities and identify critical social and ethical issues. Furthermore, we highlight the paucity of COVID-19 data and clinical trials in this region and the lack of child participants in ongoing studies. Lastly, approaches and interventions to mitigate the pandemic's impact on child health outcomes are discussed. IMPACT: Children in sub-Saharan Africa bear a disproportionate burden of communicable and non-communicable diseases globally; this remains true even as the COVID-19 pandemic persists. Amidst the fast-expanding COVID-19 literature, there is little comprehensive coverage of the pandemic's indirect impact on child health in sub-Saharan Africa. This article comprehensively outlines the threat that the pandemic poses to major disease prevention and control for children in sub-Saharan Africa. It discusses the potential impact of SARS-CoV-2 co-infections/co-morbidities, highlights research gaps, and advocates for data and action to mitigate the ripple effects of the pandemic on this population.

Phylogenetic analyses of SARS-CoV-2 B.1.1.7 lineage suggest a single origin followed by multiple exportation events versus convergent evolution

The emergence of new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) herald a new phase of the pandemic. This study used state-of-the-art phylodynamic methods to ascertain that the rapid rise of B.1.1.7 “Variant of Concern” most likely occurred by global dispersal rather than convergent evolution from multiple sources.