A Novel and Expanding SARS-CoV-2 Variant, B.1.1.318, dominates infections in Mauritius medrxiv.org/content/10.110…
Mauritius is an example of controlling #COVID19 in Africa, with 1,700 infections and only 18 deaths. However, one variant seems to have caused the great majority of all of the infections
Mauritius has stopped dozens of introductions of the Beta (501Y.V2/B.1.351) and Alpha (B.1.1.7) but the B.1.1.318, which has the 484K mutation (common to Beta) and the 681H mutation (common to Alpha) has caused all local transmitted cases.
The B.1.1.318 has its origins traced to Nigeria. This variant has been highlighted as a variant of interest (VOI) in the U.K. and seems to be also transmitted at high level in Europe, which was identified as the source to introduction to Mauritius.
This variant, B.1.1.318, is now spreading in over 35 countries and over 3,200 genomes are available at @GISAD
Immune evasion properties introduced by Spike substitutions (e.g. E484K and Y144del) are unlikely to explain local transmission as there was presumably a low level of population immunity following a small first wave. However, it is important to detect its effect in vaccines.
At the end of May 2021, close to 20% of the population of Mauritius had received the first dose and half of those had also received the second dose of one of the vaccines.
Strong outbreak response, with widespread testing (positivity rate < 1%) seems to be able to slow the spread of this variant in Mauritius. However, public health response needs to keep focused as this variant is spreading in many other countries (>35).
Mauritius also used genomics surveillance to follow outbreaks, and in spite of a limited number of genomes, it allows the country to rank as one of the top 5 countries in genomics coverage in the world with 12% of the infections genotyped.
In conclusion, SARS-CoV-2 genomic surveillance in Mauritius demonstrated a second wave that was dominated by a VUI, despite PCR testing and quarantine effectively preventing local transmission of other variants.
This report also highlights the need for continuous genomic surveillance to fully to understand the transmission dynamics of the VUI in Mauritius.

Pre-print open at: medrxiv.org/content/10.110…
This work was done in close collaboration with the Ministry of Health and Wellness, Mauritius. The Central Health Laboratory, Victoria Hospital, Candos, Mauritius. The #franciscrickinstitute, the @nicd_sa , @krisp_news, @ceri_news and the @AfricaCDC and @WHOAFRO
Thanks to @houzhou @rjlessells @EduanWilkinson @Mittenavoig and many other colleagues from Mauritius. Together, we can expand genomics surveillance to detect and control new variants in Africa!
More information on the expanding variant in Mauritius. medrxiv.org/content/10.110…

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More from @Tuliodna

3 Jun
In this online pre-print, we present a case of persistent SARS-CoV-2 infection with accelerated intra-host evolution in a patient with advanced HIV and antiretroviral treatment failure in South Africa.

Paper deposited at medRxiv &available at: krisp.org.za/publications.p… @sigallab
SARS-CoV-2 RT-PCR was positive for 216 days (27 weeks). At all time-points between day 0 and day 216 there was a mean Ct ranging from 16.4 to 31.6. The patient had HIV drug resistance and was not responding to therapy.
Over 30 mutations accumulated over time, many of them changing aminoacids that are common of variants of concern.
Read 15 tweets
14 May
A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa medrxiv.org/content/10.110…
By 5 May 2021, 14,504 SARS-CoV-2 genomes had been submitted to the GISAID database from 38 African countries and two overseas territories (Mayotte and Réunion) (Fig. 1A). Overall, this corresponds to approximately one sequence per ~300 reported cases.
Overall, the number of sequences correlates closely with the number of reported cases per country. lmost half of the sequences were from South Africa, consistent with it being responsible for almost half of the reported cases in Africa.
Read 21 tweets
13 May
Confirmed Detection of eight (8) more genomes B.1.617.2 and two (2) community transmission of B.1.1.7 in South Africa, By Network for Genomic Surveillance in South Africa (NGS-SA), 13 May 2021
The eight new cases of B.1.617.2 variant have been detected from KwaZulu-Natal province. More specifically, these were cases in crew members of a commercial vessel that arrived in Durban Port from India.
The cases were isolated on the vessel, and other crew members have been quarantined according to national COVID-19 case management guidelines. The individuals who tested positive for COVID-19 did not disembark in South Africa, with exception of one that was admitted to hospital
Read 9 tweets
9 May
Confirmed Detection of B.1.617.2 and B.1.1.7 in South Africa by NGS-SA

This report was sent to our Health Minister @DrZweliMkhize yesterday.

In this Twitter thread, we highlight the details and repercussion of the discovery to South Africa
In response to the continued emergence and spread of new variants around the world, the Network for Genomic Surveillance in South Africa (NGS-SA) recently intensified the monitoring of confirmed COVID-19 cases in recent arrivals to the country.
We can now confirm that today we detected four cases of the B.1.617.2 variant. The four cases have been detected from Gauteng (n=2) and KwaZulu-Natal (n=2) provinces and all have a history of recent arrivals from India.
Read 17 tweets
4 May
First genomic surveillance results from a traveler to India in South Africa. A patient at Tygerberg Hospital who tested positive for SARS-CoV-2 about 3 days after traveling to SA from India. This first genome is a 501Y.V2 (B.1.351) and not the B.1.617 described in India.
The 501Y.V2 (B.1.351) is the 3rd most common variant in India after the B.1.617 and the B.1.1.7. Below a graph from @trvrb showing the spread of the variants in India.
The 501Y.V2 (B.1.351) was firstly identified in South Africa by the network for genomic surveillance in South Africa (NGS-SA). It shows how variants can be introduced back and forth between countries.
Read 8 tweets
29 Mar
Today paper on neutralization of 501Y.V2 (B.1.351) - Show effective neutralization of other SARS-CoV-2 lineages by 501Y.V2 @nature


All start with a good cohort... We obtained convalescent plasma & sequenced the matching infecting virus of 1st & 2nd wave
A first wave variant lacking the 501Y.V2 RBD and NTD mutations (B.1.1.177) was outgrown from one participant infected in the first South African infection wave, and 501Y.V2 was outgrown from a participant at the beginning of the second wave.
A focus forming live virus neutralization assay (LVNA) was used to quantify neutralization.
Read 14 tweets

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