黑死病源于天山北麓今Kyrgyzstan

choi

(1)
(a) Yersinia pestis or "Y pestis was discovered in 1894 by Alexandre Yersin, a Swiss/French physician and bacteriologist from the Pasteur Institute, during an epidemic of the plague in Hong Kong."  en.wikipedia.org for "Yersinia pestis."
(b) Alexandre Yersin
https://en.wikipedia.org/wiki/Alexandre_Yersin   
(1863 – 1943; born Swiss; :From 1883 to 1884 he studied medicine at Lausanne, followed by Marburg [in Germany, where University of Marburg is located], and Paris (1884–1886). * * * In 1886, Yersin entered Louis Pasteur's research laboratory * * * In 1888 he received his doctorate [likely in medicine, as he was not a PhD] * * * He joined the recently created Pasteur Institute in 1889 * * * In order to practice medicine in France, Yersin applied for and obtained French nationality in 1888 [maybe this sentence should precede the previous quoted sentence, but this is the order in this Wiki page]. * * * In 1894 Yersin was sent by request of the French government and the Pasteur Institute to Hong Kong, to investigate the plague happening there.  There [in 1894, see (4)(a) below)], in a small hut since he was denied access to British hospitals at his arrival, he made his greatest discovery: that of the pathogen which causes the disease")


(2) Robert L Dillard and Andrew L Juergens, Plague, StatPearls, last updated on May 3, 2022
https://www.ncbi.nlm.nih.gov/books/NBK549855/

Quote:

"The typical life-cycle of Y Pestis starts within an insect vector [flea] followed by transmission to a mammalian host, typically rodents or other wild animals. Humans are only affected as incidental hosts [rodents being the primary hosts for the bacteria].

"The bacterium is enzootic in rodents with insects serving as the primary vector. Rattus rattus (the domestic black rat) and Rattus novegicus [Norwegian rat; rattus is Latin noun masculine for 'rat'] (the brown sewer rat) are the most common hosts

"The plague has arguably been most impactful as three historical pandemics. The first [started] throughout the Mediterranean in the 6th Century during the reign of the Roman emperor Justinian. The second was the black death * * * and the third began in China in the late 19th century, leading to the deaths of millions in China and India [continues in Africa today].

"The most common presentation of Y pestis infection in humans is bubonic plague * * * the next day [after flea bite], a bubo develops. The bubo begins as intense pain in an area of regional lymph nodes, most commonly inguinal, followed by axillary or cervical [neck] nodes

"Early antibiotics are the cornerstone of effective treatment for the plague due to the rapid progression of each disease subtype. Given these potentially poor clinical outcomes, treatment should begin based on clinical suspicion pwithout waiting for confirmation from laboratory, such as bacterial culture], as described above. Aminoglycosides ['Streptomycin is the first-in-class aminoglycoside antibiotic' but others in the class are gentamicin and neomycin] are considered first-line treatment * * *

Note:
(a) StatPearls are written for physicians, not laypersons. I am unsure if you can understand text. However, try: sections of Introduction, Etiology, Epidemiology, Pathophysiology, History and Physical (paragraph 1 only).
(b) bubo
https://en.wikipedia.org/wiki/Bubo
(photo)
(c) first plague pandemic
https://en.wikipedia.org/wiki/First_plague_pandemic

choi

(3)
(a) DNA ends to mutate with time. Some DNAs are more stable, not liable for mutation. On the other hand, some others mutate frequently, such as HIV (causing AIDS) and coronavirus (each variant has the change of a base) which causes Covid-19. Therefore, even identical twins accumulate DNA mutations that can tell them apart.
(b) Prior to the latest reports (see (4) ), there were hints that Black Death, the second pandemic of Y pestis, originated in Kyrgyzstan.

Monica H Green, How a microbe becomes a pandemic: a new story of the Black Death. Lancet, December 2020.
https://www.thelancet.com/journals/lanmic/article/PIIS2666-5247(20)30176-2/fulltext

Quote:

"In 2011, palaeogeneticists at McMaster University, Canada, and Tübingen University, Germany, [for the first time; see note (a) below] reconstructed the genomes of Yersinia pestis, the causative organism of plague, from two 14th-century cemeteries below the centre of London.

Note:
(i) Bos KI et al, A Draft Genome of Yersinia pestis from Victims of the Black Death. Nature, 478: 506 (2011).
https://www.nature.com/articles/nature10549

Quote:

"from Black Death victims securely dated to episodes of pestilence-associated mortality in London, England, 1348–1350.

"Y pestis is a recently evolved descendent of the soil-dwelling bacillus Yersinia pseudotuberculosis [footnote omitted], which in the course of its evolution acquired two additional plasmids (pMT1 and pPCP1) that provide it with specialized mechanisms for infiltrating mammalian hosts.

"The genome of Y pestis, like that of all organisms, carries indelible marks. Its single nucleotide polymorphisms (SNPs) allow researchers to join the history of this horrifically lethal microbe [to create family tree for this virus AND] to the history of human activities that have facilitated its transport and replication.

"The living Y pestis strains most closely related to those implicated in late-medieval Europe's Black Death [ie second pandemic of plague] are found in marmots, hibernating animals that normally live far from human habitation. Yet the marmots carrying these closely related strains are found nowhere near Europe. Rather, they are tightly clustered in adjacent habitats in and near the Tian Shan mountain range, on the eastern border of Kyrgyzstan. The lineages of Y pestis that are hosted in Tian Shan marmots are, moreover, living relatives of at least three other lineages descended from the Big Bang psee (4)(a) and (b) below]. This late-medieval proliferation scattered new plague lineages in every direction around the Tian Shan, taking the bacterium into marmot populations separated by 1000 km or more.

"To date, historiography has barely associated the Mongols with plague, save for the now-discredited fiction that they spread the Black Death to Europe by throwing plague-ridden bodies over the walls during a siege of Caffa on the Black Sea[footnote omitted]. The spread of plague in the 1340s was hardly an act of bioterrorism; instead, its introduction into the commercial routes of the Black Sea and Mediterranean was due to grain shipments unrelated to the siege.

(ii) marmot
https://en.wikipedia.org/wiki/Marmot
(iii) Feodosia
https://en.wikipedia.org/wiki/Feodosia   (in Crimea; "During much of its history, the city was known as Caffa * * * or Kaffa")

choi

(4) The (4)(a) is news witten with scientists (as well as general population) in mind, whereas is for top scientist) and hard to understand). So I choose (a) first, supplemented and explained with part of (4)(b).
(a) Ann Gibbons, Ancient DNA Reveals Black Death Source; Graves in Kyrgyzstan hold early victims of plague that swept medieval Europe. Science 376: 1254 (June 17, 2022, which is tomorrow).
https://www.science.org/doi/epdf/10.1126/science.add4865

Quote:

"The  strain  that killed them [in two cemeteries of Kyrgyzstan] was ancestral [judging from accumulation of mutations] to all the strains that rampaged across Europe a decade later and continued to kill for the next 500 years. The bacterium jumped from rodents to hu-mans just before  the  Kyrgyzstan  burials, perhaps after sudden changes in rainfall or temperature, the researchers propose this week in Nature [I read Nature which did not say this]. * * * In 1894, microbiologists  identified Y pestis as the cause.

"One branch  of  the [viral family] tree underwent a 'big bang' explosion of diversity at the time of the Black Death, creating a starlike pattern of four new lineages of Y pestis whose descendant strains still persist in 40 species of rodents around the world. One of those lineages was the source of the Black Death and later outbreaks in Europe until the 18th century.

Maria "Spyrou extracted DNA from the pulp of seven individuals' teeth and found three were infected with Y pestis. * * * The  strain was closely related to ones found  in  rodents [marmots included] near Issyk Kul today.

Note:
(i) A picture is worth a thousand words. Hence, view the figure first.
(ii) Dr Philip Slavin is an Associate Professor in History at the University of Stirling.
https://www.stir.ac.uk/people/951608
(iii) University of Stirling
https://en.wikipedia.org/wiki/University_of_Stirling
(1967-; a public university in Sterling p25 mile northeast of Glasgow], Scotland)

(b) Spyrou A et al, The Source of the Black Death in Fourteenth-Century Central Eurasia. Nature, _: _ (June 15, 2022)
https://www.nature.com/articles/s41586-022-04800-3.pdf
("Excavations of these cemeteries between 1885 and 1892 [by Russians] revealed a unique archaeological assemblage potentially associated with an epidemic that affected the region during the fourteenth century (Fig 1 * * *). On the basis of tombstone inscriptions, these cemeteries showed a disproportionally [sic] high number of burials dating between 1338 and 1339, with some inscriptions stating that the cause of death was due to an unspecified pestilence")

My comment:
(i) There is no need to read this article. Just follow me and read selected portions.
(ii) The authorship of this article includes both Bos KI, first author of (3)(b)(i), and second last author Philip Slavin.
(iii) Figure1 caption:
"b, Area within the Kara-Djigach cemetery [one of the two cemeteries at issue] * * * Individuals from graves 6, 9, 20, 22 and 28 (the numbers in bold) were investigated using aDNA [ancient DNA] in this study. Burials shown with stripe patterns [9, 20, 28] were associated with individuals BSK001, BSK003 and BSK007 [BSK acronym is not explained in this Article], which showed evidence of Y pestis infections.   
"d, Tombstone from the Kara-Djigach cemetery with legible pestilence-associated inscription. The inscription is translated as 'In the Year 1649 [=AD 1338], and it was the Year of the Tiger, in Turkic Bars. This is the tomb of the believer Sanmaq. [He] died of pestilence [=mawtānā].' " (insertions in this sentence are original).
(iii) Figure 2:
(A) View Figure 2(a), which is explained in (2)(b).
(B) Figure 2)(b) starts at the intersection of three line segments: one up and two on the right; the intersection has a dotted (broken) line pointing downward toward "Other branch 0." The intersection is ground 0, so the three individuals died of plague are identified as BSK001, BSK003 and BSK007. BSK001 and BSK003 are represented in Figure (2)(b) as a SINGLE pink circle, which gives out four branches: 1, 2, 3, 4. Branch 1, further upward AS TIME PROGRESSED, branched out, first as blue circles, then yellow circles, and finally dark green circles -- the same circles in Figure (2)(a). (Though blue circles in Figure (2)(a) and (b), respectively, have slightly different shades (of blue), they are meant to be the same.) Other parts of Branch 1 (represented by dark gray circles) are other Y pestis DNA from other victims (not from these two cemeteries) not used in this article.  

Now return to quotation 2 of (4)(a) above, the Science news: "a starlike pattern of four new lineages of Y pestis * * * One of those lineages was the source of the Black Death." I believe the four lineages means the four BRANCHES in Nature article, and that "[o]ne of those lineages was the source of the Black Death" refers to branch 1 in Figure 2 of the Nature article. The Science writer should not do this and befuddle readers.  
(iv) At last, at the page 4 (page numbers are at the lower right or left corners) of the online Nature article, is this statement: "BSK001/003 [the pink circle in Figure (2)(b)] carries the ancestral state in all covered diagnostic SNPs defining branches 1–4 and 0.ANT3 [the '0' signals Branch 0], which is the closest related branch 0 lineage to BSK001/003 * * *