Upper ocean water masses and transports in the western tropical Pacific (165E

ABSTRACT As part of the international TOGA program, the ORSTOM Center in Nouméa (New Caledonia) initiated in January 1984 a series of semi-annual cruises along the 165"E meridian from 20"s to 10"N, across the equatorial current system of the western Pacific. This paper presents an analysis of the first six hydrographic (0-1000 m) and current (0-600 m) sections. A detailed description of "typical" January 1986 vertical structures of temperature, salinity and zonal measured velocity is offered. Differences are noted with structures previously obtained in the tropical Pacific. Compared to the central and eastern Pacific, the 165"E dataset evidences a much weaker equatorial upwelling and deeper surface isothermal layer and subsurface currents. Compared to the few western Pacific measurements, the two speed cores of the Equatorial Undercurrent (EUC) previously reported at 100 and 200 m are not observed here. Special attention is given to the eastward equatorial jet (2OS-2"N 0-75 m) measured in January 1985 when westerly winds were present from the north of New Guinea to 160"E. For the purpose of volume transport calculations, eastward flows at 165"E are not sufficiently separated to be easily differentiated. A definition based on an isodensity surface (sigma-t = 23.5 kg m-3) is thus adopted to discriminate the EUC and the North and South Subsurface Countercurrents (NSCC, SSCC) from the North and South Equatorial Countercurrents (NECC, SECC).' The EUC is assumed to lie within 2 degrees of the equator below sigma-t = 23.5 kg m-3. Using these current boundaries, transports of the South Equatorial Current (SEC), EUC and NECC agree within 30% with estimates previously computed in the westem, central and eastern Pacific; e.g., the mean NECC transport is 27 f 13 lo6 m3 s-l. A noticeable exception is the SECC transport which is two to four times as much as that estimated for the central Pacific. The weaker (stronger) EUC and the farthest northern (southern) NECC were observed during the three January (June-July) cruises. Large transport variability was observed and calls for a denser time-space sampling rate of observation. Hence, the credibility of dynamic height and geostrophic currents calculated from XBT (0-400 m) and mean temperature-salinity (T-S) curves are investigated. Major limitations, stressed by the semiannual transects, are caused b y 1) notable density variations in the 400-1000 m layer, and 2) the effects of variability of the T-S relation in the 0-400 m layer. These two points can each result in signals of as much as 6 dyn cm in the surface dynamic height and therefore significant errors in geostrophic velocities calculated from individual cruises. These errors are generally not accounted for when the geostrophic method is applied to XBT data. However, poleward of 2" latitude, a fair agreement is observed between mean geostrophic and measured currents (5 cm s-' rms difference), after eliminating the errors introduced by the 400 db reference level and mean T-S curves. In the 2"S-2"N band, the agreement is only qualitative (30 cm s-' rms difference) and better in the EUC than in surface flows. Deeper temperature sampling and a better knowledge of T-S variability than the present one are particularly recommended to monitor the equatorial current system from XBTs in the western tropical Pacific Ocean

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century